Contacts of the helix formed by residues 125 - 150 (chain S) 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 ASP 125 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S THR* 3.4 24.4 - - - +
63S ARG* 2.8 29.0 + - - -
67S ILE* 4.3 7.9 - - - +
120S THR* 2.8 43.9 + - + +
123S GLU* 3.3 6.7 - - + +
124S GLY* 1.3 72.6 - - - +
126S ASP* 1.3 62.2 + - - +
128S THR* 2.9 27.9 + - - -
129S ASN* 3.2 2.8 + - - +
136Y LYS* 5.6 0.9 + - - +
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Residues in contact with ASP 126 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124S GLY* 3.4 14.2 + - - +
125S ASP* 1.3 73.1 + - - +
127S VAL* 1.3 58.7 + - + +
129S ASN* 3.7 7.5 - - - +
130S ASP* 3.1 28.6 + - - +
114Y LYS* 3.4 35.6 + - - +
117Y ILE* 3.9 15.3 - - + +
133Y ILE* 3.8 29.2 - - + +
136Y LYS* 5.3 4.7 - - - +
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Residues in contact with VAL 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S ARG* 3.1 41.1 - - + +
125S ASP* 3.4 0.6 + - - -
126S ASP* 1.3 74.6 - - + +
128S THR* 1.3 66.8 + - - +
129S ASN 3.2 0.2 + - - -
130S ASP* 3.3 3.6 + - - +
131S MET* 3.0 24.5 + - + +
133Y ILE* 3.8 18.6 - - + +
136Y LYS* 3.9 22.0 - - + -
137Y ALA* 3.7 44.0 - - + +
140Y ASP* 4.2 2.0 - - - +
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Residues in contact with THR 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S THR* 4.5 2.2 - - + -
13S LEU* 3.7 39.9 - - + +
63S ARG* 2.9 24.8 + - - +
67S ILE* 4.6 1.0 - - - +
120S THR* 3.8 15.7 - - - +
125S ASP* 2.9 28.2 + - - +
127S VAL* 1.3 77.6 - - - +
129S ASN* 1.3 62.5 + - - +
131S MET* 3.3 13.1 + - + +
132S LEU* 3.1 26.0 + - + +
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Residues in contact with ASN 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N ASP* 5.3 0.4 + - - -
117S ILE* 3.0 44.6 + - - +
120S THR* 3.1 25.8 - - + +
121S ASP* 3.8 16.6 + - - +
125S ASP 3.2 7.7 + - - +
126S ASP* 3.7 8.5 - - - +
127S VAL 3.2 0.6 - - - -
128S THR* 1.3 76.4 - - - +
130S ASP* 1.3 63.7 + - - +
132S LEU* 3.4 5.8 + - - +
133S ILE* 3.1 36.7 + - - +
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Residues in contact with ASP 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N ASP* 3.6 13.7 - - - +
126S ASP 3.1 17.0 + - - +
127S VAL 3.8 3.7 - - - +
129S ASN* 1.3 76.2 + - - +
131S MET* 1.3 70.4 + - - +
133S ILE* 3.1 10.7 + - - +
134S ALA* 3.0 25.8 + - - +
130Y ASP* 3.6 20.7 - - - +
133Y ILE* 4.2 19.3 - - + +
134Y ALA* 6.0 2.4 - - - +
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Residues in contact with MET 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 4.2 9.4 - - + -
59S GLU* 4.0 21.3 - - + +
60S VAL* 4.3 11.4 - - + -
63S ARG* 3.9 27.4 - - + -
127S VAL* 3.0 20.8 + - + +
128S THR* 3.3 19.9 + - + +
130S ASP* 1.3 80.1 + - - +
132S LEU* 1.3 83.7 + - + +
134S ALA* 3.3 5.6 + - - +
135S PHE* 3.1 49.2 + - + -
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Residues in contact with LEU 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S PHE* 3.9 22.7 - - + -
13S LEU* 4.3 7.0 - - + -
16S GLN* 5.8 0.4 - - + -
60S VAL* 5.3 2.7 - - + -
113S TYR* 4.3 20.3 - - + +
116S GLY* 3.4 39.9 - - - +
117S ILE* 3.7 13.9 - - + +
120S THR* 4.2 7.4 - - - +
128S THR* 3.1 18.7 + - + +
129S ASN 3.7 4.7 - - - +
130S ASP 3.2 0.2 - - - -
