Contacts of the helix formed by residues 85 - 107 (chain A) in PDB entry 2VM6
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 ASN 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 3.9 14.9 - - + +
84A ILE* 1.3 75.5 - - - +
86A TRP* 1.3 63.2 + - - +
87A GLY* 3.1 6.9 + - - -
88A ARG* 2.9 36.5 + - - +
89A ILE* 3.1 23.9 + - - +
133A TRP* 3.7 15.5 - - + -
156B GLY 3.9 0.5 - - - +
157B ASP* 3.0 26.6 + - - +
160B ASN* 3.5 31.5 - - - +
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 1.3 72.0 - - - +
87A GLY* 1.3 65.9 + - - +
89A ILE* 3.2 18.9 + - + +
90A VAL* 2.9 25.8 + - - +
133A TRP* 3.6 26.4 - + - -
134A ILE* 3.8 32.8 - - + -
137A ASN* 3.5 22.2 + - + +
139A GLY 3.2 32.5 - - - -
140A TRP* 3.8 24.5 - + - -
143A GLY* 3.6 10.9 - - - -
144A PHE* 3.6 33.7 - + + -
147A LYS* 4.0 23.1 - - + -
148A PHE* 3.6 19.7 - + + -
1150A SO4 5.2 3.6 - - - -
160B ASN* 3.7 1.8 + - - -
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 3.1 3.8 + - - -
86A TRP* 1.3 78.9 - - - +
88A ARG* 1.3 61.2 + - - +
90A VAL* 3.1 15.8 + - - +
91A THR* 3.3 14.4 + - - +
148A PHE* 4.1 11.3 - - - -
156B GLY* 3.2 24.1 - - - -
159B PHE* 4.7 4.2 - - - +
160B ASN* 3.6 14.7 + - - -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 3.3 25.0 + - - +
79A PHE* 3.8 21.6 - - + +
81A ASP* 2.7 42.2 + - - -
83A ILE* 3.0 40.9 + - - +
85A ASN* 2.9 26.7 + - - +
87A GLY* 1.3 72.2 - - - +
89A ILE* 1.3 65.6 + - - +
91A THR* 2.5 26.7 + - - -
92A ILE* 3.4 8.3 + - - +
153B ARG* 3.3 20.3 - - - +
156B GLY* 3.7 9.6 + - - -
157B ASP* 2.8 38.8 + - - +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 6.2 0.4 - - + -
79A PHE* 5.3 0.9 - - + -
84A ILE* 3.9 12.3 - - + -
85A ASN 3.1 15.8 + - - +
86A TRP* 3.2 20.8 + - + +
88A ARG* 1.3 75.6 - - - +
90A VAL* 1.3 66.4 + - + +
91A THR 3.2 0.7 + - - -
92A ILE* 3.2 28.0 + - + +
93A PHE* 3.4 11.7 - - + -
126A ILE* 5.0 4.5 - - + -
130A THR* 4.1 16.2 - - + +
133A TRP* 3.7 31.4 - - + -
134A ILE* 4.0 13.0 - - + -
140A TRP* 3.6 34.1 - - + -
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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
----------------------------------------------------------
37A LEU* 4.1 3.8 - - + -
40A VAL* 3.8 14.4 - - + -
41A ALA* 3.5 33.7 - - + +
44A VAL* 3.6 22.2 - - + -
86A TRP 2.9 17.9 + - - +
87A GLY* 3.1 9.8 + - - +
89A ILE* 1.3 75.8 - - + +
91A THR* 1.3 56.3 + - - +
93A PHE* 3.0 26.6 + - - +
94A ALA* 3.1 10.2 + - - +
144A PHE* 3.7 28.5 - - + -
148A PHE* 4.3 10.1 - - + -
159B PHE* 6.1 0.4 - - + -
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Residues in contact with THR 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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44A VAL* 4.0 8.5 - - + -
78A GLU* 2.6 22.7 + - - -
87A GLY 3.3 13.6 + - - +
88A ARG 2.5 18.5 + - - -
90A VAL* 1.3 73.5 - - - +
92A ILE* 1.3 54.4 + - - +
94A ALA* 3.7 9.2 - - - +
95A PHE* 2.8 35.9 + - - +
152B LEU* 3.3 37.5 - - - +
155B ILE* 3.8 12.8 - - + -
156B GLY* 3.6 12.1 - - - +
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Residues in contact with ILE 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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71A PHE* 3.7 29.7 - - + -
75A MET* 3.7 21.5 - - + -
79A PHE* 3.9 22.4 - - + -
88A ARG 3.6 9.0 - - - +
89A ILE* 3.4 25.1 - - + +
91A THR* 1.3 78.3 + - - +
93A PHE* 1.3 55.7 + - - +
95A PHE* 3.4 2.1 + - - +
96A GLU* 3.0 27.1 + - - +
122A VAL* 3.7 15.5 - - + -
125A PHE* 4.0 13.2 - - + -
