Contacts of the helix formed by residues 85 - 107 (chain B) in PDB entry 1VGO
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 TYR 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY* 2.6 35.8 + - - +
71B THR* 3.3 41.0 + - + +
83B ILE* 3.5 3.5 + - + -
84B TYR* 1.3 70.3 - - - +
86B ALA* 1.3 65.1 + - - +
88B TYR* 3.1 9.8 + - - +
89B ALA* 3.0 21.2 + - - +
128B LEU* 4.1 20.4 - - + -
132B LEU* 4.2 33.6 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA* 3.5 32.2 - - + +
63B ALA* 4.3 14.4 - - + -
64B MET* 3.6 12.6 - - + +
69B GLY* 4.1 8.6 + - - -
84B TYR* 5.4 0.2 - - + -
85B TYR* 1.3 78.3 - - - +
87B ARG* 1.3 53.4 + - - +
89B ALA* 3.8 7.2 - - - +
90B ASP* 2.7 37.6 + - - +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 5.4 1.6 - - - +
61B TYR* 5.6 3.0 + - - -
64B MET* 3.8 31.9 - - + +
84B TYR* 3.4 29.3 + - + +
85B TYR 3.1 0.6 - - - -
86B ALA* 1.3 77.9 - - - +
88B TYR* 1.3 70.2 + - + +
90B ASP* 3.3 7.0 - - - +
91B TRP* 3.2 66.4 + - + +
209B GLU* 4.1 8.3 + - - -
210B THR* 4.3 24.0 + - - +
213B PHE* 3.3 46.1 - - - +
217B ASP* 5.5 2.2 + - - +
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.6 5.8 - - + -
84B TYR 3.5 19.3 - - - -
85B TYR 3.1 6.7 + - - +
87B ARG* 1.3 88.8 + - - +
89B ALA* 1.3 61.8 + - - +
90B ASP 3.1 1.8 - - - -
91B TRP* 4.1 22.1 - + - +
92B LEU* 2.9 29.7 + - - +
124B ILE* 3.3 32.7 - - + +
127B GLY 3.7 21.3 - - - -
128B LEU* 3.7 34.8 - - + -
131B ALA* 3.6 15.6 - - + +
194B TRP* 3.2 28.6 + - - -
199B GLU* 5.0 0.3 + - - +
261B RET 4.1 6.7 - - + -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 5.8 0.2 - - - -
85B TYR 3.0 15.6 + - - +
86B ALA* 3.8 8.1 - - - +
88B TYR* 1.3 73.4 - - - +
90B ASP* 1.3 65.6 + - - +
92B LEU* 3.4 10.2 + - + -
93B PHE* 2.9 40.0 + - + -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 4.7 8.5 - - - +
57B ALA* 3.6 25.6 + - - +
60B ALA* 3.6 21.0 - - + +
61B TYR* 4.2 12.5 - - - -
64B MET* 5.3 0.5 - - - +
86B ALA 2.7 17.8 + - - +
87B ARG* 3.3 7.5 - - - +
89B ALA* 1.3 78.2 - - - +
91B TRP* 1.3 69.3 + - - +
93B PHE* 3.0 5.0 + - - +
94B THR* 2.8 44.5 + - - -
217B ASP* 4.7 0.2 - - - +
221B LYS* 3.8 9.1 + - - -
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Residues in contact with TRP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.2 50.0 + - + +
88B TYR* 3.5 21.1 + + - +
90B ASP* 1.3 85.7 + - - +
92B LEU* 1.3 58.4 + - - +
94B THR* 3.9 1.8 - - - -
95B THR* 2.4 40.0 + - + -
124B ILE* 3.6 20.0 - - + +
190B TYR* 3.7 17.7 - + - -
213B PHE* 3.8 27.8 - + - -
217B ASP* 3.2 28.7 + - - -
221B LYS* 3.9 4.7 - - - -
261B RET 3.3 63.3 - - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR 2.9 19.3 + - - +
89B ALA* 3.5 11.2 - - + +
