Contacts of the helix formed by residues 92 - 121 (chain A) in PDB entry 2DPD
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 ASP 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.4 15.9 - - - +
69A ILE* 3.0 11.1 + - - +
91A LYS* 1.3 79.5 - - + +
93A TYR* 1.3 57.5 + - - +
94A GLU* 3.1 15.3 + - - +
95A ALA* 3.1 34.0 + - + +
96A ALA* 3.1 21.3 + - - +
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Residues in contact with TYR 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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28A GLU* 3.1 28.8 + - + +
90A PHE* 3.6 55.8 - + + +
91A LYS 3.9 3.2 + - - -
92A ASP* 1.3 71.4 + - - +
94A GLU* 1.3 61.5 + - + +
96A ALA* 3.6 7.2 - - + -
97A LYS* 2.9 56.7 + - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 3.1 10.2 + - - +
93A TYR* 1.3 75.6 - - + +
95A ALA* 1.3 66.3 + - - +
97A LYS* 3.1 21.2 + - - +
98A LEU* 2.9 28.7 + - + +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP 5.3 2.0 - - - +
68A GLY 4.8 1.3 - - - +
69A ILE* 3.9 20.1 - - + +
92A ASP* 3.1 39.4 + - + +
94A GLU* 1.3 77.0 - - - +
96A ALA* 1.3 60.7 - - - +
98A LEU* 3.5 11.1 + - - +
99A TYR* 3.1 23.6 + - - +
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Residues in contact with ALA 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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24A ILE* 4.4 13.4 - - + +
69A ILE* 3.7 19.4 - - + +
90A PHE* 3.6 31.2 - - + -
92A ASP 3.1 8.7 + - - +
93A TYR* 3.4 12.6 - - + +
94A GLU 3.1 0.4 - - - -
95A ALA* 1.3 72.2 - - - +
97A LYS* 1.3 57.7 + - - +
98A LEU 3.0 0.5 + - - -
99A TYR* 3.0 5.6 + - - +
100A LYS* 2.8 35.8 + - - +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 5.4 2.9 - - - +
93A TYR* 2.9 55.2 + - + +
94A GLU* 3.1 19.9 + - - +
96A ALA* 1.3 74.4 - - - +
98A LEU* 1.3 63.5 + - + +
100A LYS* 3.4 8.2 + - - +
101A LYS* 3.1 46.0 + - - +
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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
----------------------------------------------------------
94A GLU* 2.9 18.5 + - + +
95A ALA* 3.6 11.9 - - - +
97A LYS* 1.3 77.4 - - + +
99A TYR* 1.3 62.1 + - - +
101A LYS* 3.1 22.8 + - + +
102A GLN* 3.1 25.2 + - + +
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Residues in contact with TYR 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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16A ARG* 5.5 0.2 - - - -
17A ALA* 3.9 17.8 - - - +
20A LYS* 3.2 50.4 + - + -
24A ILE* 3.5 21.1 - - + -
64A LEU* 4.4 6.5 - - + -
67A ASP* 5.9 1.8 - - - -
69A ILE* 5.2 10.1 - - + -
95A ALA 3.1 13.1 + - - +
96A ALA* 3.0 5.5 + - - +
98A LEU* 1.3 75.4 - - - +
100A LYS* 1.3 65.6 + - - +
102A GLN* 3.4 26.7 + - + +
103A LEU* 3.1 53.0 + - + +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.8 16.2 - - + -
24A ILE* 3.7 24.4 - - + +
25A THR* 3.4 26.1 - - - +
28A GLU* 3.5 25.9 + - - +
96A ALA 2.8 18.1 + - - +
97A LYS* 3.6 10.1 - - - +
99A TYR* 1.3 72.8 - - - +
101A LYS* 1.3 59.3 + - + +
103A LEU* 3.3 3.9 + - - +
104A LYS 3.0 21.8 + - - -
121B ASN 2.8 28.8 + - - -
122B PHE* 3.5 24.6 - - + -
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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
----------------------------------------------------------
97A LYS* 3.1 32.1 + - - +
98A LEU* 3.1 15.5 + - + +
100A LYS* 1.3 76.1 - - + +
102A GLN* 1.3 66.5 + - - +
