Contacts of the helix formed by residues 94 - 129 (chain A) in PDB entry 5CXV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 2.8 28.5 + - - +
92A ALA 3.4 4.4 + - - -
93A LEU* 1.3 79.3 - - - +
95A THR* 1.3 62.0 + - - -
96A LEU 3.4 2.5 - - - -
97A ALA 4.0 0.2 - - - -
98A CYS* 2.9 12.3 + - - +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY* 1.3 72.3 - - - -
96A LEU* 1.3 60.5 + - - +
98A CYS* 3.2 2.8 + - - +
99A ASP* 2.9 36.1 + - - +
165A GLN* 5.7 1.3 - - - -
171A ARG* 3.5 42.2 - - + +
175A ALA* 6.2 3.8 - - - -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 3.4 0.2 - - - -
95A THR* 1.3 83.2 + - - +
97A ALA* 1.3 59.1 + - - +
99A ASP* 3.3 11.5 + - + +
100A LEU* 2.9 50.6 + - + +
162A LEU* 5.8 1.8 - - + -
166A TYR* 6.0 1.1 - - - +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 3.7 4.9 - - + -
93A LEU* 3.3 43.0 + - + +
94A GLY 3.5 1.6 + - - -
95A THR 3.3 0.4 - - - -
96A LEU* 1.3 75.7 - - - +
98A CYS* 1.3 66.5 + - - +
100A LEU* 3.8 8.7 - - - +
101A TRP* 2.9 25.5 + - - +
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Residues in contact with CYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 3.5 14.5 - - + +
94A GLY 2.9 15.6 + - - +
95A THR 3.2 9.8 + - - +
97A ALA* 1.3 76.3 - - - +
99A ASP* 1.3 66.7 + - - +
101A TRP* 3.1 4.3 + - - +
102A LEU* 3.0 29.2 + - - +
171A ARG* 3.8 17.0 - - - +
173A VAL* 5.6 0.2 - - - -
177A GLN 4.9 0.4 - - - +
178A CYS* 2.0 59.2 - - + -
179A TYR 4.2 2.7 - - - -
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 2.9 24.4 + - - +
96A LEU* 3.7 11.7 - - + +
98A CYS* 1.3 78.9 - - - +
100A LEU* 1.3 57.6 + - - +
102A LEU* 3.4 4.0 + - - +
103A ALA* 2.9 24.9 + - - +
161A ILE* 3.7 17.2 - - - +
162A LEU* 3.3 30.4 - - + +
165A GLN* 3.1 19.4 + - - +
166A TYR* 6.0 0.2 - - - -
171A ARG* 2.8 26.7 + - - -
179A TYR 5.3 2.1 - - - +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 2.9 42.3 + - + +
97A ALA* 3.8 7.6 - - - +
99A ASP* 1.3 75.8 - - - +
101A TRP* 1.3 58.8 + - - +
103A ALA* 3.8 2.9 - - + +
104A LEU* 2.9 33.1 + - - +
162A LEU* 4.3 19.5 - - + -
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Residues in contact with TRP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 5.5 1.6 - - + -
78A SER* 3.8 26.6 + - - +
81A LEU* 3.6 28.8 - - + +
82A TYR* 3.5 47.8 - + + -
85A TYR* 4.9 7.6 - + - -
91A TRP* 3.6 23.8 - + + -
97A ALA 2.9 18.7 + - - +
98A CYS 3.5 0.4 - - - +
100A LEU* 1.3 78.3 - - - +
102A LEU* 1.3 77.9 + - + +
104A LEU* 3.3 7.8 + - + +
105A ASP* 2.9 35.9 + - + +
178A CYS* 3.4 42.2 - - + -
404A TYR* 4.6 6.1 - + - -
408A TYR* 4.4 4.9 - - - -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A CYS* 3.0 15.1 + - - +
99A ASP* 4.1 6.1 - - - +
101A TRP* 1.3 103.8 - - + +
103A ALA* 1.3 63.9 + - - +
105A ASP* 3.3 3.1 + - + -
106A TYR* 2.9 49.0 + - + +
161A ILE* 3.9 12.8 - - + -
178A CYS* 3.5 23.6 - - - +
179A TYR* 3.5 34.3 - - - +
180A ILE* 4.0 14.1 - - + +
404A TYR* 4.4 6.1 - - - +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP 2.9 19.0 + - - +
100A LEU* 3.8 6.1 - - + +
102A LEU* 1.3 76.8 - - - +
