Contacts of the helix formed by residues 93 - 117 (chain A) in PDB entry 5C6P
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 ALA 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.2 15.9 - - + +
84A LEU* 3.9 28.2 - - + +
89A LYS 2.6 18.8 + - - +
90A THR* 3.6 11.2 - - - +
92A GLU* 1.3 71.5 - - - +
94A GLY* 1.3 51.0 - - - +
96A THR* 2.8 12.1 + - - -
97A GLY 2.6 29.8 + - - -
227A PHE* 3.1 15.5 - - + -
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Residues in contact with GLY 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 THR 2.6 23.4 + - - -
91A GLY* 3.1 9.0 - - - -
93A ALA* 1.3 70.6 - - - +
95A GLU* 1.3 53.0 + - - +
96A THR 2.8 4.5 - - - -
97A GLY 2.7 4.0 + - - -
98A ARG* 2.6 34.5 + - - +
227A PHE* 3.3 18.4 - - - -
229A PRO* 3.6 11.3 - - - +
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Residues in contact with GLU 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 GLY 2.5 21.3 + - - +
92A GLU* 3.6 39.0 - - + +
94A GLY* 1.3 71.3 - - - +
96A THR* 1.3 54.0 + - - +
98A ARG* 2.9 44.8 + - - +
99A GLN* 2.4 37.1 - - - +
229A PRO* 3.8 2.2 - - + +
241A TRP* 4.3 14.3 - - - -
243A VAL* 4.4 18.9 - - - +
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 5.2 4.6 - - + +
80A MET* 5.5 13.2 - - + -
81A ILE* 5.3 6.3 - - + -
84A LEU* 4.6 4.4 - - + +
92A GLU* 2.7 24.4 + - - -
93A ALA* 2.8 13.2 + - - -
95A GLU* 1.3 78.1 + - - +
97A GLY* 1.3 52.2 + - - +
99A GLN* 2.6 7.7 + - - +
100A GLY* 2.5 35.5 + - - -
243A VAL* 3.9 32.3 - - + +
246A GLN* 5.3 7.4 - - - +
247A ILE* 5.1 7.4 - - + +
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Residues in contact with GLY 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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77A LEU* 5.7 0.7 - - - -
81A ILE* 4.2 6.9 - - - +
93A ALA 2.6 14.3 + - - -
94A GLY 2.7 3.0 + - - -
96A THR* 1.3 67.2 - - - +
98A ARG* 1.3 62.0 + - - -
101A ILE* 2.8 2.6 + - - -
157A HIS* 2.5 41.7 + - - -
227A PHE* 3.0 28.5 - - - -
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Residues in contact with ARG 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 GLY 2.6 11.2 + - - +
95A GLU* 2.9 54.0 + - - +
97A GLY* 1.3 67.3 - - - -
99A GLN* 1.3 83.2 + - - +
101A ILE* 2.7 33.9 + - - +
102A TRP* 2.8 13.7 + - - +
227A PHE* 4.0 3.4 + - - -
229A PRO* 3.3 50.4 + - + +
230A PHE* 4.1 3.4 - - + +
231A GLY 4.3 7.3 + - - -
232A LEU 5.5 0.4 + - - -
233A THR* 3.2 24.1 - - + +
234A ALA 5.3 0.6 - - - +
241A TRP* 5.5 3.6 - - - -
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Residues in contact with GLN 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 GLU* 2.4 28.0 - - - +
96A THR* 2.6 14.0 + - - +
98A ARG* 1.3 101.5 - - - +
100A GLY* 1.3 51.7 + - - -
102A TRP* 3.1 5.7 - - - +
103A PHE 2.8 8.1 + - - -
233A THR* 3.5 7.3 - - - +
234A ALA 2.5 46.7 + - - +
241A TRP* 2.8 27.7 + - - +
243A VAL* 3.2 24.9 - - + +
244A PHE* 2.5 37.9 - - + -
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Residues in contact with GLY 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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74A MET* 4.0 1.7 - - - +
77A LEU* 4.1 6.1 - - - -
96A THR 2.5 15.7 + - - -
99A GLN* 1.3 69.1 - - - +
101A ILE* 1.3 50.3 + - - +
102A TRP 2.9 5.6 - - - -
103A PHE* 3.0 10.6 - - - +
104A GLY* 2.2 37.2 + - - -
157A HIS* 3.0 19.3 - - - -
247A ILE* 3.9 14.1 - - - +
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Residues in contact with ILE 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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97A GLY 2.8 5.2 + - - +
98A ARG* 2.7 16.9 + - - +
