Contacts of the helix formed by residues 86 - 118 (chain A) in PDB entry 1T0R
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 ASP 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ARG 3.6 2.7 + - - -
85A ALA* 1.3 74.0 - - - +
87A PRO* 1.3 68.0 - - - +
88A GLY* 2.4 35.6 + - - +
89A TRP* 2.8 29.2 + - + +
90A VAL* 3.1 10.4 + - - +
215A ALA* 6.4 1.1 - - + -
280A TYR 4.4 1.0 - - - +
282A PRO* 3.8 27.9 - - + +
483A HIS* 3.3 18.6 + - - -
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Residues in contact with PRO 87 (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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85A ALA 3.7 6.3 - - - +
86A ASP* 1.3 91.4 - - - +
88A GLY* 1.3 61.2 + - - +
90A VAL* 3.9 9.2 - - + +
91A SER* 2.9 30.0 + - - -
482A ALA* 3.2 32.8 - - + +
483A HIS* 3.8 17.7 - - + +
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Residues in contact with GLY 88 (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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86A ASP* 2.4 24.9 + - - -
87A PRO* 1.3 69.6 - - - +
89A TRP* 1.3 51.5 + - - -
91A SER* 3.7 4.8 + - - -
92A THR* 2.8 31.1 + - - -
280A TYR* 3.4 29.4 - - - +
347A ALA* 4.4 16.8 - - - -
483A HIS* 4.0 3.2 - - - -
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Residues in contact with TRP 89 (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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81A PHE* 4.1 4.5 - + - -
85A ALA* 4.0 15.9 - - + -
86A ASP* 2.8 22.8 + - + +
88A GLY* 1.3 73.2 - - - +
90A VAL* 1.3 67.7 + - - +
91A SER 3.1 1.6 - - - -
92A THR* 2.7 44.9 + - + -
93A MET* 3.0 31.1 + - + +
208A LEU* 4.3 9.0 - - + -
211A ASP* 4.5 9.0 - - + -
212A ALA* 3.4 42.8 - - + -
215A ALA* 4.1 20.2 - - + -
217A ASP* 2.7 31.6 + - + +
220A PHE* 3.7 25.1 - + - -
276A ILE* 5.9 0.4 - - + -
280A TYR 4.3 1.0 + - - -
281A THR* 5.4 10.8 - - + -
282A PRO* 5.9 2.8 - - + +
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Residues in contact with VAL 90 (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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82A VAL* 3.8 26.7 - - + +
85A ALA* 3.9 17.5 - - + +
86A ASP 3.1 12.0 + - - +
87A PRO* 3.4 9.2 + - + +
89A TRP* 1.3 77.3 - - - +
91A SER* 1.3 63.6 + - - +
93A MET* 3.3 11.8 + - + +
94A GLN* 3.1 34.9 + - - +
155A TRP* 3.9 23.7 - - + +
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Residues in contact with SER 91 (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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87A PRO* 2.9 18.3 + - - +
88A GLY* 3.8 6.1 - - - -
90A VAL* 1.3 76.6 - - - +
92A THR* 1.3 64.4 + - - +
94A GLN* 3.3 12.4 + - - +
95A LEU* 2.9 26.4 + - - +
280A TYR* 4.1 10.8 - - - -
344A TRP* 3.8 6.6 - - - +
345A ASP* 2.5 45.7 + - - +
482A ALA* 4.1 0.5 - - - +
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Residues in contact with THR 92 (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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88A GLY 2.8 19.6 + - - -
89A TRP* 2.7 44.6 + - + -
91A SER* 1.3 73.5 - - - +
93A MET* 1.3 55.8 + - + +
95A LEU* 3.5 7.0 + - - +
96A HIS* 3.0 28.9 + - + +
208A LEU* 4.7 11.4 - - + -
220A PHE* 6.0 0.9 - - + -
