Contacts of the helix formed by residues 94 - 123 (chain D) in PDB entry 2BKC
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 94 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 1.3 76.7 - - - +
95D MET* 1.3 70.2 + - + +
96D ASP* 3.6 20.6 - - + +
97D GLN* 3.3 26.1 + - - -
98D LEU* 3.1 23.5 + - - +
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Residues in contact with MET 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D MET* 3.6 43.1 - - + -
35D ARG 3.6 32.1 + - - +
36D GLY* 5.3 1.3 - - - -
38D ASN* 4.2 21.8 - - + +
39D PHE 4.4 0.9 - - - +
42D LEU* 3.1 38.1 - - + -
93D LYS 3.9 0.4 + - - -
94D THR* 1.3 76.7 - - + +
96D ASP* 1.3 64.9 + - - +
98D LEU* 3.4 9.2 + - - +
99D MET* 3.1 32.9 + - - +
149D PHE* 4.2 11.2 - - + -
37I HIS* 5.7 3.4 - - + -
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D THR* 3.2 14.2 - - + +
95D MET* 1.3 77.4 - - - +
97D GLN* 1.3 57.1 + - + +
99D MET* 3.0 5.0 + - - +
100D GLU* 2.9 35.1 + - - +
149D PHE* 4.2 3.6 - - - -
150D LEU* 3.9 30.0 - - + +
37I HIS* 2.7 39.2 + - - -
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Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D PRO 4.9 0.7 - - - +
93D LYS* 3.7 35.7 + - + +
94D THR* 3.3 37.5 + - - +
96D ASP* 1.3 77.6 - - + +
98D LEU* 1.3 62.3 + - - +
100D GLU* 3.2 18.1 + - - +
101D ASP* 3.1 20.6 + - - +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 5.6 5.8 - - + +
30D ILE* 3.7 43.7 - - + +
33D TYR* 4.7 4.7 - - + +
34D MET* 4.0 34.3 - - + +
35D ARG 5.4 0.2 - - - +
89D TYR* 4.1 17.7 - - + +
93D LYS* 4.1 31.4 - - + +
94D THR 3.1 16.9 + - - +
95D MET* 3.7 12.6 - - - +
96D ASP 3.3 0.2 - - - -
97D GLN* 1.3 78.6 - - - +
99D MET* 1.3 61.9 + - + +
101D ASP* 3.2 10.0 + - + +
102D LEU 3.1 21.0 + - - -
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Residues in contact with MET 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ILE* 3.6 30.5 - - + -
34D MET* 4.7 2.0 - - + -
42D LEU* 4.1 15.7 - - + -
46D MET* 4.2 13.7 - - + -
95D MET* 3.1 22.4 + - - +
96D ASP 3.0 9.4 + - - +
98D LEU* 1.3 76.2 - - + +
100D GLU* 1.3 60.8 + - - +
102D LEU* 3.2 9.8 + - + +
103D VAL* 2.9 33.3 + - - +
146D PHE* 3.7 35.2 - - + +
149D PHE* 3.8 21.1 - - + -
150D LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ASP* 2.9 20.2 + - - +
97D GLN* 3.2 20.8 + - - +
99D MET* 1.3 74.2 - - - +
101D ASP* 1.3 61.2 + - - +
103D VAL* 4.1 4.0 - - + +
104D GLY* 3.0 24.9 + - - -
150D LEU* 4.2 21.1 - - + +
152D LYS* 5.5 12.0 + - - +
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Residues in contact with ASP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LYS* 2.3 44.8 + - + +
29D GLN* 5.0 3.8 + - - -
30D ILE* 5.2 3.1 - - + +
93D LYS* 5.2 10.1 - - - +
97D GLN 3.1 12.6 + - - +
98D LEU* 3.2 12.5 + - + +
100D GLU* 1.3 75.5 - - - +
102D LEU* 1.3 61.2 + - - +
104D GLY* 3.9 1.4 - - - +
105D THR* 2.8 33.3 + - - -
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.3 39.3 - - + -
26D LYS* 5.3 1.3 - - - -
27D ILE* 4.6 2.9 - - + -
30D ILE* 4.2 16.1 - - + +
46D MET* 4.2 7.6 - - + -
49D LEU* 3.7 26.7 - - + -
98D LEU 3.1 12.3 + - - +
99D MET* 3.2 15.0 + - + +
101D ASP* 1.3 75.5 - - - +
103D VAL* 1.3 58.1 + - - +
105D THR* 3.1 8.1 + - - -
106D LEU* 2.9 32.2 + - + +
146D PHE* 3.8 38.8 - - + -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D MET 2.9 17.3 + - - +
