Contacts of the helix formed by residues 78 - 104 (chain A) in PDB entry 3V2W
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 ARG 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS 4.1 9.8 + - - +
76A PHE 3.0 1.8 - - - -
77A HIS* 1.3 78.3 - - - +
79A PRO* 1.4 76.3 - - + +
80A MET* 3.3 3.6 - - + +
81A TYR* 3.1 36.0 + - + +
82A TYR* 3.2 12.2 + - - -
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Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A HIS 4.5 2.2 - - - +
78A ARG* 1.4 84.5 - - + +
80A MET* 1.4 62.7 + - - +
82A TYR* 3.1 27.4 + - + +
83A PHE* 3.3 22.5 - - + -
141A GLU* 5.8 1.6 - - + -
156A ASN* 5.2 10.8 - - - +
157A ASN* 5.3 6.3 - - - +
160A LEU* 3.7 24.9 - - + +
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.2 3.1 + - + +
79A PRO* 1.4 77.9 - - - +
81A TYR* 1.3 80.1 + - + +
83A PHE* 3.1 24.0 + - - +
84A ILE* 3.2 37.8 + - + +
138A ILE* 4.3 13.0 - - + -
141A GLU* 4.6 12.9 - - + +
142A ARG* 3.4 41.1 - - - +
254A LEU* 3.6 35.9 - - + -
258A VAL* 4.1 13.5 - - - -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.6 26.3 - - + +
75A LYS 4.1 6.3 - - - -
76A PHE* 3.2 75.7 - + + +
78A ARG* 3.1 27.1 + - + +
80A MET* 1.3 92.2 - - + +
82A TYR* 1.4 57.2 + - - +
84A ILE* 3.3 9.8 + - + +
85A GLY* 3.0 24.4 + - - -
254A LEU* 4.1 15.8 - - + +
317A GLU* 4.1 15.9 + - - -
318A MET* 3.7 25.9 - - + +
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 5.3 7.2 - - + -
76A PHE 5.4 1.3 - - - -
77A HIS* 3.2 54.5 + + - +
78A ARG 3.2 21.7 + - - -
79A PRO* 3.1 18.0 + - + +
81A TYR* 1.4 76.7 - - + +
83A PHE* 1.4 58.2 + - + +
85A GLY* 3.6 2.1 + - - +
86A ASN* 3.1 26.0 + - - +
157A ASN* 5.9 2.5 - - + -
160A LEU* 4.4 15.3 - - + -
161A PHE* 3.6 36.4 - + - -
164A ILE* 4.0 20.5 - - + +
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.3 29.6 - - + -
80A MET* 3.1 13.3 + - - +
82A TYR* 1.4 74.2 - - + +
84A ILE* 1.4 59.0 + - - +
86A ASN* 3.5 8.6 + - + +
87A LEU* 3.2 26.2 + - - +
134A SER* 4.1 6.0 - - - +
137A ALA* 3.5 36.6 - - + -
138A ILE* 3.6 20.8 - - + +
140A ILE* 6.2 1.3 - - + -
141A GLU* 3.7 20.0 - - + -
160A LEU* 3.6 33.0 - - + -
163A LEU* 4.4 20.2 - - + -
164A ILE* 4.5 22.2 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 4.6 1.3 - - + -
70A ILE* 4.0 14.4 - - + -
80A MET* 3.2 46.8 + - + +
81A TYR* 3.5 13.7 - - + +
83A PHE* 1.4 74.5 - - - +
85A GLY* 1.3 58.7 + - - +
87A LEU* 3.4 7.7 - - - +
88A ALA* 3.1 24.6 + - - +
138A ILE* 3.8 21.8 - - + -
258A VAL* 4.9 7.6 - - + -
311A TYR* 3.4 35.7 + - + +
318A MET* 4.0 20.2 - - + -
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 4.9 0.9 - - - -
67A LEU* 3.2 29.7 - - - +
70A ILE* 4.4 11.4 - - - -
81A TYR 3.0 15.5 + - - -
82A TYR* 3.9 1.8 - - - -
83A PHE 3.3 0.2 - - - -
84A ILE* 1.3 74.3 - - - +
86A ASN* 1.4 54.0 + - - +
88A ALA* 3.0 6.0 + - - +
89A LEU* 2.8 30.0 + - - +
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Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR 3.1 17.4 + - - +
83A PHE* 3.8 8.7 - - - +
84A ILE 3.5 0.2 - - - -
85A GLY* 1.4 74.2 - - - +
87A LEU* 1.4 52.9 + - - +
89A LEU* 3.3 13.2 + - - +