276A ILE* 3.7 40.2 - - + +
280A TYR* 3.9 8.1 - - - +
281A THR* 5.5 1.0 - - - +
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Residues in contact with MET 93 (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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81A PHE* 5.4 0.7 - - + -
82A VAL* 5.0 11.4 - - + -
85A ALA* 5.5 0.4 - - + -
89A TRP* 3.0 40.3 + - + +
90A VAL* 3.8 14.1 - - + +
92A THR* 1.3 76.2 - - - +
94A GLN* 1.3 60.1 + - - +
96A HIS* 3.0 7.4 + - - +
97A PHE* 2.8 47.0 + - + -
148A ASN* 6.1 0.7 - - - -
155A TRP* 4.0 18.2 - - + -
217A ASP* 2.9 30.3 - - - +
220A PHE* 3.5 34.1 - - + -
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Residues in contact with GLN 94 (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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90A VAL* 3.1 27.5 + - - +
91A SER* 3.7 13.1 + - - +
93A MET* 1.3 74.9 - - - +
95A LEU* 1.3 60.0 + - - +
97A PHE* 4.2 2.2 - - - +
98A GLY* 3.2 13.7 + - - -
152A SER* 4.3 4.4 + - - -
154A LYS* 3.5 46.6 + - + +
155A TRP* 3.7 46.9 - - + +
158A ALA 5.6 0.9 + - - -
343A TRP* 2.9 24.3 + - + -
344A TRP* 4.0 13.8 - - + -
345A ASP* 4.5 2.1 + - - +
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Residues in contact with LEU 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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91A SER 2.9 17.3 + - - +
92A THR 3.6 4.0 - - - +
94A GLN* 1.3 78.5 - - - +
96A HIS* 1.3 64.5 + - - +
99A ALA* 3.1 21.5 + - + +
271A VAL 5.0 1.3 - - - +
272A LEU* 3.3 38.8 - - + +
276A ILE* 3.3 37.7 - - + -
280A TYR* 5.0 1.3 - - + -
343A TRP* 3.7 12.8 - - + +
344A TRP* 3.6 47.5 - - + +
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Residues in contact with HIS 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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92A THR* 3.0 20.4 + - + +
93A MET* 3.4 7.4 - - - +
95A LEU* 1.3 79.8 - - + +
97A PHE* 1.3 68.9 + + - +
99A ALA* 5.2 0.9 - - - -
100A ILE* 3.0 46.6 + - + +
141A GLN* 3.1 30.3 + - - -
204A GLN* 5.3 5.8 + - - -
205A PHE* 3.7 23.6 - + - -
208A LEU* 3.6 26.6 - - + +
220A PHE* 3.8 22.9 - + + -
224A ILE* 3.9 6.3 - - - +
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Residues in contact with PHE 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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93A MET* 2.8 38.2 + - + +
94A GLN* 4.3 3.4 - - - +
96A HIS* 1.3 76.0 - + - +
98A GLY* 1.3 58.6 + - - +
101A ALA* 3.1 35.6 + - - +
141A GLN* 3.4 35.0 - - + -
144A PHE* 4.3 3.1 - + + -
145A PRO* 3.5 37.9 - - + -
148A ASN* 5.8 0.4 - - - -
155A TRP* 4.0 10.5 - + + -
158A ALA* 3.4 20.0 - - + +
220A PHE* 3.5 34.3 - + - -
223A LEU* 3.7 23.8 - - + -
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Residues in contact with GLY 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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94A GLN 3.2 16.5 + - - -
97A PHE* 1.3 79.0 - - - +
99A ALA* 1.3 60.6 + - - +
100A ILE 3.7 0.2 + - - -
101A ALA 4.8 0.7 + - - -
102A LEU 5.4 0.5 + - - -
157A TRP 3.4 23.7 - - - +
158A ALA* 3.7 4.5 - - - +
161A ALA* 3.1 25.3 - - - +
162A ILE* 3.8 11.8 - - - +
343A TRP* 3.9 7.9 - - - -