90B ASP 3.1 0.4 - - - -
91B TRP* 1.3 77.7 - - - +
93B PHE* 1.3 80.6 + - + +
95B THR* 4.6 0.2 - - - -
96B PRO* 2.9 20.5 - - - +
121B ALA* 4.0 37.4 - - + +
124B ILE* 4.0 11.9 - - + +
125B VAL* 5.2 4.3 - - + +
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ILE* 4.0 26.7 - - + -
89B ALA* 2.9 32.7 + - + -
90B ASP 3.0 4.4 + - - +
92B LEU* 1.3 96.6 - - + +
94B THR* 1.3 61.7 + - - +
96B PRO* 3.1 14.8 - - - +
97B LEU* 3.0 27.5 + - + +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.5 33.1 + - + +
56B ILE* 4.2 8.5 - - - +
90B ASP* 2.8 29.0 + - - -
91B TRP* 4.4 0.7 - - - -
93B PHE* 1.3 76.4 - - - +
95B THR* 1.3 66.5 + - - +
97B LEU* 3.1 17.8 + - - +
98B LEU* 3.1 18.3 + - + +
221B LYS* 3.1 26.8 - - - -
261B RET 3.4 14.4 - - + -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TRP* 2.4 30.8 + - + +
94B THR* 1.3 75.2 - - - +
96B PRO* 1.3 67.6 - - - +
98B LEU* 3.4 4.3 + - - +
99B LEU* 3.1 26.7 + - - +
120B ASP* 2.6 31.5 + - - -
123B MET* 5.0 0.4 - - + -
124B ILE* 4.0 7.8 - - + +
187B TRP* 3.8 13.6 - - + -
261B RET 3.7 48.7 - - + -
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Residues in contact with PRO 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TRP 3.5 0.2 - - - +
92B LEU* 2.9 22.9 - - + +
93B PHE* 3.1 19.7 - - - +
95B THR* 1.3 99.2 - - - +
97B LEU* 1.3 59.7 + - + +
99B LEU* 3.4 7.2 + - + +
100B LEU* 3.0 27.4 + - - +
117B ILE* 4.2 34.1 - - + +
120B ASP* 3.7 12.3 - - - +
121B ALA* 5.6 3.1 - - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.4 26.8 - - + +
52B LEU* 3.9 28.0 - - + -
53B VAL* 3.8 19.5 - - + +
56B ILE* 3.8 26.2 - - + -
93B PHE 3.0 19.5 - - - +
94B THR* 3.1 8.0 + - - +
96B PRO* 1.3 77.7 - - + +
98B LEU* 1.3 63.0 + - - +
100B LEU* 3.2 16.7 + - + +
101B ASP* 3.1 17.0 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR* 5.6 1.8 - - + -
53B VAL* 4.0 22.2 - - + -
94B THR* 3.1 33.2 + - + +
95B THR* 3.9 4.0 - - - +
96B PRO 3.4 0.2 - - - -
97B LEU* 1.3 73.4 - - - +
99B LEU* 1.3 66.8 + - - +
101B ASP* 3.1 24.0 + - - +
102B LEU* 3.4 12.2 + - + +
187B TRP* 4.0 16.4 - - + +
220B ALA 3.7 21.3 - - - +
221B LYS* 4.8 2.0 - - - +
224B PHE* 3.6 40.1 - - + -
261B RET 4.0 19.3 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR 3.1 15.4 + - - +
96B PRO* 3.6 7.6 - - + +
98B LEU* 1.3 76.7 - - - +
100B LEU* 1.3 56.5 + - - +
102B LEU* 3.1 15.3 + - + +
103B ALA* 2.8 28.5 + - - +
116B LEU* 3.6 35.1 - - + +
117B ILE* 4.8 5.6 - - + -
120B ASP* 3.3 44.2 - - + +
153B VAL* 4.3 10.8 - - + -
157B LEU* 4.3 15.9 - - + -
183B VAL* 5.3 0.2 - - + -
187B TRP* 3.6 25.4 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.3 24.2 - - + -
96B PRO 3.0 15.0 + - - +