104A LYS* 3.1 9.5 + - - +
105A VAL* 3.1 23.5 + - - +
122B PHE* 5.4 0.4 - - - -
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.1 23.5 + - + +
99A TYR* 3.6 32.5 + - + +
101A LYS* 1.3 75.8 - - + +
103A LEU* 1.3 57.9 + - + +
105A VAL* 3.0 13.4 + - - +
106A GLU* 2.9 32.2 + - + +
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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
----------------------------------------------------------
13A VAL* 4.7 3.4 - - + -
17A ALA* 3.5 34.1 - - + +
21A LEU* 3.7 43.3 - - + +
24A ILE* 4.9 0.2 - - + -
99A TYR* 3.1 59.7 + - + +
100A LYS* 3.6 5.6 - - - +
101A LYS 3.2 0.2 - - - -
102A GLN* 1.3 72.0 - - - +
104A LYS* 1.3 60.9 + - - +
106A GLU* 3.5 17.3 - - + +
107A LEU* 2.9 34.1 + - + +
122B PHE* 4.2 2.5 - - - -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS 3.0 7.6 + - - +
101A LYS* 3.1 13.4 + - - +
103A LEU* 1.3 75.5 - - - +
105A VAL* 1.3 53.8 + - + +
107A LEU* 3.2 3.5 + - - +
108A ASP* 2.8 69.7 + - - +
118B LEU* 3.7 17.9 - - + +
122B PHE* 3.6 54.2 - - + -
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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 LYS 3.1 10.1 + - - +
102A GLN* 3.0 13.1 + - - +
104A LYS* 1.3 81.4 - - + +
106A GLU* 1.3 64.6 + - + +
108A ASP* 3.1 10.4 + - - +
109A ARG* 3.0 34.0 + - + +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE 5.2 1.6 - - - +
12A LEU 5.6 0.3 - - - -
13A VAL* 3.9 33.9 + - + +
14A LYS* 5.0 2.8 + - - +
17A ALA* 4.6 4.3 - - - +
102A GLN* 2.9 18.4 + - + +
103A LEU* 3.5 22.7 - - + +
105A VAL* 1.3 78.4 - - + +
107A LEU* 1.3 59.0 + - - +
109A ARG* 3.3 22.0 + - - +
110A SER* 2.9 31.6 + - - -
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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
----------------------------------------------------------
13A VAL* 3.8 33.4 - - + -
18A PHE* 4.6 12.6 - - + -
21A LEU* 3.8 26.2 - - + -
103A LEU* 2.9 20.5 + - + +
104A LYS 3.7 0.7 - - - +
106A GLU* 1.3 74.7 - - - +
108A ASP* 1.3 59.5 + - - +
110A SER* 3.1 3.6 + - - -
111A LYS* 2.8 31.4 + - - +
114B ILE* 3.8 14.8 - - + +
117B ALA* 3.8 23.1 - - + -
118B LEU* 3.5 33.9 - - + +
122B PHE* 4.1 1.6 - - + -
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Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 2.8 51.8 + - - +
105A VAL* 3.4 12.2 - - - +
106A GLU 3.1 0.2 - - - -
107A LEU* 1.3 77.2 - - - +
109A ARG* 1.3 61.5 + - - +
111A LYS* 3.5 11.5 + - - +
112A LYS* 3.0 29.3 + - - +
118B LEU* 3.8 12.3 - - - +
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Residues in contact with ARG 109 (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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10A GLY* 2.3 40.7 + - - -
11A PHE 2.7 18.4 + - - -
105A VAL* 3.0 22.9 + - + +
106A GLU* 3.6 20.5 + - - +
108A ASP* 1.3 71.5 - - - +
110A SER* 1.3 59.8 - - - +
112A LYS* 2.8 30.6 + - + +
113A LEU* 2.8 20.2 + - - +
48B ILE* 2.9 45.6 + - + +
49B GLY* 3.4 16.4 + - - -
50B PHE 3.7 0.6 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE 4.8 1.1 + - - -
12A LEU* 3.4 19.2 - - - +
13A VAL* 3.0 37.1 + - - +
106A GLU 2.9 12.9 + - - -
107A LEU* 3.4 11.9 - - - -
109A ARG* 1.3 76.6 - - - +
111A LYS* 1.3 66.0 + - - +
113A LEU* 3.4 2.1 + - - -
114A ILE* 3.1 26.3 + - - +
114B ILE* 3.8 19.3 - - - -
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 2.8 12.8 + - - +
108A ASP* 3.6 15.0 - - - +
