Contacts of the helix formed by residues 86 - 115 (chain A) in PDB entry 3AEV
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 THR 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG 4.3 4.3 - - - +
85A VAL* 1.3 77.0 - - - +
87A GLN* 1.3 66.3 + - - +
88A GLN* 3.4 12.3 + - - +
89A GLN* 2.7 49.5 + - - +
90A ARG* 2.8 20.9 + - - +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 1.3 72.6 - - - +
88A GLN* 1.3 63.1 + - - +
90A ARG* 3.3 15.2 + - - +
91A LYS* 3.0 24.1 + - - +
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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
----------------------------------------------------------
86A THR* 3.2 9.0 + - - +
87A GLN* 1.3 79.6 - - - +
89A GLN* 1.3 82.6 + - - +
91A LYS* 3.2 9.0 + - - +
92A ALA* 2.9 35.3 + - + +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.4 41.7 - - + -
65A VAL* 4.9 0.2 - - - +
67A LYS* 5.3 3.0 + - - +
84A ARG 3.2 16.0 + - - -
85A VAL* 3.3 6.6 - - + +
86A THR* 2.7 48.4 + - - +
88A GLN* 1.3 94.1 + - - +
90A ARG* 1.3 65.8 + - - +
92A ALA* 3.9 3.5 - - - +
93A LYS* 3.0 25.8 + - - +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS 5.0 3.2 + - - -
64A VAL* 5.5 0.8 - - - +
65A VAL* 4.1 29.9 + - + +
82A LEU* 6.3 0.6 - - - +
85A VAL* 3.7 13.3 - - + +
86A THR 2.8 12.6 + - - +
87A GLN* 3.6 19.1 - - - +
89A GLN* 1.3 77.1 - - - +
91A LYS* 1.3 63.1 + - - +
93A LYS* 3.3 2.1 + - - +
94A LEU* 3.1 40.3 + - + +
30B GLU* 2.7 44.2 + - - -
31B PHE* 4.0 21.4 - - - -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN 3.0 16.3 + - - +
88A GLN* 3.2 9.2 + - - +
90A ARG* 1.3 76.4 - - - +
92A ALA* 1.3 64.0 + - - +
94A LEU* 3.3 8.8 + - - +
95A GLN* 3.0 43.4 + - + +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 2.9 25.8 + - + +
89A GLN* 3.9 4.5 - - - +
91A LYS* 1.3 74.9 - - - +
93A LYS* 1.3 66.8 + - - +
94A LEU 3.1 0.5 + - - -
95A GLN* 3.1 11.9 + - - +
96A GLU* 2.8 25.3 + - - +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 5.5 2.6 + - - +
14A PHE* 3.2 38.1 + - + +
15A VAL* 4.0 3.4 - - - +
16A VAL* 4.0 10.3 - - + -
33A GLU* 2.5 37.1 + - - -
65A VAL* 3.7 29.6 - - + -
89A GLN 3.0 18.7 + - - +
90A ARG 3.8 3.4 - - - +
92A ALA* 1.3 78.1 - - - +
94A LEU* 1.3 57.8 + - - +
96A GLU* 3.0 34.1 + - - +
97A PHE* 2.8 30.5 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 5.0 4.9 - - + -
65A VAL* 3.8 14.1 - - + -
90A ARG* 3.1 48.3 + - + +
91A LYS* 3.6 7.4 - - - +
93A LYS* 1.3 75.2 - - - +
95A GLN* 1.3 67.4 + - - +
97A PHE* 3.3 5.1 + - + +
98A LYS* 3.0 31.9 + - - +
30B GLU* 3.3 28.7 - - + +
31B PHE* 3.7 37.2 - - + -
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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 LYS* 3.0 41.9 + - + +
92A ALA* 3.1 10.4 + - - +
94A LEU* 1.3 76.1 - - - +
96A GLU* 1.3 62.4 + - - +
98A LYS* 3.1 9.2 + - - +
99A ARG* 3.0 36.4 + - - +
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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
----------------------------------------------------------
14A PHE 5.1 0.5 - - - +
92A ALA 2.8 16.8 + - - +
93A LYS* 3.0 36.5 + - - +
94A LEU 3.3 0.2 - - - -
95A GLN* 1.3 76.0 - - - +
97A PHE* 1.3 61.9 + - - +
99A ARG* 3.3 6.2 + - - +
100A ALA* 3.0 22.7 + - + +
135A GLU* 4.0 27.9 - - + +
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.6 40.4 - - + -
32A ASP* 4.8 10.3 - - + -
33A GLU* 3.9 27.1 - - + -
93A LYS* 2.8 19.1 + - - +
94A LEU* 3.7 8.5 - - + +