90A SER* 2.8 36.0 + - - -
134A SER* 3.5 17.8 + - - +
164A ILE* 3.5 32.1 - - + +
167A CYS* 4.0 16.0 - - - +
168A TRP* 2.7 33.4 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 5.7 0.2 - - - +
83A PHE 3.2 13.6 + - - +
84A ILE* 3.4 9.4 - - - +
86A ASN* 1.4 75.2 - - - +
88A ALA* 1.4 60.6 + - + +
90A SER* 3.3 7.4 + - - -
91A ASP* 3.0 30.4 + - - +
131A SER* 4.4 6.5 - - - +
134A SER* 3.6 18.3 + - - -
135A LEU* 3.7 37.0 - - + -
138A ILE* 3.9 15.9 - - + -
261A VAL* 4.5 6.3 - - + -
265A PHE* 6.5 0.7 - - + -
307A ASN* 3.4 31.0 - - + +
311A TYR* 3.9 18.4 - - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 3.5 31.9 - - + +
66A VAL* 3.8 26.7 - - + -
67A LEU* 4.3 3.6 - - + -
84A ILE 3.1 12.8 + - - +
85A GLY* 3.0 10.4 + - - +
87A LEU* 1.4 77.3 - - + +
89A LEU* 1.4 55.3 + - - +
91A ASP* 3.6 1.7 - - - +
92A LEU* 2.7 35.6 + - - +
311A TYR* 5.9 1.1 - - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.0 20.6 - - + +
85A GLY 2.8 12.9 + - - +
86A ASN* 3.4 22.9 - - - +
88A ALA* 1.4 72.8 - - - +
90A SER* 1.3 60.3 + - - +
92A LEU* 3.6 14.2 - - + +
93A LEU* 3.0 51.8 + - + +
164A ILE* 6.3 0.7 - - + -
168A TRP* 4.4 14.8 - - + +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 2.8 20.0 + - - -
87A LEU 3.3 9.6 + - - -
89A LEU* 1.3 77.3 - - - +
91A ASP* 1.4 56.8 + - - +
93A LEU* 3.4 2.3 + - - +
94A ALA* 3.0 26.2 + - - +
127A ALA* 3.8 11.7 - - - +
130A ALA* 3.3 25.3 - - - +
131A SER* 3.4 27.6 - - - -
134A SER* 3.9 1.7 + - - -
168A TRP* 3.4 13.9 - - - -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.1 1.6 - - - +
63A ASN* 4.0 10.5 + - - +
87A LEU* 3.0 21.8 + - - +
88A ALA 3.6 4.0 - - - +
90A SER* 1.4 71.9 - - - +
92A LEU* 1.4 58.2 + - - +
94A ALA* 3.5 10.1 - - - +
95A GLY* 3.2 20.4 + - - -
131A SER* 3.1 22.9 + - - -
265A PHE* 5.7 1.7 - - - -
303A ASN* 5.4 4.0 + - - -
304A SER* 3.6 44.0 + - - +
307A ASN* 2.8 31.7 + - - +
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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
----------------------------------------------------------
59A ILE 5.1 1.1 - - - -
60A ILE* 3.4 27.5 - - + +
63A ASN* 4.1 8.7 - - + +
64A ILE* 3.8 32.3 - - + +
67A LEU* 3.9 22.9 - - + -
88A ALA 2.7 20.7 + - - +
89A LEU* 3.6 13.2 - - + +
90A SER 3.3 0.2 - - - -
91A ASP* 1.4 72.2 - - - +
93A LEU* 1.3 80.2 + - + +
95A GLY 3.3 2.4 + - - -
96A VAL* 3.3 31.5 + - + +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.0 28.4 + - + +
90A SER 3.9 3.6 - - - +
92A LEU* 1.3 86.4 - - + +
94A ALA* 1.4 54.9 + - - +
96A VAL* 3.3 13.5 + - + +
97A ALA* 2.8 35.8 + - - +
127A ALA* 4.8 5.4 - - + -
168A TRP* 3.8 32.5 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 3.0 17.5 + - - +
91A ASP* 3.5 15.3 - - - +
92A LEU 3.2 0.2 - - - -
93A LEU* 1.4 75.9 - - - +
95A GLY* 1.3 51.8 + - - +
97A ALA* 3.4 5.0 + - - +
98A TYR* 2.8 37.5 + - - +
124A MET* 4.3 9.4 - - + +
127A ALA* 3.8 19.9 - - + +
301A VAL* 6.0 1.8 - - - -
304A SER* 3.9 12.8 - - - +
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS* 3.5 17.8 - - - +
59A ILE* 4.9 9.6 - - - +
60A ILE* 3.5 15.8 - - - +
91A ASP 3.2 10.5 + - - -