100A GLY* 1.3 73.9 - - - +
102A TRP* 1.3 65.7 + - - +
104A GLY* 3.4 3.0 + - - +
105A LEU* 3.2 18.9 + - - +
154A ARG* 3.5 41.5 - - + +
157A HIS* 2.9 34.5 + - + +
217A LEU* 3.7 24.5 - - + -
218A TRP* 4.7 19.1 - - + -
230A PHE* 3.2 34.5 - - + -
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Residues in contact with TRP 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 ARG 2.8 11.0 + - - +
99A GLN* 3.1 12.8 - - - +
101A ILE* 1.3 75.8 - - - +
103A PHE* 1.3 68.6 + - - +
105A LEU* 2.8 27.8 + - + +
106A ILE* 3.2 20.1 - - + +
230A PHE* 3.6 16.6 - + + -
232A LEU* 5.4 10.1 - - + +
233A THR* 2.8 42.7 + - - +
234A ALA* 3.2 33.0 - - - -
235A LYS* 3.3 28.5 - - + -
244A PHE* 3.7 21.1 - + - -
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Residues in contact with PHE 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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73A ILE* 4.2 9.9 - - + -
74A MET* 3.4 9.4 - - + -
77A LEU* 5.7 0.2 - - + -
99A GLN 2.8 15.4 + - - +
100A GLY* 3.0 15.3 - - - +
102A TRP* 1.3 74.4 - - - +
104A GLY* 1.4 50.4 + - - +
105A LEU 2.8 11.4 + - - -
106A ILE* 3.0 26.9 - - + +
107A LEU* 3.0 51.2 + - + +
244A PHE* 3.4 41.3 - + + -
247A ILE* 3.6 42.8 - - + -
248A TRP* 5.1 15.7 - + - -
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Residues in contact with GLY 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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74A MET* 3.1 19.4 - - - +
100A GLY 2.2 25.1 + - - -
101A ILE* 3.4 7.9 - - - -
102A TRP 3.1 0.2 - - - -
103A PHE* 1.4 64.4 - - - +
105A LEU* 1.3 57.9 + - - +
108A GLY 4.5 0.2 - - - -
150A ALA 3.1 6.1 - - - +
153A HIS* 2.6 27.3 - - - +
154A ARG* 3.1 20.7 + - - -
157A HIS* 4.9 0.7 - - - -
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Residues in contact with LEU 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 ILE 3.2 10.7 + - - +
102A TRP* 2.8 15.7 + - + +
103A PHE 2.8 3.0 + - - -
104A GLY* 1.3 69.1 - - - +
106A ILE* 1.3 58.4 + - + +
107A LEU 2.5 20.0 + - - -
108A GLY* 2.5 17.8 + - - -
109A ILE* 2.9 25.9 + - + -
150A ALA* 3.5 23.3 - - + +
151A MET* 4.8 3.8 - - + +
154A ARG* 4.1 27.8 - - + +
230A PHE* 4.8 14.8 - - + -
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Residues in contact with ILE 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 TRP* 3.2 30.5 - - + +
103A PHE* 3.0 17.7 - - + +
105A LEU* 1.3 75.7 - - + +
107A LEU* 1.3 78.2 + - + +
109A ILE* 3.3 12.5 - - - +
110A PHE* 2.8 29.6 + - - +
235A LYS* 5.5 8.1 - - + +
244A PHE* 3.1 40.2 - - + -
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Residues in contact with LEU 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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70A PHE* 3.8 27.9 - - + -
73A ILE* 3.7 17.5 - - + -
74A MET* 3.1 29.2 - - + -
103A PHE* 3.0 50.1 + - + +
105A LEU 2.5 4.0 + - - -
106A ILE* 1.3 76.3 - - + +
108A GLY* 1.3 55.6 + - - +
110A PHE* 2.7 11.3 + - + +
111A GLY* 2.5 35.5 + - - -
153A HIS* 4.3 6.1 - - - +
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Residues in contact with GLY 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 GLY 3.9 3.2 + - - -
105A LEU 2.5 11.9 + - - -
107A LEU* 1.3 74.3 - - - +
109A ILE* 1.3 55.4 + - - -
111A GLY* 4.6 0.9 - - - -
112A MET* 2.9 24.9 + - - +
149A ALA* 2.9 21.8 - - - -
150A ALA* 3.0 21.7 + - - -
153A HIS* 3.6 17.4 - - - -
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Residues in contact with ILE 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 LEU* 2.9 50.0 + - + -
106A ILE* 3.3 13.5 - - - +
108A GLY* 1.3 73.6 - - - +
