Contacts of the helix formed by residues 85 - 107 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY* 3.2 24.0 + - - +
70A VAL 5.3 0.2 - - - -
71A THR* 3.6 32.4 + - + +
83A ILE* 3.1 10.5 + - + -
84A TYR* 1.3 70.1 - - - +
86A ALA* 1.3 60.8 + - - +
88A TYR* 3.1 12.0 + - - +
89A ALA* 3.1 21.3 + - - +
128A LEU* 4.2 22.7 - - + +
132A LEU* 4.0 34.7 - - + +
309A BNG 3.5 46.2 - - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 3.7 17.5 - - - +
63A ALA* 4.4 13.7 - - + -
64A MET* 3.7 24.0 - - + -
68A ILE 4.8 7.9 - - - +
69A GLY* 4.4 2.7 + - - -
84A TYR 2.9 1.0 + - - -
85A TYR* 1.3 76.6 - - - +
87A ARG* 1.3 64.3 + - - +
89A ALA* 3.7 10.1 - - - +
90A ASP* 3.0 24.6 + - - +
309A BNG 6.1 1.8 - - - -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.4 3.8 - - - +
61A TYR* 5.6 2.4 + - - -
64A MET* 4.0 31.9 - - + +
84A TYR* 2.8 25.3 + - + +
86A ALA* 1.3 77.8 - - - +
88A TYR* 1.3 75.5 + - + +
90A ASP* 3.3 6.9 - - - +
91A TRP* 3.1 67.4 + - + +
194A TRP* 6.2 0.6 - - - -
199A GLU* 4.0 14.5 + - - -
206A LEU* 6.2 2.4 - - - +
209A GLU* 4.2 2.4 + - - -
210A THR* 4.7 18.2 + - - +
213A PHE* 3.7 42.7 - - - +
217A ASP* 5.5 1.6 + - - -
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 4.5 6.7 - - + -
84A TYR 3.8 15.9 - - - -
85A TYR 3.1 6.2 + - - +
87A ARG* 1.3 95.8 + - - +
89A ALA* 1.3 61.7 + - - +
90A ASP 3.3 0.2 - - - -
91A TRP* 4.0 22.3 - + - -
92A LEU* 2.9 30.7 + - - +
124A ILE* 3.3 18.4 - - + +
127A GLY 3.9 4.5 - - - -
128A LEU* 3.7 62.8 - - + -
131A ALA* 3.7 16.8 - - + +
194A TRP* 3.2 27.1 + - - -
199A GLU* 4.8 4.9 + - - +
260A RET 4.1 7.0 - - + -
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Residues in contact with ALA 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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56A ILE* 5.2 1.2 - - - +
60A ALA* 6.1 0.4 - - + -
85A TYR 3.1 12.9 + - - +
86A ALA* 3.7 13.2 - - - +
87A ARG 3.3 0.2 - - - -
88A TYR* 1.3 74.4 - - - +
90A ASP* 1.3 68.5 + - - +
92A LEU* 3.4 7.7 + - - -
93A PHE* 3.1 31.7 + - + +
309A BNG 4.3 29.6 - - + -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.4 9.3 - - - +
57A ALA* 3.7 27.9 + - - +
60A ALA* 3.6 15.5 - - + +
61A TYR* 4.4 12.5 - - - -
64A MET* 5.3 0.9 - - - +
86A ALA 3.0 13.8 + - - +
87A ARG* 3.3 12.3 - - - +
89A ALA* 1.3 80.3 - - - +
91A TRP* 1.3 66.3 + - - +
93A PHE* 3.0 1.9 + - - +
94A THR* 2.8 53.0 + - - -
217A ASP* 4.9 0.5 - - - +
221A LYS* 3.7 10.1 + - - -
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Residues in contact with TRP 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 ARG* 3.1 52.4 + - + +
88A TYR* 4.0 17.3 - + - +
90A ASP* 1.3 91.5 + - - +
92A LEU* 1.3 60.7 + - - +
94A THR* 4.3 4.0 - - - -
95A THR* 2.7 35.7 + - + +
124A ILE* 3.5 20.4 - - + -
190A TYR* 3.6 30.7 - + - -
194A TRP* 5.8 0.4 - + - -
213A PHE* 3.9 18.6 - + - -
217A ASP* 3.2 25.4 + - - -
260A RET 3.4 67.9 - - + +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR 2.9 20.6 + - - +
89A ALA* 3.5 8.7 - - - +
90A ASP 3.1 0.4 + - - -
91A TRP* 1.3 75.8 - - - +
93A PHE* 1.3 84.2 + - + +
96A PRO* 3.0 22.2 - - - +
120A ASP* 4.8 0.3 - - - +
121A ALA* 4.2 35.2 - - + +
124A ILE* 3.8 14.1 - - + +
125A VAL* 5.0 5.6 - - + +