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Residues in contact with ALA 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 LEU* 3.1 26.0 + - + +
96A HIS* 4.3 1.3 - - - +
98A GLY* 1.3 75.3 - - - +
100A ILE* 1.3 71.1 + - + +
103A GLU* 3.4 21.7 - - - +
162A ILE* 4.2 8.9 - - - +
168A ALA* 6.0 1.1 - - + +
172A ALA* 4.4 9.6 - - + +
176A PHE* 4.3 3.3 - - - -
272A LEU* 4.5 19.3 - - + -
343A TRP* 3.8 12.9 - - + -
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Residues in contact with ILE 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 HIS* 3.0 42.6 + - + +
99A ALA* 1.3 91.6 - - + +
101A ALA* 1.3 57.2 + - - +
102A LEU 3.4 2.0 - - - -
103A GLU* 2.9 4.0 + - + -
104A GLU* 2.6 60.9 + - + +
141A GLN* 4.1 7.4 - - - +
176A PHE* 4.0 24.5 - - + -
196A PHE* 5.6 5.2 - - + -
205A PHE* 4.9 7.0 - - + -
268A LEU* 5.8 1.1 - - + -
272A LEU* 5.6 9.0 - - + -
502A AZI 5.9 4.0 - - - +
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Residues in contact with ALA 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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96A HIS 4.3 0.2 + - - -
97A PHE* 3.1 22.4 + - - +
98A GLY 4.8 0.2 - - - -
100A ILE* 1.3 79.7 - - - +
102A LEU* 1.3 67.2 + - + +
104A GLU* 3.2 16.3 + - - +
105A TYR* 3.2 5.2 + - - +
138A GLY* 3.8 9.8 - - - -
141A GLN* 3.8 36.5 - - + +
142A LEU* 4.6 4.9 - - + -
158A ALA 3.1 17.0 - - - +
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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 GLY 5.4 0.6 + - - -
100A ILE 3.4 0.2 - - - -
101A ALA* 1.3 80.4 - - + +
103A GLU* 1.3 62.5 + - - +
105A TYR* 3.4 7.5 + - + +
106A ALA* 2.9 26.7 + - - +
142A LEU* 4.3 7.2 - - + -
158A ALA 3.7 19.7 + - - +
159A HIS* 3.4 27.8 - - + +
162A ILE* 4.1 27.1 - - + +
163A HIS* 3.6 18.4 - - + +
34B ASN 4.3 0.7 - - - +
35B LEU* 3.4 53.8 - - + +
37B TYR* 4.5 4.6 - - + -
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Residues in contact with GLU 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 ALA 3.4 19.7 - - - +
100A ILE* 2.9 9.0 + - + +
102A LEU* 1.3 75.2 - - - +
104A GLU* 1.3 66.6 + - - +
106A ALA* 3.2 6.5 + - - +
107A ALA* 3.0 18.9 + - - +
162A ILE* 4.0 13.4 - - + +
172A ALA* 3.5 1.1 - - + +
173A ARG* 3.4 29.5 + - - +
176A PHE* 2.9 52.3 - - + +
180A MET* 3.6 7.6 - - - +
502A AZI 5.5 1.5 + - - -
37B TYR* 3.1 29.4 + - - -
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Residues in contact with GLU 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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100A ILE* 2.6 39.2 + - + +
101A ALA* 3.2 9.6 - - - +
103A GLU* 1.3 73.8 - - - +
105A TYR* 1.3 62.8 + - - +
107A ALA* 3.0 21.9 + - - +
134A GLU* 3.0 19.0 - - - +
137A HIS* 3.6 12.1 + - + +
138A GLY* 4.0 13.7 - - - +
141A GLN* 3.0 20.9 - - - +
205A PHE* 4.2 15.6 - - - -
227A ILE* 4.4 0.2 - - - +
500A FE 2.2 30.3 - - - -
502A AZI 3.3 16.0 + - - +
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Residues in contact with TYR 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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101A ALA 3.2 8.4 + - - +
102A LEU* 3.6 11.9 - - - +
104A GLU* 1.3 80.5 - - - +
106A ALA* 1.3 59.2 + - - +
108A SER* 2.9 34.4 - - - -
109A THR* 4.0 2.4 + - - -
134A GLU 4.0 7.0 - - - -
135A ASN* 4.3 21.1 - - - -