110A PHE* 1.3 58.1 + - + +
112A MET* 3.5 8.6 - - + +
113A ILE* 2.7 53.5 + - + +
150A ALA* 3.5 18.3 - - + +
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Residues in contact with PHE 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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70A PHE* 4.3 20.6 - + - -
106A ILE* 2.8 17.3 + - + +
107A LEU* 2.7 13.8 + - + +
109A ILE* 1.3 75.7 - - + +
111A GLY* 1.3 60.5 + - - +
113A ILE* 3.5 21.4 - - + +
114A LEU* 3.4 23.9 + - + +
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Residues in contact with GLY 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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66A VAL* 4.9 8.7 - - - -
70A PHE* 3.9 27.6 - - - -
107A LEU 2.5 19.1 + - - -
108A GLY* 4.1 0.9 - - - -
110A PHE* 1.3 69.0 - - - +
112A MET* 1.3 51.7 + - - +
113A ILE 2.5 4.3 + - - -
114A LEU* 2.5 33.9 + - - +
115A MET* 3.2 8.1 + - - +
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Residues in contact with MET 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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66A VAL* 5.1 0.8 - - - +
108A GLY 2.9 10.6 + - - +
109A ILE* 3.5 15.7 - - + +
111A GLY* 1.3 68.4 - - - -
113A ILE* 1.3 68.4 + - + +
115A MET* 3.3 10.9 - - - +
116A TRP* 2.4 52.0 + - + +
146A ALA 2.9 20.6 - - - +
147A MET* 3.5 22.6 - - - +
149A ALA* 3.0 32.8 - - + +
150A ALA* 3.9 25.6 - - - +
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Residues in contact with ILE 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 ILE* 2.7 33.8 + - + +
110A PHE* 3.5 26.7 - - + +
111A GLY 2.5 8.5 + - - -
112A MET* 1.3 83.0 - - + +
114A LEU* 1.3 59.8 + - - +
116A TRP* 3.2 27.9 - - + +
117A ALA* 2.6 35.4 + - + +
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Residues in contact with LEU 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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66A VAL* 3.7 28.0 - - + -
70A PHE* 6.2 5.8 - - + -
110A PHE* 3.4 19.6 + - + +
111A GLY* 2.5 16.8 + - - +
113A ILE* 1.3 73.8 - - - +
115A MET* 1.3 72.0 + - + +
117A ALA* 3.1 1.2 - - - -
118A ALA* 2.6 42.1 + - + +
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Residues in contact with MET 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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59A GLY 5.9 0.9 - - - +
62A ALA 5.1 6.5 - - - +
63A PHE* 3.3 44.0 - - + -
66A VAL* 3.5 24.9 - - + -
111A GLY 3.2 1.4 + - - -
112A MET* 3.3 13.9 - - - +
114A LEU* 1.3 81.7 - - + +
116A TRP* 1.3 57.2 + - - +
117A ALA 2.5 25.6 + - - +
119A ILE* 3.0 38.1 - - + +
142A PHE* 3.7 18.2 - - + +
145A LEU* 4.5 1.6 - - + +
146A ALA* 3.1 34.1 - - + +
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Residues in contact with TRP 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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112A MET* 2.4 37.6 + - + +
113A ILE* 3.2 44.6 - - + -
115A MET* 1.3 69.6 - - - +
117A ALA* 1.3 72.1 + - + +
119A ILE* 4.6 5.5 - - - +
143A THR* 5.1 6.7 - - - -
147A MET* 3.6 33.1 - - + +
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Residues in contact with ALA 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 ILE* 2.6 20.3 + - + +
114A LEU* 3.8 1.3 - - - +
115A MET 2.5 9.9 + - - +
116A TRP* 1.3 85.7 - - + +
118A ALA* 1.3 56.6 + - - +
119A ILE* 2.6 23.2 + - - +
120A THR* 3.4 11.4 + - - -
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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
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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