126A ILE* 3.8 27.1 - - + -
130A THR* 4.6 4.0 - - + -
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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
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9A ILE* 4.7 2.7 - - + -
12A LEU* 4.2 7.4 - - + -
13A ALA* 3.6 32.5 - - + -
16A TYR* 3.1 19.6 - - + -
37A LEU* 3.7 33.7 - - + -
41A ALA* 4.1 13.2 - - + -
89A ILE* 3.4 18.2 - - + -
90A VAL 3.0 6.9 + - - +
92A ILE* 1.3 75.6 - - - +
94A ALA* 1.3 64.2 + - - +
96A GLU* 2.9 38.0 - - - +
97A GLY 3.0 6.2 + - - -
122A VAL* 4.9 0.9 - - + -
126A ILE* 3.5 29.6 - - + -
140A TRP* 3.7 27.6 - + - -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 4.1 1.7 - - - -
41A ALA* 3.6 16.2 - - - +
44A VAL* 3.5 33.0 - - + -
45A GLN* 3.4 28.4 - - - +
48A VAL* 5.4 1.6 - - + -
90A VAL 3.1 8.5 + - - +
91A THR* 3.7 6.3 - - - +
93A PHE* 1.3 74.6 - - - +
95A PHE* 1.3 62.3 + - - +
97A GLY 3.2 2.1 + - - -
98A ILE* 3.1 20.0 + - - +
152B LEU* 5.4 3.1 - - + -
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.9 3.6 - - + -
70A LEU* 4.3 5.6 - - + -
71A PHE* 3.9 26.7 - + - -
74A VAL* 3.9 32.5 - - + -
75A MET* 4.3 2.5 - - + -
91A THR 2.8 21.6 + - - +
92A ILE* 3.8 5.6 - - - +
94A ALA* 1.3 75.0 - - - +
96A GLU* 1.3 62.3 + - - +
98A ILE* 3.1 30.7 + - + +
99A LEU* 3.0 48.8 + - + +
148B ILE* 3.6 37.7 - - + -
152B LEU* 3.8 14.9 - - + +
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Residues in contact with GLU 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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13A ALA* 2.9 42.0 - - - +
16A TYR* 3.6 10.5 - - + +
17A LEU* 3.7 18.8 - - - +
71A PHE* 5.1 0.4 - - - -
92A ILE 3.0 10.2 + - - +
93A PHE* 2.9 36.5 - - - +
95A PHE* 1.3 75.8 - - - +
97A GLY* 1.3 56.2 + - - +
99A LEU* 3.2 12.2 + - - +
100A ILE* 2.9 29.9 + - - +
118A ILE* 4.0 9.2 - - + +
119A SER* 4.0 5.0 + - - -
122A VAL* 3.6 33.7 - - + +
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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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16A TYR* 4.0 8.5 - - - -
17A LEU* 5.9 0.7 - - - -
20A VAL* 3.9 5.5 - - - +
45A GLN* 3.4 23.9 + - - -
93A PHE 3.0 12.7 + - - -
95A PHE 3.2 0.2 - - - -
96A GLU* 1.3 78.0 - - - +
98A ILE* 1.3 60.0 + - - +
100A ILE* 3.3 25.2 - - - +
101A LYS* 3.3 15.1 + - - +
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Residues in contact with ILE 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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45A GLN* 3.8 8.5 - - + +
48A VAL* 3.5 33.4 - - + -
49A GLU* 3.7 32.8 - - + +
52A LEU* 5.7 0.2 - - + -
56A LEU* 4.0 27.6 - - + -
94A ALA 3.1 14.5 + - - +
95A PHE* 3.1 28.1 + - + +
97A GLY* 1.3 74.4 - - - +
99A LEU* 1.3 65.6 + - + +
101A LYS* 3.5 4.2 + - - +
102A LYS* 3.2 37.3 + - + +
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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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61A VAL* 4.1 24.3 - - + +
67A ALA* 3.9 22.4 - - + +
70A LEU* 4.1 11.2 - - + -
71A PHE* 3.8 35.7 - - + -
95A PHE* 3.0 46.9 + - + +
96A GLU* 3.2 10.0 + - - +
98A ILE* 1.3 75.7 - - + +
100A ILE* 1.3 67.2 + - - +
102A LYS* 3.9 4.2 - - + +
103A LEU* 3.0 25.7 + - - +
118A ILE* 4.8 7.3 - - + +
121A PHE* 4.6 9.2 - - + -
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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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17A LEU* 3.7 37.5 - - + -
20A VAL* 4.1 15.3 - - + -