138A GLY* 4.0 8.2 - - - -
139A GLN* 5.5 2.5 - - + -
142A LEU* 6.4 0.2 - - + -
35B LEU* 3.4 53.2 - - + -
36B HIS* 3.5 25.8 - + - -
149B SER* 3.2 17.1 + - - -
152B THR* 3.5 13.7 - - + +
153B ASN* 2.6 36.5 + - - -
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Residues in contact with ALA 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 14.9 + - - +
103A GLU* 3.4 14.6 - - - +
104A GLU 3.2 0.2 - - - -
105A TYR* 1.3 79.1 - - - +
107A ALA* 1.3 54.6 + - - +
109A THR* 2.7 38.7 + - - -
110A ALA 3.3 2.3 + - - -
180A MET* 4.1 2.2 - - + -
181A MET* 3.4 19.4 - - - +
36B HIS* 6.2 1.3 - - - -
37B TYR* 3.8 24.2 - - + +
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Residues in contact with ALA 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 GLU 3.0 8.3 + - - +
104A GLU* 3.0 16.7 + - - +
106A ALA* 1.3 75.5 - - - +
108A SER* 1.3 61.8 + - - +
110A ALA* 3.0 5.1 + - + +
111A GLU* 2.9 26.0 + - - +
134A GLU* 3.7 23.6 - - + +
180A MET* 3.3 30.0 - - + +
192A LEU* 5.0 4.8 - - + +
502A AZI 4.7 7.2 - - - +
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Residues in contact with SER 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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104A GLU 3.5 2.2 + - - -
105A TYR* 2.9 27.6 + - - -
107A ALA* 1.3 78.7 - - - +
109A THR* 1.3 54.5 + - - +
111A GLU 3.3 1.2 + - - -
112A ALA* 3.0 23.4 + - - +
131A MET* 3.4 31.7 + - - +
134A GLU* 3.6 14.3 - - - +
135A ASN* 4.4 10.0 + - - +
143B HIS* 2.9 26.3 - - - -
156B THR* 4.7 0.5 + - - -
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Residues in contact with THR 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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105A TYR* 4.5 3.5 + - - -
106A ALA* 2.7 18.8 + - - -
108A SER* 1.3 71.0 - - - +
110A ALA* 1.3 65.3 + - - -
111A GLU 3.1 0.2 - - - -
112A ALA* 3.1 3.5 + - - +
113A ARG* 2.9 28.6 + - - +
181A MET* 4.4 9.4 - - - -
36B HIS* 4.5 15.8 + - - -
38B PHE* 6.6 0.2 - - + -
46B TRP* 5.7 2.9 - - + -
58B TYR* 3.9 13.9 - - - +
143B HIS* 3.6 17.1 + - - -
144B GLN* 3.5 30.4 - - + +
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Residues in contact with ALA 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 ALA 3.3 2.2 + - - -
107A ALA* 3.0 10.9 + - - +
109A THR* 1.3 77.6 - - - +
111A GLU* 1.3 63.1 + - - +
113A ARG* 3.2 20.0 + - - +
114A MET* 3.6 3.7 + - - +
180A MET* 3.4 32.8 - - + +
181A MET* 3.3 23.6 - - + +
188A VAL* 3.9 14.2 - - + +
192A LEU* 4.0 11.2 - - + -
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Residues in contact with GLU 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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107A ALA* 2.9 15.1 + - + +
108A SER 3.4 6.7 - - - +
110A ALA* 1.3 79.3 - - + +
112A ALA* 1.3 61.9 + - - +
114A MET* 2.9 19.6 + - - +
115A ALA* 2.9 21.0 + - - +
127A ALA* 3.2 17.2 - - - +
130A GLY* 3.1 32.9 - - - +
131A MET* 3.3 15.9 - - - +
134A GLU* 4.2 7.8 - - + +
192A LEU* 4.7 7.0 - - + +
193A THR* 4.1 5.5 + - - -
197A GLU* 4.5 1.2 - - - +
234A HIS* 3.9 15.3 - - - -
237A GLN* 3.1 29.0 + - - -
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Residues in contact with ALA 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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108A SER 3.0 14.5 + - - +
