Contacts of the helix formed by residues 82 - 111 (chain A) in PDB entry 3BVI
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 GLY 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.5 19.1 - - - -
80A PHE 3.5 2.0 - - - -
81A GLU* 1.3 82.8 - - - +
83A LEU* 1.3 66.8 + - - -
84A THR* 3.3 2.9 - - - -
85A GLN* 3.3 5.6 + - - +
86A ILE* 3.1 25.3 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.1 7.6 - - - -
31A CYS* 4.6 5.4 - - - -
36A LEU* 3.8 20.6 - - + +
39A ALA* 4.0 16.6 - - + -
82A GLY* 1.3 70.5 - - - -
84A THR* 1.3 63.9 + - - +
86A ILE* 3.3 4.6 + - + +
87A PHE* 3.2 49.5 + - + -
141A ILE* 3.9 28.0 - - + +
151A LEU* 3.8 29.7 - - + +
154A ALA* 4.1 17.0 - - + -
155A ASP* 5.0 6.5 - - - +
158A VAL* 5.8 2.0 - - + -
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 3.3 0.6 - - - -
83A LEU* 1.3 77.5 - - - +
85A GLN* 1.3 57.8 + - - +
87A PHE* 3.4 2.8 + - - +
88A GLN* 2.9 46.8 + - + +
138A LEU* 4.2 3.8 - - + +
141A ILE* 3.5 23.3 - - + +
142A GLU* 3.8 32.9 - - + +
146A ASN* 4.9 8.0 + - - +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS 4.2 1.4 - - - +
80A PHE* 3.4 12.8 - - - +
81A GLU* 2.8 58.0 + - + +
82A GLY* 3.3 16.2 + - - +
84A THR* 1.3 76.0 - - - +
86A ILE* 1.3 60.6 + - - +
88A GLN* 3.6 18.3 - - + +
89A LYS* 2.9 54.9 + - + +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.6 30.9 - - + +
30A TRP* 3.3 45.8 - - + -
31A CYS* 3.9 13.0 - - - -
43A LEU* 4.0 16.2 - - + -
80A PHE* 3.6 28.5 - - + -
82A GLY 3.1 15.2 + - - +
83A LEU* 3.6 9.0 - - - +
84A THR 3.3 0.4 - - - -
85A GLN* 1.3 76.2 - - - +
87A PHE* 1.3 65.2 + - + +
89A LYS* 3.6 5.3 - - - +
90A ALA* 2.8 29.5 + - + +
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 4.1 9.2 - - + -
42A PHE* 3.9 23.3 - + - -
43A LEU* 4.2 18.4 - - + -
83A LEU* 3.2 31.9 + - + +
84A THR 4.1 2.2 - - - +
86A ILE* 1.3 80.4 - - + +
88A GLN* 1.3 58.7 + - - +
90A ALA* 3.8 2.8 - - + +
91A TYR* 2.9 30.3 + - - +
134A PHE* 3.7 36.5 - + - +
137A ILE* 3.5 27.1 - - + -
138A LEU* 3.8 16.4 - - + +
141A ILE* 3.5 28.9 - - + -
158A VAL* 4.4 8.3 - - + -
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 2.9 31.5 + - + +
85A GLN* 3.6 26.0 - - + +
86A ILE 3.4 0.2 - - - -
87A PHE* 1.3 74.3 - - - +
89A LYS* 1.3 63.1 + - + +
91A TYR* 3.6 2.3 + - - +
92A GLU* 3.2 34.1 + - - +
138A LEU* 3.9 26.4 - - + +
142A GLU* 4.2 9.5 - - - +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.6 0.4 - - + +
27A MET* 3.9 10.5 - - + -
77A GLU* 2.8 32.8 + - - +
79A LYS 4.9 3.1 - - - -
80A PHE* 3.9 22.0 - - + -
85A GLN* 2.9 48.2 + - + +
86A ILE 3.6 3.8 - - - +
88A GLN* 1.3 73.8 - - + +
90A ALA* 1.3 61.1 + - - +
92A GLU* 3.4 10.3 + - - +
93A HIS* 2.9 29.1 + - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.5 16.4 + - + -
27A MET* 3.9 11.0 - - + +
43A LEU* 5.2 1.3 - - + -
86A ILE 2.8 21.3 + - - +
87A PHE* 3.8 7.0 - - + +
88A GLN 3.3 0.2 - - - -
89A LYS* 1.3 73.8 - - - +
91A TYR* 1.3 57.4 + - - +
93A HIS* 3.2 6.0 + - - +
94A GLU* 2.9 32.6 + - - +
134A PHE* 3.7 31.2 - - + -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE 2.9 18.3 + - - +
88A GLN 4.0 3.6 - - - +
90A ALA* 1.3 74.2 - - - +
92A GLU* 1.3 67.7 + - + +
94A GLU* 3.3 2.3 + - + +
95A GLN* 3.0 54.6 + - + +
131A GLU* 3.7 32.8 + - + -
134A PHE* 4.3 14.8 - - + +
135A LYS* 3.6 30.0 - - + +