309A BNG 4.7 20.9 - - + -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.1 22.2 - - + -
89A ALA* 3.1 25.8 + - + +
90A ASP 3.0 3.7 + - - +
92A LEU* 1.3 99.9 - - + +
94A THR* 1.3 60.9 + - - +
96A PRO* 3.5 9.2 - - - +
97A LEU* 3.3 27.3 + - + +
309A BNG 4.2 36.6 - - + -
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Residues in contact with THR 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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53A VAL* 3.5 29.9 + - + +
56A ILE* 4.1 10.6 - - - +
90A ASP* 2.8 28.9 + - - -
91A TRP* 4.3 1.3 - - - -
93A PHE* 1.3 76.6 - - - +
95A THR* 1.3 67.1 + - - +
96A PRO 3.2 2.0 - - - -
97A LEU* 3.2 10.8 + - - +
98A LEU* 3.1 23.0 + - + +
221A LYS* 3.2 27.6 - - - -
260A RET 3.4 13.0 - - + -
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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
----------------------------------------------------------
91A TRP* 2.7 27.0 + - + +
94A THR* 1.3 74.1 - - - +
96A PRO* 1.4 61.2 - - - +
98A LEU* 3.3 6.4 + - - +
99A LEU* 2.9 32.3 + - - +
120A ASP* 2.4 35.6 + - - +
123A MET* 4.7 3.4 - - + -
124A ILE* 4.0 4.3 - - - +
187A TRP* 3.7 13.2 - - + -
260A RET 3.7 48.9 - - + -
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Residues in contact with PRO 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 LEU 3.0 27.4 - - - +
93A PHE* 3.5 8.1 - - - +
94A THR 3.3 3.8 - - - -
95A THR* 1.4 98.8 - - - +
97A LEU* 1.3 57.2 + - + +
99A LEU* 3.2 10.5 + - + +
100A LEU* 2.9 28.1 + - - +
117A ILE* 4.3 32.5 - - + +
120A ASP* 3.4 13.9 - - + +
121A ALA* 5.4 3.6 - - + +
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Residues in contact with LEU 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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49A ILE* 3.4 32.1 - - + +
52A LEU* 3.9 38.1 - - + +
53A VAL* 3.8 12.3 - - + -
56A ILE* 4.0 15.3 - - + -
93A PHE* 3.3 20.2 - - + +
94A THR* 3.2 8.3 + - - +
96A PRO* 1.3 76.6 - - + +
98A LEU* 1.3 65.3 + - - +
100A LEU* 3.1 23.6 + - + +
101A ASP* 3.2 9.7 + - - +
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Residues in contact with LEU 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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50A THR* 5.9 2.0 - - + -
53A VAL* 3.9 23.3 - - + -
94A THR* 3.1 27.0 + - + +
95A THR* 3.7 5.8 - - - +
97A LEU* 1.3 76.9 - - - +
99A LEU* 1.3 64.0 + - - +
101A ASP* 3.1 22.0 + - - +
102A LEU* 3.3 15.9 + - + +
183A VAL* 6.3 0.2 - - + -
187A TRP* 3.8 16.4 - - + +
220A ALA 3.7 17.5 - - - +
221A LYS* 4.8 2.9 - - - +
224A PHE* 3.6 37.5 - - + -
260A RET 3.7 29.8 - - + -
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Residues in contact with LEU 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 13.6 + - - +
96A PRO* 3.2 8.3 + - + +
98A LEU* 1.3 76.9 - - - +
100A LEU* 1.3 57.3 + - - +
102A LEU* 3.3 20.6 + - + +
103A ALA* 2.9 26.6 + - - +
116A LEU* 3.8 39.7 - - + +
117A ILE* 4.5 5.8 - - + -
120A ASP* 3.4 44.0 - - + +
153A VAL* 4.3 11.4 - - + -
157A LEU* 4.8 6.1 - - + -
183A VAL* 5.7 0.2 - - + -
187A TRP* 3.4 30.1 - - + -
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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
----------------------------------------------------------