104A LEU* 1.3 57.1 + - - +
107A VAL* 2.9 37.9 + - - +
158A ALA* 4.4 13.0 - - + -
161A ILE* 3.7 18.0 - - + +
162A LEU* 3.8 25.1 - - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.7 22.7 - - + -
77A PHE* 3.8 41.5 - - + -
78A SER* 5.5 1.3 - - - +
100A LEU 2.9 19.7 + - - +
101A TRP* 3.6 6.3 - - + +
103A ALA* 1.3 75.1 - - - +
105A ASP* 1.3 58.4 + - - +
107A VAL* 4.0 3.1 - - + +
108A ALA* 2.9 32.4 + - - +
502A Y01 4.0 30.1 - - + -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.9 7.3 - - - +
78A SER* 2.7 32.4 + - - +
101A TRP* 2.9 24.2 + - + +
102A LEU* 3.8 5.4 - - - +
103A ALA 3.3 0.2 - - - -
104A LEU* 1.3 78.3 - - - +
106A TYR* 1.3 61.8 + - + +
108A ALA* 3.8 2.2 - - - +
109A SER* 2.8 34.2 + - - -
404A TYR* 3.4 7.6 + - - +
408A TYR* 2.6 27.6 + - - -
501A 0HK 3.0 24.1 - - - -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 2.9 30.0 + - + +
105A ASP* 1.3 78.4 - - + +
107A VAL* 1.3 61.7 + - - +
109A SER* 4.0 0.3 - - - -
110A GLN* 2.9 32.9 + - - +
157A TRP* 3.5 36.5 + + + -
161A ILE* 3.9 14.1 - - + -
180A ILE* 3.5 28.3 - - + +
183A LEU* 4.8 3.1 - - + +
381A TYR* 4.4 3.1 + - - -
404A TYR* 3.6 29.6 - - - -
501A 0HK 3.4 66.6 - + + +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA 2.9 22.3 + - - +
104A LEU* 4.0 5.4 - - + +
106A TYR* 1.3 77.2 - - - +
108A ALA* 1.3 59.2 + - - +
111A ALA* 2.9 28.1 + - - +
150A TRP* 4.6 8.5 - - + -
153A SER* 3.6 8.4 - - - -
154A PHE* 3.7 36.6 - - + +
157A TRP* 3.9 17.9 - - + -
158A ALA* 4.0 15.0 - - + +
502A Y01 3.8 27.8 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA* 3.5 11.9 - - - +
73A ILE* 3.7 31.9 - - + -
74A ILE* 4.0 18.2 - - + -
104A LEU* 2.9 19.7 + - + +
105A ASP* 3.8 3.4 - - - +
107A VAL* 1.3 78.4 - - - +
109A SER* 1.3 56.0 + - - +
111A ALA* 3.2 7.8 + - - +
112A SER* 2.9 23.4 + - - -
150A TRP* 4.4 7.0 - - - -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.8 17.2 - - - +
105A ASP* 2.8 16.1 + - - -
106A TYR 4.0 0.7 - - - -
108A ALA* 1.3 73.2 - - - +
110A GLN* 1.3 65.6 + - - +
112A SER* 2.9 15.9 + - - +
113A VAL* 3.0 15.8 + - - +
378A TRP* 3.5 18.2 - - - -
408A TYR* 5.4 0.2 - - - -
501A 0HK 3.2 45.2 + - - -
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Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR 2.9 19.0 + - - +
107A VAL 4.1 2.5 - - - +
109A SER* 1.3 75.3 - - - +
111A ALA* 1.3 56.2 + - - +
113A VAL* 3.3 13.7 + - - +
114A MET* 2.9 40.7 + - - +
153A SER* 3.5 17.9 - - - +
156A LEU* 4.2 16.0 - - + +
157A TRP* 3.3 28.1 + - + +
196A ALA* 3.3 43.7 + - - +
200A PRO* 5.3 0.6 - - - +
501A 0HK 3.9 10.1 - - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA* 4.8 0.4 - - - -
107A VAL 2.9 20.1 + - - +
108A ALA 3.3 6.7 - - - +
109A SER 3.1 0.2 - - - -
110A GLN* 1.3 77.0 - - - +
112A SER* 1.3 55.6 + - - +
114A MET* 3.1 2.6 + - - +
115A ASN* 2.7 38.7 + - - +
149A ALA 5.2 0.4 - - - -
150A TRP* 3.8 42.0 - - + +
153A SER* 3.2 14.9 + - - +
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.8 25.6 - - - +
70A ALA* 4.2 10.3 - - - +
71A ASP* 4.5 7.1 + - - -
74A ILE* 5.3 3.6 - - - -
108A ALA 2.9 13.2 + - - -