138A LEU* 3.9 17.7 - - + -
1C MET* 3.6 24.4 - - + +
1001C ASP 4.6 2.4 + - - -
1002C GLN* 3.3 33.6 - - + +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 3.2 23.0 + - - +
89A LYS* 3.8 9.4 - - - +
90A ALA 3.4 0.2 - - - -
91A TYR* 1.3 78.6 - - + +
93A HIS* 1.3 62.2 + - - +
95A GLN* 3.4 23.2 - - - +
96A HIS* 3.1 21.1 + - - +
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 5.3 0.2 - - - -
19A ASN* 4.4 13.9 - - - -
20A SER* 2.5 38.4 + - - -
23A LEU* 3.9 22.5 - - + +
24A TYR* 3.6 26.5 - + - -
89A LYS 2.9 15.8 + - - +
90A ALA* 3.2 11.4 + - - +
92A GLU* 1.3 77.2 - - - +
94A GLU* 1.3 57.9 + - - +
96A HIS* 3.1 14.1 + - - +
97A ILE* 2.9 44.5 + - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 2.5 32.1 + - - +
46A HIS* 2.8 23.2 + - - -
50A GLU* 3.4 1.4 - - - +
90A ALA 2.9 14.2 + - - +
91A TYR* 3.3 6.0 + - - +
93A HIS* 1.3 74.4 - - - +
95A GLN* 1.3 60.2 + - - +
97A ILE* 4.3 3.3 - - - +
98A SER* 2.8 27.6 + - - -
127A GLN* 2.8 32.6 + - - +
130A GLU* 3.9 4.2 - - - +
131A GLU* 4.2 17.7 - - + -
134A PHE* 3.7 21.5 - - + -
1007A FE 2.4 25.8 - - - -
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Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.0 44.5 + - + +
92A GLU* 3.4 33.6 - - - +
94A GLU* 1.3 76.7 - - - +
96A HIS* 1.3 55.8 + - - +
98A SER* 3.2 3.7 + - - -
99A GLU* 3.0 28.8 + - - +
131A GLU* 3.6 24.4 - - - +
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Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 4.0 35.4 + - + -
92A GLU 3.1 9.4 + - - +
93A HIS* 3.1 17.9 + - - +
95A GLN* 1.3 75.7 - - - +
97A ILE* 1.3 74.6 + - + +
99A GLU* 3.4 19.8 + - - +
100A SER* 3.0 23.0 + - - -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 4.2 8.5 - - - +
16A LYS* 4.1 34.5 - - + +
17A GLU* 4.1 10.1 - - - +
20A SER* 3.8 16.2 - - - +
50A GLU* 5.4 1.6 - - - +
93A HIS* 2.9 39.7 + - + +
94A GLU* 3.7 9.2 - - - +
96A HIS* 1.3 81.8 - - + +
98A SER* 1.3 62.1 - - - +
100A SER* 2.8 20.3 + - - +
101A ILE* 3.0 11.2 + - + +
127A GLN* 3.7 25.8 - - - +
1006A FE 3.8 10.1 - - - -
1007A FE 4.5 0.7 - - - -
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 2.8 17.2 + - - -
95A GLN* 3.2 5.8 + - - -
97A ILE* 1.3 76.5 - - - +
99A GLU* 1.3 57.1 + - - +
101A ILE* 3.4 5.3 + - - +
102A ASN* 3.0 38.3 + - - +
127A GLN* 3.2 25.6 + - - +
128A HIS* 5.2 0.5 + - - -
131A GLU* 2.5 30.2 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN 3.0 13.2 + - - +
96A HIS* 3.5 25.2 - - - +
98A SER* 1.3 75.3 - - - +
100A SER* 1.3 64.0 + - - +
102A ASN* 3.3 12.8 + - + +
103A ASN* 3.0 22.7 + - - +
----------------------------------------------------------
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 26.7 + - - -
16A LYS* 3.9 24.4 - - - +
96A HIS* 3.0 18.2 + - - -
97A ILE* 2.8 18.2 + - - -
99A GLU* 1.3 76.4 + - - +
101A ILE* 1.3 60.1 + - - +
103A ASN* 3.3 21.3 + - - +
104A ILE* 3.3 14.9 + - - +
----------------------------------------------------------
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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
----------------------------------------------------------
13A GLN* 3.5 16.6 - - - +
97A ILE* 3.0 13.7 + - + +
98A SER* 3.6 6.5 - - - +
100A SER* 1.3 78.6 + - - +
102A ASN* 1.3 66.1 + - - +
104A ILE* 3.1 10.0 + - + +
105A VAL* 3.0 24.7 + - + +