109A THR 3.3 9.2 - - - +
111A GLU* 1.3 76.7 - - - +
113A ARG* 1.3 61.3 + - - +
115A ALA* 3.5 3.6 - - - +
116A ARG* 3.1 18.4 + - - +
131A MET* 4.2 4.0 - - - +
140B VAL* 3.8 24.8 - - + +
143B HIS* 3.6 24.9 - - + -
144B GLN* 2.9 22.1 - - + +
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Residues in contact with ARG 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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33A MET* 4.1 32.1 - - - +
109A THR* 2.9 20.8 + - - +
110A ALA* 3.3 13.9 - - - +
111A GLU 3.0 0.6 - - - -
112A ALA* 1.3 77.9 - - - +
114A MET* 1.3 56.9 + - - +
117A PHE* 2.9 38.1 + - + +
180A MET 4.9 2.4 + - - -
181A MET* 2.9 31.9 + - - +
183A ARG 4.1 16.1 + - - +
185A SER* 4.2 4.7 - - - +
188A VAL* 5.0 5.4 - - + -
46B TRP* 4.8 1.6 - - - -
54B MET* 3.7 17.6 - - - +
57B TRP* 6.0 0.2 - - - -
58B TYR* 2.9 39.4 + - - -
144B GLN* 2.8 48.4 + - - +
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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 ALA 3.6 4.0 + - - +
111A GLU* 2.9 34.3 + - - +
113A ARG* 1.3 75.6 - - - +
115A ALA* 1.3 65.9 + - - +
118A ALA* 2.9 28.0 + - + +
123A ASN* 3.9 17.5 - - - +
124A ARG* 3.7 2.7 - - - +
127A ALA* 3.8 8.7 - - + -
185A SER* 3.0 31.0 - - - +
188A VAL* 4.0 16.8 - - + -
189A SER* 3.6 34.5 - - - -
192A LEU* 5.6 0.7 - - + -
193A THR* 4.2 7.4 - - - +
237A GLN* 3.9 19.5 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU 2.9 12.3 + - - +
112A ALA* 3.5 10.3 - - - +
113A ARG 3.3 0.2 - - - -
114A MET* 1.3 76.9 - - - +
116A ARG* 1.3 55.8 + - - +
124A ARG* 3.3 42.8 - - - +
127A ALA* 3.6 7.3 - - + +
128A THR* 3.9 13.6 + - - +
133B HIS* 5.2 1.2 - - - -
136B GLN* 5.8 1.9 + - - +
137B MET* 4.2 6.4 - - - +
140B VAL* 3.7 27.1 - - + +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.0 37.9 + - - +
29A PHE* 3.8 8.7 - - - -
112A ALA 3.1 9.8 + - - +
114A MET 3.1 0.6 - - - -
115A ALA* 1.3 79.9 - - - +
117A PHE* 1.3 90.5 + - + +
118A ALA 3.6 0.9 - - - -
124A ARG* 4.3 1.7 - - - +
137B MET* 3.3 54.7 + - - +
140B VAL* 3.3 18.8 - - + -
141B TYR* 4.0 13.4 - - + +
144B GLN* 3.9 5.8 - - - +
210B LEU* 2.9 37.6 + - - +
213B TRP* 3.4 8.5 - - - -
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 4.4 0.7 - - - -
29A PHE* 3.6 8.0 - - - -
30A PRO* 4.1 13.5 - - + -
33A MET* 3.4 56.1 - - + +
34A SER* 2.3 34.9 + - - -
113A ARG* 2.9 25.7 + - - +
116A ARG* 1.3 101.6 - - + +
118A ALA* 1.3 56.5 + - - +
119A LYS 3.6 0.2 + - - -
185A SER* 4.1 3.4 - - - -
57B TRP* 4.6 0.9 - + - -
141B TYR* 3.8 10.1 - + - -
144B GLN* 3.4 26.9 - - - -
213B TRP* 3.5 40.4 - + - -
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.8 2.4 - - - -
34A SER* 4.4 1.3 - - - -
114A MET 2.9 21.6 + - - +
116A ARG 3.6 0.2 - - - -
117A PHE* 1.3 77.3 - - - +
119A LYS* 1.3 54.7 + - - +
120A ALA* 4.2 0.9 - - + +
123A ASN* 3.9 30.7 - - + +
124A ARG* 2.5 41.6 + - + +
185A SER* 3.4 16.7 + - - +
186A VAL* 6.0 3.1 - - + -
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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
------------------------------------------------------------
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