109A SER* 2.9 13.0 + - - -
111A ALA* 1.3 76.2 - - - +
113A VAL* 1.3 63.2 + - - +
115A ASN* 3.3 3.1 + - - +
116A LEU* 3.0 31.3 + - - +
374A PHE* 5.0 1.7 - - - -
378A TRP* 4.9 8.0 - - - -
410A ASN* 4.6 12.5 + - - -
414A ASN* 5.0 0.2 + - - -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A SER 3.0 16.0 + - - +
110A GLN* 3.6 17.9 - - - +
112A SER* 1.3 74.2 - - - +
114A MET* 1.3 60.4 + - - +
116A LEU* 3.1 11.9 + - - +
117A LEU* 2.9 27.6 + - + +
196A ALA 3.7 16.2 - - - +
197A PHE* 5.1 1.3 - - + -
200A PRO* 3.6 32.8 - - + -
204A MET* 4.7 5.3 - - + +
374A PHE* 3.7 29.2 - - + -
378A TRP* 3.8 13.9 - - + -
501A 0HK 4.8 1.8 - - - -
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 2.9 35.0 + - - +
111A ALA 3.1 4.7 + - - +
113A VAL* 1.3 76.9 - - - +
115A ASN* 1.3 59.1 + - - +
117A LEU* 3.3 24.7 + - + +
118A LEU* 2.9 28.4 + - - +
149A ALA* 4.1 31.5 - - + +
152A VAL* 3.9 24.0 - - + -
153A SER* 4.1 6.5 - - - +
156A LEU* 4.9 8.1 - - + -
200A PRO* 5.9 1.1 - - - -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.2 7.1 - - + +
66A SER* 2.3 39.9 + - - +
67A LEU* 3.3 23.5 + - + -
111A ALA* 2.7 28.5 + - - +
112A SER* 3.7 4.7 - - - +
114A MET* 1.3 77.4 - - - +
116A LEU* 1.3 60.0 + - - +
118A LEU* 3.7 10.5 - - - +
119A ILE* 2.9 38.5 + - + +
146A ILE* 5.7 1.8 - - - +
149A ALA* 4.1 17.2 - - - +
150A TRP* 3.9 8.2 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.2 17.0 - - + -
112A SER* 3.0 22.9 + - - +
113A VAL* 3.3 8.3 - - - +
115A ASN* 1.3 77.2 - - - +
117A LEU* 1.3 62.1 + - - +
119A ILE* 3.4 8.4 + - + +
120A SER* 2.8 29.5 + - - -
204A MET* 3.5 14.1 - - + -
367A LEU* 5.4 3.1 - - + +
370A ILE* 4.0 21.5 - - + -
371A LEU* 3.8 21.2 - - + +
374A PHE* 3.6 52.5 - - + -
410A ASN* 5.6 0.9 - - - +
414A ASN* 5.8 1.3 - - - +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL 2.9 12.0 + - - +
114A MET* 3.5 31.0 - - + +
115A ASN 3.3 0.2 - - - -
116A LEU* 1.3 77.5 - - - +
118A LEU* 1.3 56.1 + - - +
120A SER* 3.2 5.3 + - - -
121A PHE* 2.9 49.9 + - + -
200A PRO* 3.7 43.3 - - + +
203A VAL* 3.8 30.7 - - + -
204A MET* 4.0 8.7 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 3.9 23.8 - - + -
114A MET 2.9 15.4 + - - +
115A ASN* 3.7 11.0 - - - +
116A LEU 3.3 0.2 - - - -
117A LEU* 1.3 76.9 - - - +
119A ILE* 1.3 57.2 + - - +
121A PHE* 4.0 7.1 - - + +
122A ASP* 2.9 31.6 + - - +
145A MET* 3.5 55.9 - - + +
146A ILE* 3.9 12.3 - - + +
149A ALA* 4.1 12.3 - - + -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 3.7 36.3 - - + +
64A LEU* 4.6 12.8 - - + -
67A LEU* 4.3 23.1 - - + -
115A ASN* 2.9 22.4 + - + +
116A LEU* 3.8 9.0 - - + +
118A LEU* 1.3 75.2 - - - +
120A SER* 1.3 64.9 + - - +
122A ASP* 3.3 5.9 + - - +
123A ARG* 2.9 23.4 + - - +
367A LEU* 3.7 30.1 - - + -
370A ILE* 6.4 0.4 - - + -
504A PGE 3.7 28.1 - - - +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU 2.8 21.5 + - - -
117A LEU* 3.2 5.4 + - - -
119A ILE* 1.3 78.8 - - - +
121A PHE* 1.3 58.5 + - - +
123A ARG* 3.4 5.4 + - - +
124A TYR* 2.9 28.4 + - - +
204A MET* 3.7 24.4 + - - +
207A LEU* 3.8 24.4 - - - +