120A LEU* 5.4 3.4 - - + +
123A TYR* 3.4 44.0 - - + +
124A VAL* 3.8 30.5 - - + -
127A GLN* 3.7 36.6 - - + -
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.0 26.5 + - - +
99A GLU* 3.3 12.9 + - + +
101A ILE* 1.3 76.2 - - - +
103A ASN* 1.3 53.0 + - - +
105A VAL* 3.4 3.4 + - - +
106A ASP* 2.8 36.4 + - - +
124A VAL* 5.0 3.6 - - - +
112C LYS* 3.2 32.1 + - + +
113C ASP* 4.8 3.2 + - - +
114C HIS* 3.4 33.5 + - - +
115C ALA* 4.3 4.5 + - - +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.7 28.2 - - - +
99A GLU 3.0 11.9 + - - +
100A SER* 3.3 15.3 + - - +
102A ASN* 1.3 73.6 - - - +
104A ILE* 1.3 59.8 + - - +
106A ASP* 3.5 7.4 + - - +
107A HIS* 3.0 28.2 + - - +
112C LYS* 4.7 16.2 + - - +
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.5 8.1 - - + +
9A LEU* 3.8 48.9 - - + +
10A LEU* 4.1 19.1 - - + -
13A GLN* 3.4 37.5 - - + +
100A SER 3.3 10.5 - - - +
101A ILE* 3.1 10.4 + - + +
103A ASN* 1.3 72.0 - - + +
105A VAL* 1.3 61.1 + - - +
107A HIS* 3.1 2.9 + - - +
108A ALA* 2.8 27.5 + - - +
116A THR* 5.0 1.1 - - + -
120A LEU* 3.7 25.1 - - + -
123A TYR* 5.6 0.7 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.0 17.4 + - + +
102A ASN* 3.7 4.3 - - - +
104A ILE* 1.3 76.5 - - - +
106A ASP* 1.3 61.4 + - - +
108A ALA* 3.3 8.3 + - - +
109A ILE* 3.1 22.5 + - - +
117A PHE* 3.4 25.1 - - + -
120A LEU* 3.8 23.3 - - + -
121A GLN* 4.5 3.4 - - - +
124A VAL* 3.8 26.5 - - + -
114C HIS* 3.4 34.3 - - + +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASN 2.8 18.5 + - - +
103A ASN* 3.7 6.3 - - - +
105A VAL* 1.3 76.7 - - - +
107A HIS* 1.3 57.4 + - - +
109A ILE* 3.2 13.3 + - - +
110A LYS* 2.8 63.9 + - - +
109C ILE* 4.4 9.2 - - - +
112C LYS* 3.5 38.1 + - + +
114C HIS* 4.0 8.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 5.3 0.2 - - - -
5A ASP* 3.3 40.4 + - + +
6A ILE* 3.8 12.5 - - + +
9A LEU* 3.7 20.3 - - + +
103A ASN* 3.0 19.2 + - - +
104A ILE 3.1 4.5 + - - +
106A ASP* 1.3 74.0 + - - +
108A ALA* 1.3 58.6 + - - +
110A LYS* 3.3 15.0 + - + +
111A SER* 2.8 62.6 + - - -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.9 16.4 - - + +
104A ILE 2.8 17.1 + - - +
105A VAL* 3.4 12.8 - - - +
106A ASP 3.3 0.2 - - - -
107A HIS* 1.3 71.3 - - - +
109A ILE* 1.3 56.8 + - - +
111A SER 3.3 0.7 + - - -
112A LYS* 3.0 7.1 + - - -
113A ASP* 2.8 48.4 + - - +
114A HIS* 5.1 0.6 + - - -
116A THR* 4.5 7.0 - - + -
117A PHE* 4.1 19.1 - - + +
120A LEU* 5.1 0.7 - - + -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL 3.1 11.2 + - - +
106A ASP* 3.2 13.0 + - - +
108A ALA* 1.3 73.1 - - - +
110A LYS* 1.3 68.6 + - + +
112A LYS* 3.2 15.6 + - - +
114A HIS* 4.7 18.5 + - + +
117A PHE* 3.6 23.3 - - + -
109C ILE* 4.2 28.9 - - + -
114C HIS* 3.4 34.3 - - + +
----------------------------------------------------------
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASP* 2.8 49.1 + - - +
107A HIS* 3.3 18.3 + - + +
109A ILE* 1.3 80.0 - - + +
111A SER* 1.3 62.0 + - - +
112A LYS* 3.5 7.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 4.8 7.4 + - - -
6A ILE* 4.5 6.6 - - - +
107A HIS* 2.8 45.0 + - - -
108A ALA* 3.8 4.0 - - - -
109A ILE 3.2 0.2 - - - -
110A LYS* 1.3 76.3 - - - +
112A LYS* 1.3 69.9 + - - +
113A ASP* 3.3 12.7 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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