96A GLU* 1.3 76.4 - - - +
98A LYS* 1.3 61.9 + - - +
100A ALA* 3.1 18.0 + - + +
101A GLN* 3.1 42.9 + - + +
31B PHE* 3.5 33.4 - + + -
32B PHE* 4.0 18.4 - + - -
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.0 22.5 + - - +
95A GLN* 3.7 6.1 - - - +
97A PHE* 1.3 77.3 - - + +
99A ARG* 1.3 61.5 + - + +
101A GLN* 3.5 7.3 + - - +
102A LYS* 3.3 16.9 + - - +
29B GLU 2.9 25.5 + - - -
30B GLU* 3.5 20.6 + - - +
31B PHE 3.6 24.5 - - - +
32B PHE 3.6 1.1 - - - +
33B LYS* 3.0 29.1 + - - +
34B GLN* 3.2 30.4 + - - +
35B GLU* 4.7 7.9 + - - -
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Residues in contact with ARG 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 29.9 + - - +
96A GLU* 3.7 2.4 - - - +
97A PHE 3.2 0.2 - - - -
98A LYS* 1.3 74.8 - - + +
100A ALA* 1.3 61.0 + - - +
102A LYS* 3.2 17.7 + - - +
103A ALA* 2.9 28.2 + - - +
135A GLU* 2.8 48.4 + - - +
137A TYR* 3.4 35.6 - - + +
138A ALA* 4.3 4.8 - - - +
141A GLU* 2.9 42.8 + - - -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 6.2 0.4 - - - +
96A GLU* 3.0 14.3 + - + +
97A PHE* 3.1 13.4 + - + +
99A ARG* 1.3 78.7 - - - +
101A GLN* 1.3 55.1 + - - +
103A ALA* 4.4 2.2 - - - +
104A GLU* 3.0 29.3 + - - +
126A TRP* 3.5 21.8 - - + -
135A GLU* 5.0 3.3 + - + -
137A TYR* 5.5 2.0 - - - +
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Residues in contact with GLN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 3.1 39.3 + - + +
98A LYS* 3.5 10.9 + - - +
99A ARG 3.3 0.2 - - - -
100A ALA* 1.3 73.6 - - - +
102A LYS* 1.3 63.4 + - - +
104A GLU* 3.5 6.8 + - - +
105A ASN* 2.9 37.0 + - - +
31B PHE 2.9 21.2 - - - +
32B PHE* 3.4 40.0 + - - +
34B GLN* 3.9 9.5 + - - +
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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
----------------------------------------------------------
98A LYS 3.3 12.1 + - - +
99A ARG* 3.2 19.2 + - - +
101A GLN* 1.3 74.3 - - - +
103A ALA* 1.3 69.5 + - - +
105A ASN* 3.1 8.7 + - - +
106A LEU* 2.8 34.6 + - + +
137A TYR* 3.8 35.6 + - + +
170A TYR 5.5 2.4 + - - +
34B GLN* 4.0 16.3 - - - +
35B GLU 5.8 0.8 + - - -
36B GLU* 4.0 13.5 + - - -
88B LEU* 6.5 0.9 - - + -
91B TRP* 3.3 47.0 - - + +
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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
----------------------------------------------------------
99A ARG 2.9 15.7 + - - +
100A ALA* 4.5 1.1 - - - -
101A GLN 3.4 0.2 - - - -
102A LYS* 1.3 77.2 - - - +
104A GLU* 1.3 58.3 + - - +
106A LEU* 3.1 3.1 + - - +
107A LEU* 2.8 30.0 + - - +
126A TRP* 3.7 20.4 - - + -
136A VAL* 3.8 19.1 - - + -
137A TYR* 3.9 18.6 - - + +
140A PHE* 3.9 15.3 - - + -
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 3.0 17.6 + - - +
101A GLN* 3.8 7.6 - - - +
103A ALA* 1.3 78.2 - - - +
105A ASN* 1.3 60.4 + - - +
107A LEU* 3.3 3.4 + - - +
108A ARG* 2.9 63.6 + - - +
118A PHE* 4.2 13.9 - - + -
122A TRP* 4.4 13.6 - - + -
126A TRP* 3.4 18.7 - - + -
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Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLN* 2.9 27.8 + - - +
102A LYS* 3.1 7.9 + - - +
104A GLU* 1.3 77.4 - - - +
106A LEU* 1.3 66.7 + - - +
108A ARG* 3.4 17.3 + - - +
109A LEU* 3.1 24.3 + - - +
34B GLN* 6.4 0.2 - - - +
87B PRO* 3.5 41.6 + - + +
88B LEU* 4.1 14.6 - - + +
91B TRP* 6.0 1.8 - - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 2.8 28.7 + - + +
103A ALA 3.4 4.5 - - - +
105A ASN* 1.3 76.0 - - + +