208A TYR 5.8 0.2 - - - -
211A ILE* 4.5 5.0 - - - +
367A LEU* 5.3 5.1 - - - +
371A LEU* 4.6 12.8 - - - +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 2.9 38.1 + - + +
118A LEU* 4.0 8.7 - - + +
120A SER* 1.3 73.1 - - - +
122A ASP* 1.3 66.2 + - - +
124A TYR* 3.2 6.4 + + - +
125A PHE* 2.9 59.6 + + + -
203A VAL* 3.9 31.2 - - + -
207A LEU* 3.9 21.5 - - + -
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.1 22.4 - - + -
118A LEU 2.9 18.8 + - - +
119A ILE* 3.3 7.6 + - - +
121A PHE* 1.3 76.9 - - - +
123A ARG* 1.3 58.2 + - - +
125A PHE* 3.4 0.6 + - - -
126A SER* 2.9 34.0 + - - -
133A TYR* 2.6 33.0 + - - +
137A ARG* 3.0 39.9 + - - -
504A PGE 4.2 14.6 + - - +
1C ASP 4.4 1.4 + - - -
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Residues in contact with ARG 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE 2.9 17.0 + - - +
120A SER* 3.8 3.4 - - - +
122A ASP* 1.3 78.7 + - - +
124A TYR* 1.3 63.7 + - - +
126A SER* 3.2 6.9 + - - -
127A VAL* 3.0 25.3 + - - +
208A TYR* 4.0 29.1 + - - -
211A ILE* 4.1 34.5 - - + +
212A TYR* 5.4 1.2 - - - +
364A ALA* 3.5 28.3 - - - +
367A LEU* 3.5 29.8 - - - +
504A PGE 2.7 74.7 + - - +
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER 2.9 18.7 + - - +
121A PHE* 3.2 9.4 + + - +
123A ARG* 1.3 76.6 - - - +
125A PHE* 1.3 75.2 + + - +
127A VAL* 3.3 1.6 + - - +
128A THR* 2.5 60.7 + - + +
129A ARG* 3.6 24.6 + - - -
207A LEU* 4.1 26.7 - - + -
210A ARG* 4.1 32.6 - - + -
211A ILE* 3.8 22.4 - - + -
214A GLU* 5.6 0.4 - - + -
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 2.9 58.0 + + + +
124A TYR* 1.3 90.5 - + - +
126A SER* 1.3 61.3 + - - +
128A THR* 3.6 2.5 - - - -
129A ARG* 2.9 64.7 + - + +
133A TYR* 3.5 41.0 - + + +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 2.9 20.6 + - - -
123A ARG* 3.2 8.9 + - - -
125A PHE* 1.3 78.1 - - - +
127A VAL* 1.3 61.1 + - - +
129A ARG 4.9 1.1 - - - -
130A PRO* 3.4 21.1 - - - +
133A TYR* 3.6 17.4 - - - -
134A ARG* 5.6 5.9 - - - +
137A ARG* 4.2 4.7 - - - -
218A ARG* 4.9 2.4 + - - +
1C ASP* 3.7 35.0 + - - +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG 3.0 17.4 + - - +
124A TYR 4.0 2.5 - - - +
126A SER* 1.3 80.0 - - - +
128A THR* 1.3 65.0 + - + +
129A ARG 3.4 0.2 - - - -
130A PRO* 3.4 11.8 - - - +
211A ILE* 3.7 26.5 - - + -
214A GLU* 3.9 38.0 - - + +
215A THR* 4.0 8.7 - - - +
218A ARG* 3.5 39.7 + - + +
360A GLU* 5.1 0.2 - - - +
504A PGE 4.0 10.5 - - - -
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 2.5 53.8 + - + +
125A PHE* 3.6 1.4 - - - -
127A VAL* 1.3 78.9 - - + +
129A ARG* 1.3 92.6 + - - +
130A PRO* 3.4 6.7 - - - +
211A ILE* 6.2 0.7 - - - -
214A GLU* 4.0 32.5 - - + +
1063A GLU* 5.1 1.0 - - - +
1067A ASN* 5.9 1.2 + - - -
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 3.6 22.2 + - - -
125A PHE* 2.9 39.7 + - + +
126A SER 4.4 0.3 - - - +
128A THR* 1.3 108.3 + - - +
130A PRO* 1.3 65.9 - - - +
131A LEU 2.9 5.0 + - - -
132A SER* 3.5 19.5 - - - +
133A TYR* 3.1 27.4 + - + +
134A ARG 3.9 0.5 + - - -
1063A GLU* 3.2 12.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il