97B LEU* 3.3 21.1 - - + +
99B LEU* 1.3 75.5 - - - +
101B ASP* 1.3 67.7 + - - +
103B ALA* 3.1 10.7 + - + -
104B LEU* 2.8 47.2 + - + +
113B ILE* 4.6 17.5 - - + -
117B ILE* 5.2 6.0 - - + +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.4 27.8 - - + +
49B ILE* 3.7 17.9 - - - +
50B THR* 2.9 30.2 + - - +
53B VAL* 5.3 0.5 - - - +
97B LEU 3.1 11.8 + - - +
98B LEU* 3.1 14.6 + - - +
100B LEU* 1.3 80.7 - - - +
102B LEU* 1.3 57.4 + - + +
104B LEU* 3.3 1.3 + - - -
105B LEU* 2.8 30.6 + - - +
224B PHE* 3.9 15.2 - - + -
228B LEU* 3.5 21.7 - - + +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU 3.7 13.0 - - - +
99B LEU* 3.1 14.1 + - + +
101B ASP* 1.3 76.1 - - - +
103B ALA* 1.3 58.6 + - - +
105B LEU* 3.1 7.2 + - + +
106B ALA* 2.9 31.4 + - - +
157B LEU* 3.9 38.6 - - + -
161B LEU* 3.7 2.8 - - + +
176B PHE* 3.7 16.3 - - + -
179B LEU* 3.9 33.4 - - + -
180B THR* 4.3 13.7 - - - +
183B VAL* 4.1 18.2 - - + -
224B PHE* 4.1 11.0 - - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU 2.8 13.4 + - - +
100B LEU* 3.1 15.2 + - + +
102B LEU* 1.3 76.2 - - - +
104B LEU* 1.3 58.8 + - - +
106B ALA 3.4 0.3 + - - -
107B LYS* 3.0 23.0 + - - -
108B VAL* 3.4 14.5 + - + +
113B ILE* 3.8 33.4 - - + +
116B LEU* 4.9 6.3 - - + -
161B LEU* 3.3 15.4 - - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLU* 4.3 21.3 - - + +
46B TYR* 3.1 26.9 + - + +
49B ILE* 3.5 32.5 - - + -
100B LEU* 2.8 32.6 + - + +
101B ASP 3.6 3.4 - - - +
103B ALA* 1.3 78.7 - - + +
105B LEU* 1.3 64.3 + - - +
107B LYS* 3.4 20.0 + - - +
113B ILE* 5.2 6.7 - - + -
168B ARG* 3.9 6.4 + - - -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.1 22.8 + - + +
101B ASP 2.8 16.0 + - - +
102B LEU* 3.1 11.2 + - + +
104B LEU* 1.3 77.6 - - - +
106B ALA* 1.3 55.8 + - - +
165B ALA* 4.8 1.4 - - - +
168B ARG* 2.7 24.9 + - - +
172B VAL* 3.4 36.5 - - + +
175B THR* 4.4 3.8 - - + -
176B PHE* 4.0 26.2 - - + +
179B LEU* 4.0 15.3 - - + -
228B LEU* 3.9 26.0 - - + -
233B ALA* 3.9 19.7 - - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 2.9 15.6 + - - +
105B LEU* 1.3 76.3 - - - +
107B LYS* 1.3 71.7 + - - +
108B VAL* 3.8 3.1 - - + -
161B LEU* 3.3 44.4 - - + +
164B ALA* 3.4 23.4 - - - +
165B ALA* 3.8 14.7 - - + +
168B ARG* 4.1 1.5 - - - +
176B PHE* 3.9 4.0 - - + -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 3.2 27.0 + - - -
46B TYR* 5.7 0.4 - - - -
103B ALA 3.0 8.5 + - - -
104B LEU* 3.4 11.9 + - - +
106B ALA* 1.3 79.6 - - - +
108B VAL* 1.3 64.3 + - - +
164B ALA* 4.6 3.9 - - - +
167B LYS* 5.9 1.9 + - - -
168B ARG* 3.3 46.9 - - - +
238B THR* 3.8 20.7 - - - +
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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