107A LEU* 1.3 63.9 + - - +
109A LEU* 3.2 6.9 + - + +
110A ALA* 3.0 21.7 + - - +
137A TYR* 4.3 8.3 - - + -
140A PHE* 4.1 19.1 - - + -
163A LEU* 5.7 1.3 - - - -
166A ILE* 3.5 30.8 - - + +
167A VAL* 5.7 0.4 - - - -
170A TYR* 4.2 17.0 - - + +
171A VAL* 4.0 26.2 - - + -
88B LEU* 3.7 30.5 - - + -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 2.8 15.9 + - - +
104A GLU* 3.7 6.1 - - - +
105A ASN 3.2 0.2 - - - -
106A LEU* 1.3 78.0 - - - +
108A ARG* 1.3 56.9 + - - +
110A ALA* 3.2 3.4 + - - +
111A ALA* 2.9 26.7 + - - +
118A PHE* 4.6 9.2 - - + -
121A ALA* 3.7 33.0 - - + +
122A TRP 4.6 0.2 - - - +
125A VAL* 3.8 21.5 - - + -
126A TRP* 3.8 36.6 - - + +
140A PHE* 4.8 9.4 - - + -
159A TRP* 3.8 25.6 - - + -
163A LEU* 4.5 6.7 - - + -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 2.9 48.4 + - - +
105A ASN* 3.7 16.1 + - - +
106A LEU 3.3 0.2 - - - -
107A LEU* 1.3 75.4 - - - +
109A LEU* 1.3 58.5 + - - +
111A ALA* 3.5 7.7 + - - +
112A GLU* 3.0 41.0 + - - +
118A PHE* 3.5 55.0 - - + +
87B PRO* 6.5 0.7 - - - -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN 3.1 11.8 + - - +
106A LEU* 3.5 8.7 - - + +
107A LEU 3.2 0.2 - - - -
108A ARG* 1.3 75.9 - - - +
110A ALA* 1.3 65.7 + - - +
112A GLU* 3.2 20.2 + - + +
113A LYS* 3.0 29.9 + - + +
166A ILE* 4.1 22.9 - - + -
170A TYR* 4.6 15.0 - - + +
88B LEU* 3.8 29.8 - - + -
115B GLU* 3.8 27.6 - - - +
118B TYR* 5.9 0.9 - - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.0 8.8 + - - +
107A LEU 3.2 7.6 + - - +
109A LEU* 1.3 75.4 - - - +
111A ALA* 1.3 64.4 + - - +
113A LYS* 3.2 5.0 + - - +
114A LEU* 3.1 23.6 + - - +
159A TRP* 3.9 10.7 - - + -
162A VAL* 3.7 13.7 - - + +
163A LEU* 3.7 27.1 - - + -
166A ILE* 3.5 24.1 - - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 2.9 15.7 + - - +
108A ARG* 3.7 8.1 - - - +
110A ALA* 1.3 74.2 - - - +
112A GLU* 1.3 66.4 + - + +
114A LEU* 3.0 1.8 + - - -
115A GLY 2.9 20.1 + - - -
116A LYS 3.1 26.3 + - - +
117A ASP 4.7 2.9 - - - +
118A PHE* 5.2 3.1 - - + -
121A ALA* 4.1 12.8 - - + -
159A TRP* 3.8 22.1 - - + -
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.0 29.7 + - + +
109A LEU* 3.2 22.0 + - + +
111A ALA* 1.3 75.5 - - + +
113A LYS* 1.4 62.8 + - + +
114A LEU 3.2 1.2 + - - -
115A GLY* 3.3 10.0 + - - -
116A LYS 5.1 0.9 - - - -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.0 26.2 + - + +
110A ALA 3.5 8.5 - - - +
111A ALA 3.2 0.2 - - - -
112A GLU* 1.4 75.5 - - - +
114A LEU* 1.3 57.5 + - - +
115A GLY 3.5 0.2 - - - -
162A VAL* 3.8 24.2 - - + -
165A GLU* 3.2 30.0 + - - +
166A ILE* 4.3 10.1 - - + -
115B GLU* 3.4 28.5 + - - +
116B GLY* 4.1 9.9 - - - -
118B TYR* 4.0 10.6 + - - -
----------------------------------------------------------
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 3.1 11.6 + - - +
111A ALA* 3.0 4.1 + - - +
113A LYS* 1.3 78.1 - - - +
115A GLY* 1.3 63.0 + - - +
116A LYS* 4.0 20.8 - - + +
158A GLU* 3.8 22.2 - - + +
159A TRP* 3.6 46.9 - - + -
162A VAL* 3.6 24.5 - - + -
----------------------------------------------------------
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA 2.9 5.4 + - - -
112A GLU* 3.3 10.1 + - - -
113A LYS 3.5 0.2 - - - -
114A LEU* 1.3 79.7 - - - +
116A LYS* 1.3 62.0 + - - +
117A ASP 4.1 0.5 + - - -
----------------------------------------------------------
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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