49A ILE* 3.7 28.7 - - + -
96A PRO 2.9 12.1 + - - +
97A LEU* 3.3 19.7 - - + +
98A LEU 3.1 0.4 - - - -
99A LEU* 1.3 75.8 - - - +
101A ASP* 1.3 66.5 + - - +
103A ALA* 4.1 11.7 - - + -
104A LEU* 2.9 42.3 + - + +
113A ILE* 4.5 19.5 - - + -
117A ILE* 5.1 5.4 - - + +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 3.5 21.3 - - + +
49A ILE* 3.5 24.7 - - - +
50A THR* 3.1 24.7 + - - +
53A VAL* 5.3 0.3 - - - +
97A LEU 3.2 9.0 + - - +
98A LEU* 3.1 16.9 + - - +
100A LEU* 1.3 76.3 - - - +
102A LEU* 1.3 63.7 + - + +
104A LEU* 3.3 6.5 + - - +
105A LEU* 3.0 27.5 + - - +
179A LEU* 6.1 0.2 - - + -
224A PHE* 4.4 12.7 - - + -
228A LEU* 3.5 25.4 - - + +
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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 LEU* 3.3 13.0 + - + +
99A LEU* 3.3 16.6 + - + +
100A LEU 3.1 0.6 - - - -
101A ASP* 1.3 74.7 - - - +
103A ALA* 1.3 65.3 + - - +
105A LEU* 3.3 10.8 + - + +
106A ALA* 3.0 19.6 + - - +
157A LEU* 4.1 32.1 - - + -
161A LEU* 3.8 7.9 - - + -
176A PHE* 3.4 32.6 - - + -
179A LEU* 4.0 26.2 - - + -
180A THR* 4.4 7.6 - - - +
183A VAL* 4.3 17.5 - - + -
224A PHE* 4.1 9.0 - - + -
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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 LEU 2.9 17.1 + - - +
100A LEU* 3.6 11.0 - - + +
102A LEU* 1.3 76.1 - - - +
104A LEU* 1.3 58.2 + - - +
106A ALA 3.4 0.2 + - - -
107A LYS* 2.8 26.0 + - - -
108A VAL* 3.4 13.7 + - + +
113A ILE* 3.6 37.9 - - + +
116A LEU* 5.2 3.6 - - + -
161A LEU* 3.5 15.2 - - + +
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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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42A GLU* 5.4 2.0 - - - +
45A GLU* 4.0 26.9 - - + +
46A TYR* 3.3 30.5 - - + +
49A ILE* 3.6 30.3 - - + -
100A LEU* 2.9 32.3 + - + +
101A ASP 3.4 4.9 - - - +
103A ALA* 1.3 77.4 - - + +
105A LEU* 1.3 63.0 + - - +
107A LYS* 2.8 37.4 + - - +
113A ILE* 5.5 4.5 - - + -
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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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46A TYR* 3.2 22.1 + - + +
101A ASP 3.0 17.4 + - - +
102A LEU* 3.6 14.8 - - + +
104A LEU* 1.3 76.7 - - - +
106A ALA* 1.3 58.8 + - - +
165A ALA* 4.6 0.7 - - - +
168A ARG* 2.9 31.3 + - - +
172A VAL* 3.3 18.6 - - + +
175A THR* 4.6 1.3 - - + -
176A PHE* 4.0 25.1 - - + +
179A LEU* 3.9 16.8 - - + -
228A LEU* 3.9 23.1 - - + -
233A ALA* 3.9 35.0 - - + +
234A ILE* 4.9 0.2 - - + -
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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 3.0 16.5 + - - +
103A ALA 3.9 3.1 - - - +
105A LEU* 1.3 74.9 - - - +
107A LYS* 1.3 70.9 + - - +
108A VAL 4.3 3.6 - - - +
161A LEU* 3.2 39.0 - - + +
164A ALA* 3.4 24.7 - - + +
165A ALA* 3.8 10.2 - - + -
168A ARG* 4.3 1.5 - - - -
176A PHE* 3.7 8.9 - - + -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.1 26.6 + - - -
46A TYR* 4.1 2.2 + - - -
103A ALA 2.8 9.8 + - - -
104A LEU* 2.8 32.6 + - - +
106A ALA* 1.3 81.1 - - - +
108A VAL* 1.3 67.3 + - - +
164A ALA* 4.9 2.2 - - - +
168A ARG* 3.4 39.5 - - + +
237A GLU* 5.6 7.0 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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