92A LEU 3.3 4.8 + - - -
94A ALA* 1.3 77.9 - - - +
96A VAL* 1.3 54.1 + - - +
98A TYR* 4.0 3.4 - - - -
99A THR* 2.8 32.6 + - - -
301A VAL* 5.9 2.2 - - - -
304A SER* 5.3 1.1 + - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.7 14.4 - - + -
92A LEU* 3.3 24.1 + - + +
93A LEU* 3.3 19.5 + - + +
94A ALA 3.2 0.6 - - - -
95A GLY* 1.3 73.2 - - - +
97A ALA* 1.3 55.9 + - - +
98A TYR 3.1 3.6 - - - -
99A THR* 2.8 27.6 + - - -
100A ALA* 3.0 13.8 + - + +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU 2.8 19.9 + - - +
94A ALA* 3.8 3.1 - - - +
96A VAL* 1.3 72.9 - - - +
98A TYR* 1.4 56.9 + - - +
99A THR 3.5 0.2 - - - -
100A ALA* 4.0 7.9 - - - +
101A ASN* 3.1 23.5 + - - +
120A ARG 4.6 2.4 - - - +
123A SER* 3.4 40.3 + - - +
124A MET* 3.8 17.6 - - - +
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Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 4.8 6.2 - + + -
56A CYS* 3.8 14.4 - - - -
94A ALA 2.8 17.9 + - - +
95A GLY 4.4 2.7 - - - +
97A ALA* 1.4 74.7 - - - +
99A THR* 1.4 61.5 + - - +
100A ALA 3.3 0.7 - - - -
101A ASN* 3.5 23.4 + - + -
102A LEU* 2.9 57.7 + - + +
124A MET* 3.8 16.8 - - + -
294A GLU* 4.4 9.2 + - - -
297A LEU* 5.2 1.0 - - + +
298A VAL* 3.4 27.7 + - + +
301A VAL* 3.5 48.9 - - + -
1201A ML5 4.0 14.7 + + - -
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.8 28.7 + - + +
56A CYS* 3.2 19.1 - - - +
57A CYS* 5.3 5.0 - - - -
60A ILE* 5.4 1.0 - - - +
95A GLY 2.8 19.7 + - - -
96A VAL* 2.8 11.0 + - - -
98A TYR* 1.4 75.0 - - - +
100A ALA* 1.4 57.2 + - - +
102A LEU* 3.4 11.3 + - - +
103A LEU* 3.1 42.7 + - + +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.0 15.0 + - + +
97A ALA* 4.0 8.7 - - - +
99A THR* 1.4 74.3 - - - +
101A ASN* 1.4 58.5 + - - +
103A LEU* 3.3 10.9 + - - +
104A LEU* 2.9 46.7 + - + +
120A ARG* 5.3 0.7 - - + -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 3.1 21.3 + - - +
98A TYR* 3.4 32.7 + - + +
100A ALA* 1.4 74.8 - - - +
102A LEU* 1.4 54.2 + - - +
104A LEU 3.1 2.8 + - - -
105A SER* 2.5 44.4 + - - -
120A ARG* 4.1 21.0 + - - +
121A GLU* 2.9 32.5 + - - -
124A MET* 4.9 2.5 - - - +
1201A ML5 2.9 31.7 + - - -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 4.3 26.7 + - - +
52A PHE* 3.6 23.3 - - + +
53A ILE* 3.6 47.3 - - + +
56A CYS* 4.2 2.7 - - - -
98A TYR* 2.9 52.0 + - + +
99A THR* 3.6 7.4 - - - +
101A ASN* 1.4 76.1 + - - +
103A LEU* 1.4 59.9 - - - +
104A LEU 3.5 0.3 + - - -
105A SER* 3.5 18.7 + - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.9 25.8 - - + -
99A THR* 3.1 36.3 + - + +
100A ALA* 3.3 9.4 + - - +
102A LEU* 1.4 75.1 - - - +
104A LEU* 1.4 65.1 + - + +
105A SER 3.6 0.2 - - - -
108A THR* 3.2 19.8 + - - +
111A LYS* 5.4 0.5 - - - -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA* 2.9 29.7 + - + +
101A ASN 3.1 4.5 + - - -
103A LEU* 1.4 85.4 - - + +
105A SER* 1.4 47.6 + - - +
108A THR* 3.1 10.9 + - - -
109A THR* 3.8 3.1 - - - -
111A LYS* 4.9 14.8 - - - -
112A LEU* 3.4 34.5 - - + +
116A GLN 6.1 0.4 - - - +
120A ARG* 2.5 51.0 + - + -
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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