110A SER* 1.3 71.0 - - - +
112A LYS* 1.3 64.1 + - - +
114A ILE* 3.0 7.8 + - - +
115A GLU* 2.8 53.1 + - + +
111B LYS* 5.8 3.6 - - + +
114B ILE* 3.6 23.5 - - + +
115B GLU* 3.6 33.7 + - + +
118B LEU* 5.1 13.5 - - + -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP* 3.0 20.1 + - - +
109A ARG* 2.8 19.5 + - + +
111A LYS* 1.3 71.8 - - - +
113A LEU* 1.3 50.7 + - - +
115A GLU* 3.2 7.5 + - - +
116A LYS* 2.7 37.6 + - - +
48B ILE* 3.5 36.6 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY 4.1 8.3 - - - +
11A PHE* 3.9 33.4 - - + +
12A LEU* 3.9 19.7 - - + -
109A ARG* 2.8 20.0 + - - +
110A SER* 3.7 6.5 - - - +
112A LYS* 1.3 71.0 - - - +
114A ILE* 1.3 67.8 + - + +
116A LYS* 2.9 6.4 + - - +
117A ALA* 2.8 25.6 + - - +
18B PHE* 4.1 11.7 - - + -
45B PHE* 3.5 34.1 - - + -
48B ILE* 3.7 19.0 - - + +
50B PHE* 3.9 15.5 - - + -
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Residues in contact with ILE 114 (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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12A LEU* 3.2 44.2 - - + -
110A SER 3.1 5.6 + - - +
111A LYS* 3.0 10.8 + - - +
113A LEU* 1.3 80.8 - - + +
115A GLU* 1.3 60.8 + - - +
117A ALA* 3.3 5.5 + - - +
118A LEU* 2.8 35.9 + - + +
12B LEU* 5.6 0.7 - - + -
13B VAL* 4.6 7.9 - - + -
18B PHE* 4.9 5.2 - - + -
107B LEU* 3.7 19.1 - - + +
110B SER* 4.0 20.9 - - - +
111B LYS* 3.6 37.2 - - + +
114B ILE* 5.3 3.1 - - + -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 2.8 53.2 + - + +
112A LYS* 3.8 5.9 - - - +
114A ILE* 1.3 78.8 - - - +
116A LYS* 1.3 56.4 + - - +
118A LEU* 3.9 7.4 - - + +
119A SER* 3.1 26.9 + - - -
111B LYS* 3.4 40.2 + - + -
115B GLU* 3.9 1.4 - - - +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS 2.7 21.0 + - - +
113A LEU 3.5 3.4 - - - +
115A GLU* 1.3 72.7 - - - +
117A ALA* 1.3 64.8 + - - +
119A SER* 3.1 4.5 + - - -
120A ASP* 2.8 51.9 + - - +
22B TYR* 3.7 3.8 + - - -
44B GLU* 2.6 58.0 + - - +
45B PHE* 3.6 25.5 - - + -
48B ILE* 4.4 16.8 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU 2.8 9.0 + - - +
114A ILE* 3.5 4.0 - - - +
116A LYS* 1.3 75.5 - - - +
118A LEU* 1.3 62.4 + - - +
119A SER 3.1 1.2 + - - -
121A ASN* 3.1 31.8 + - - +
18B PHE* 3.4 35.9 - - + -
21B LEU* 5.1 2.2 - - + -
22B TYR* 3.2 18.7 + - + -
107B LEU* 3.6 17.0 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 2.8 24.7 + - + +
115A GLU* 3.9 9.2 - - + +
117A ALA* 1.3 76.8 - - - +
119A SER* 1.3 58.8 + - - +
122A PHE* 3.5 38.4 + - + +
104B LYS* 3.5 31.0 - - + +
107B LEU* 3.5 33.8 - - + +
108B ASP* 3.7 11.2 - - - +
111B LYS* 5.3 10.5 - - + -
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU 3.1 17.6 + - - -
116A LYS* 3.1 8.2 + - - -
117A ALA 3.0 1.0 - - - -
118A LEU* 1.3 77.4 - - - +
120A ASP* 1.3 67.5 + - - +
122A PHE* 3.1 18.8 - - - +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 2.8 36.1 + - - +
119A SER* 1.3 83.7 + - - +
121A ASN* 1.3 73.2 + - - +
122A PHE* 3.6 1.7 + - - +
22B TYR* 2.6 27.6 + - + -
25B THR* 4.6 7.0 - - - +
26B MET* 6.1 2.5 - - + -
44B GLU* 3.0 9.3 - - - +
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA 3.1 16.2 + - - +
120A ASP* 1.3 77.1 - - - +
122A PHE* 1.3 62.8 + - + +
21B LEU* 2.9 53.6 - - + +
22B TYR* 3.3 33.7 - - - +
25B THR* 2.4 33.6 + - - +
100B LYS* 2.8 29.5 + - - -
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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