21A LEU* 4.0 14.4 - - + -
96A GLU 2.9 14.7 + - - +
97A GLY* 3.3 20.9 - - - +
99A LEU* 1.3 78.5 - - - +
101A LYS* 1.3 59.8 + - - +
103A LEU* 4.3 2.9 - - + -
104A LEU* 3.2 21.6 + - - +
115A TYR* 3.4 47.6 - - + -
118A ILE* 3.5 16.1 - - + +
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Residues in contact with LYS 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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20A VAL* 4.0 17.0 - - + +
21A LEU* 5.0 6.5 - - + -
45A GLN* 3.5 16.5 - - - +
49A GLU* 2.6 40.2 + - - +
97A GLY 3.3 9.4 + - - +
98A ILE* 3.9 5.2 - - - +
99A LEU 3.2 0.2 - - - -
100A ILE* 1.3 75.4 - - + +
102A LYS* 1.3 61.6 + - + +
104A LEU* 3.6 8.3 + - - +
105A ARG* 3.0 32.5 + - - +
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Residues in contact with LYS 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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56A LEU* 2.9 37.3 + - + +
57A ASP* 4.8 4.0 + - - +
59A VAL* 3.1 36.3 + - + -
61A VAL* 3.7 24.9 - - + +
98A ILE* 3.2 33.3 + - + +
99A LEU* 4.1 2.2 - - + +
101A LYS* 1.3 76.1 - - + +
103A LEU* 1.3 67.6 + - - +
105A ARG* 3.8 6.0 - - - +
106A GLN* 3.3 26.0 + - - +
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Residues in contact with LEU 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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61A VAL* 3.4 24.7 - - + +
62A VAL 3.8 4.7 - - - +
63A SER* 3.7 30.3 - - - +
64A VAL* 3.9 24.7 - - + +
67A ALA* 5.2 0.4 - - + -
99A LEU 3.0 19.1 + - - +
100A ILE* 3.7 5.4 - - + +
102A LYS* 1.3 78.6 - - - +
104A LEU* 1.3 53.1 + - - +
106A GLN* 3.2 1.7 + - - +
107A GLN* 2.7 48.4 + - - +
115A TYR* 3.5 31.6 - - + -
118A ILE* 4.0 12.3 - - + -
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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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21A LEU* 3.5 35.0 - - + -
100A ILE* 3.2 14.0 + - + +
101A LYS* 4.3 5.4 - - - +
103A LEU* 1.3 75.0 - - - +
105A ARG* 1.3 65.7 + - - +
106A GLN 3.2 1.3 - - - -
107A GLN* 4.0 13.1 + - - +
110A PRO* 5.8 7.2 - - + +
112A VAL* 5.2 4.3 - - + -
115A TYR* 2.9 43.7 - - + +
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Residues in contact with ARG 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 LYS 3.0 20.8 + - - +
102A LYS* 3.8 8.5 - - - +
104A LEU* 1.3 80.5 - - - +
106A GLN* 1.3 61.9 + - + +
107A GLN 4.8 0.7 - - - +
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Residues in contact with GLN 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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60A ASN* 5.2 5.6 - - - +
61A VAL 3.0 28.0 - - - +
62A VAL* 2.7 50.6 - - - +
102A LYS 3.3 11.0 + - - +
103A LEU 3.2 0.4 + - - -
105A ARG* 1.3 82.9 - - + +
107A GLN* 1.3 68.8 + - - +
108A ILE* 3.4 6.4 + - - +
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Residues in contact with GLN 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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62A VAL 4.8 6.4 + - - +
63A SER* 5.6 1.4 - - - +
64A VAL* 5.2 4.9 - - - +
103A LEU* 2.7 40.1 + - + +
104A LEU* 4.0 10.4 - - - +
105A ARG 3.7 1.6 - - - +
106A GLN* 1.3 80.3 + - - +
108A ILE* 1.3 66.3 + - + +
109A ALA 3.7 20.7 + - - +
110A PRO* 3.8 9.6 - - + +
111A ASP* 3.3 20.2 + - - +
114A THR* 4.8 4.2 + - - -
115A TYR* 2.6 38.6 + - - -
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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