100D GLU* 4.1 6.7 - - + +
102D LEU* 1.3 77.5 - - - +
104D GLY* 1.3 63.2 + - - +
106D LEU* 3.2 10.3 + - + +
107D GLU* 3.0 45.4 + - + +
143D ILE* 4.8 9.4 - - + +
146D PHE* 3.6 34.8 - - + -
147D LYS* 3.9 24.9 - - + +
150D LEU* 4.2 13.7 - - + -
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU 3.0 18.8 + - - -
101D ASP* 3.9 2.0 - - - -
103D VAL* 1.3 75.9 - - - +
105D THR* 1.3 61.5 + - - +
107D GLU* 3.5 14.5 + - - +
108D LEU* 3.2 20.6 + - - +
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Residues in contact with THR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.6 32.5 - - + -
26D LYS* 3.6 16.1 - - - +
84D VAL* 3.8 33.9 - - + +
101D ASP* 2.8 16.8 + - - -
102D LEU 3.1 8.8 + - - -
104D GLY* 1.3 74.4 - - - +
106D LEU* 1.3 65.8 + - - +
108D LEU* 3.3 9.6 + - + +
109D LEU* 3.0 24.7 + - + +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 4.1 14.6 - - + -
49D LEU* 5.0 1.6 - - + -
53D PHE* 3.7 32.3 - - + -
102D LEU* 2.9 43.1 + - + +
103D VAL* 3.6 11.2 - - + +
105D THR* 1.3 71.4 - - - +
107D GLU* 1.3 51.4 + - - +
109D LEU* 3.3 6.8 + - + +
110D ARG* 2.7 35.3 + - - +
139D ILE* 3.5 20.1 - - + +
142D HIS* 3.9 33.4 - - + -
143D ILE* 3.8 17.3 - - + -
146D PHE* 4.6 2.9 - - + -
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D VAL* 3.0 29.5 + - + +
104D GLY* 3.7 13.2 - - - +
105D THR 3.2 0.4 - - - -
106D LEU* 1.3 71.7 - - - +
108D LEU* 1.3 67.1 + - - +
110D ARG* 3.3 30.9 + - - +
111D ASP* 2.9 32.5 + - - +
143D ILE* 4.0 14.9 - - + +
147D LYS* 3.4 29.2 + - - -
154D PRO 4.5 4.2 - - - +
155D LEU* 5.9 0.2 - - - -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASN* 4.1 4.3 - - - +
83D SER* 3.7 26.7 - - - +
84D VAL* 4.0 25.4 - - + -
85D GLU* 5.4 3.8 - - + +
104D GLY 3.2 11.2 + - - +
105D THR* 3.3 11.0 + - - +
107D GLU* 1.3 79.6 - - - +
109D LEU* 1.3 65.9 + - - +
111D ASP* 3.1 4.4 + - - +
112D GLU* 3.0 52.1 + - + +
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 3.5 23.3 - - - +
19D ASN* 4.1 16.4 - - + +
20D LEU* 3.9 23.6 - - + -
23D PHE* 3.5 41.1 - - + -
53D PHE* 4.7 6.3 - - + -
84D VAL* 4.8 3.4 - - + -
105D THR* 3.0 20.9 + - + +
106D LEU* 3.7 8.7 - - + +
108D LEU* 1.3 80.2 - - + +
110D ARG* 1.3 64.7 + - - +
112D GLU* 3.4 2.6 + - - -
113D TYR* 2.9 38.0 + - + -
139D ILE* 4.2 12.6 - - + -
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU 2.7 21.1 + - - +
107D GLU* 3.3 30.1 + - - +
109D LEU* 1.3 72.9 - - - +
111D ASP* 1.3 85.4 + - - +
113D TYR* 3.4 6.0 + - - +
114D LYS* 3.0 26.9 + - + +
136D LYS* 4.1 21.7 - - + +
139D ILE* 3.8 15.1 - - + +
140D ASP* 3.2 27.6 + - - +
143D ILE* 4.2 17.6 - - + +
154D PRO 5.1 0.6 + - - -
155D LEU* 3.7 27.5 - - - +
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Residues in contact with ASP 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D GLU* 2.9 24.2 + - - +
108D LEU* 3.9 4.7 - - - +
110D ARG* 1.3 103.7 + - - +
112D GLU* 1.3 66.4 + - + +
114D LYS* 3.3 11.0 + - - +
115D GLN* 3.2 24.8 + - - +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.2 12.6 - - + -
15D HIS* 3.4 9.5 - - - -
16D GLN* 2.7 35.2 + - - +
19D ASN* 3.1 9.2 + - - -
83D SER* 2.4 29.1 + - - -
108D LEU* 3.0 33.6 + - + +
109D LEU* 3.9 4.3 - - - +
111D ASP* 1.3 74.7 - - + +
113D TYR* 1.3 59.4 + - - +
115D GLN* 3.0 34.5 + - - +
116D GLY 3.0 10.6 + - - -
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 4.0 9.2 - + - -
16D GLN* 3.6 40.3 - - + +
20D LEU* 3.5 25.5 - - - +
56D GLN* 2.9 17.0 + - - -
60D VAL* 4.9 1.6 - - + +
109D LEU* 2.9 26.4 + - + +
110D ARG* 3.7 5.4 - - - +
112D GLU* 1.3 73.3 - - - +
114D LYS* 1.3 61.4 + - - +
116D GLY* 3.1 1.0 + - - -
117D ILE* 2.8 37.9 + - + +
132D LEU* 4.1 22.0 - - + +
135D PHE* 3.5 41.8 - + + -
136D LYS* 4.2 7.4 - - + -
139D ILE* 3.6 22.9 - - + -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.0 12.4 + - + +
111D ASP* 3.4 14.1 - - - +
112D GLU 3.2 0.2 - - - -
113D TYR* 1.3 76.2 - - - +
115D GLN* 1.3 61.6 + - + +
117D ILE* 3.3 11.8 + - + +
118D GLU* 3.2 57.9 + - - +
136D LYS* 4.2 23.7 - - - +
124K GLY* 4.2 15.4 + - - -
126K ASP* 3.3 25.9 + - - +
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 4.5 5.3 - - + -
111D ASP 3.2 9.9 + - - +
112D GLU* 3.0 32.8 + - - +
114D LYS* 1.3 76.6 - - + +
116D GLY* 1.3 56.3 + - - +
118D GLU* 3.3 14.2 + - - +
119D LEU* 3.0 30.3 + - - +
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Residues in contact with GLY 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.4 37.5 - - - -
112D GLU 3.0 10.3 + - - -
113D TYR 3.1 1.9 + - - -
115D GLN* 1.3 77.5 - - - +
117D ILE* 1.3 57.2 - - - +
119D LEU* 3.7 4.6 - - - +
120D THR* 2.9 35.1 + - - +
132D LEU* 3.8 5.9 - - - +
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TYR 2.8 21.5 + - - +
114D LYS* 3.6 12.8 - - + +
115D GLN 3.2 0.2 - - - -
116D GLY* 1.3 76.9 - - - +
118D GLU* 1.3 57.4 + - - +
120D THR* 3.7 6.3 - - - -
121D ASP* 3.1 14.8 + - + +
129D ASN* 2.9 33.5 + - - +
132D LEU* 3.7 23.3 - - + +
133D ILE* 3.6 35.7 - - + +
136D LYS* 4.1 23.3 - - + -
126K ASP* 3.6 31.0 - - + +
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LYS* 3.2 46.7 + - - +
115D GLN* 3.3 17.7 + - - +
117D ILE* 1.3 73.7 - - - +
119D LEU* 1.3 56.0 + - - +
121D ASP* 3.2 8.4 + - - +
122D LYS* 2.8 35.6 + - - +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 3.4 29.2 - - + +
8D ASP 3.6 22.7 - - - +
9D THR* 4.3 6.1 - - + +
12D PHE* 3.8 25.1 - - + -
115D GLN 3.0 16.2 + - - +
116D GLY* 3.7 3.8 - - - +
118D GLU* 1.3 78.7 - - - +
120D THR* 1.3 60.3 + - - +
122D LYS* 3.2 8.6 + - + +
123D GLU* 3.0 51.6 + - + +
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D THR* 4.0 15.5 + - - -
116D GLY 2.9 25.5 + - - +
117D ILE* 3.3 13.2 - - - +
119D LEU* 1.3 74.9 - - - +
121D ASP* 1.3 64.4 + - - +
123D GLU* 3.6 1.2 + - - +
124D GLY 3.3 2.4 + - - -
125D ASP* 3.1 52.6 + - - +
128D THR* 3.5 15.7 - - - +
129D ASN* 3.3 35.1 + - - +
132D LEU* 4.2 4.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 3.1 19.8 + - + +
118D GLU* 3.4 7.9 - - - +
120D THR* 1.3 77.5 - - - +
122D LYS* 1.3 64.1 + - - +
124D GLY* 3.0 14.8 + - - -
129D ASN* 3.7 14.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLU 2.8 14.4 + - - +
119D LEU* 3.2 13.2 + - + +
121D ASP* 1.3 80.2 + - - +
123D GLU* 1.3 58.2 + - + +
124D GLY 3.3 3.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL 4.7 0.2 - - - +
8D ASP* 3.7 22.3 - - - +
9D THR* 2.9 40.7 + - - +
119D LEU* 3.0 27.8 + - + +
120D THR 3.6 3.1 + - - +
121D ASP 3.3 0.2 - - - -
122D LYS* 1.3 76.6 - - + +
124D GLY* 1.3 61.6 + - - +
125D ASP* 3.2 5.9 + - + +
----------------------------------------------------------
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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