131S MET* 1.3 97.4 - - + +
133S ILE* 1.3 59.2 + - - +
135S PHE* 3.4 15.9 + - + +
136S LYS* 2.9 28.9 + - - +
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Residues in contact with ILE 133 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N ASP* 3.5 49.4 - - + +
127N VAL* 3.6 11.7 - - + +
130N ASP* 4.0 21.3 - - + +
117S ILE* 4.1 15.3 - - + -
129S ASN* 3.1 38.0 + - - +
130S ASP* 3.1 12.9 + - - +
132S LEU* 1.3 77.0 - - - +
134S ALA* 1.3 57.6 + - - +
136S LYS* 3.0 6.3 + - - +
137S ALA* 2.8 30.3 + - + +
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Residues in contact with ALA 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N ASP* 5.9 3.6 - - - +
130S ASP* 3.0 16.7 + - - +
131S MET* 3.6 11.0 - - - +
132S LEU 3.3 0.2 - - - -
133S ILE* 1.3 77.4 - - - +
135S PHE* 1.3 67.8 + - + +
137S ALA* 3.3 9.9 - - - +
138S SER* 3.2 19.2 + - - -
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Residues in contact with PHE 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S GLN* 3.3 54.8 + - + +
59S GLU* 3.6 28.7 - - + -
60S VAL* 3.7 24.7 - - + -
113S TYR* 3.5 21.8 - + + -
131S MET* 3.1 36.3 + - + -
132S LEU* 3.6 12.1 - - + +
133S ILE 3.3 0.2 - - - -
134S ALA* 1.3 80.7 - - + +
136S LYS* 1.3 63.2 + - - +
138S SER* 3.1 7.0 + - - -
139S ILE* 3.0 25.8 + - - +
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Residues in contact with LYS 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ARG* 4.3 6.3 - - - +
125N ASP* 5.1 2.6 + - - +
126N ASP* 5.8 4.2 + - + +
127N VAL* 4.0 17.0 - - + +
110S ARG* 4.0 26.2 - - + +
113S TYR* 4.5 9.4 - - + -
114S LYS* 3.8 30.3 - - + +
117S ILE* 3.9 22.0 - - + -
132S LEU 2.9 16.8 + - - +
133S ILE* 3.5 6.1 - - - +
135S PHE* 1.3 77.5 - - - +
137S ALA* 1.3 65.1 + - - +
139S ILE* 2.9 7.8 + - - +
140S ASP* 2.9 51.2 + - - +
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Residues in contact with ALA 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ARG* 5.2 0.9 + - - -
127N VAL* 3.6 29.6 - - + +
133S ILE* 2.8 14.3 + - + +
134S ALA* 3.3 15.7 - - - +
136S LYS* 1.3 76.6 - - - +
138S SER* 1.3 60.1 + - - +
140S ASP* 3.8 3.0 + - - +
141S LYS* 3.4 20.8 + - - +
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Residues in contact with SER 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S GLU* 2.5 32.0 + - - -
53S PHE* 5.9 0.2 - - - -
56S GLN* 4.7 3.6 - - - -
134S ALA 3.2 7.6 + - - -
135S PHE* 3.1 12.2 + - - -
137S ALA* 1.3 77.0 - - - +
139S ILE* 1.3 65.2 + - - +
141S LYS* 3.4 11.9 + - - +
142S HIS* 3.1 29.7 + - - -
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Residues in contact with ILE 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S PHE* 4.2 26.2 - - + -
56S GLN* 4.4 0.7 - - - +
106S LEU* 3.3 33.0 - - + +
109S LEU* 4.1 17.7 - - + -
110S ARG* 4.0 12.3 - - + +
113S TYR* 3.5 39.5 - - + -
135S PHE 3.0 13.1 + - - +
136S LYS* 2.9 9.2 + - - +
138S SER* 1.3 72.9 - - - +
140S ASP* 1.3 56.3 + - - +
142S HIS* 3.0 10.0 + - - +
143S ILE* 2.8 42.3 + - + +
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Residues in contact with ASP 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ARG* 3.1 32.3 + - - +
66N ALA* 4.2 15.5 - - + +
127N VAL* 4.3 2.4 - - - +
110S ARG* 3.3 33.4 + - - +
136S LYS* 2.9 44.3 + - - +
137S ALA 4.0 2.9 - - - +
139S ILE* 1.3 74.5 - - - +
141S LYS* 1.3 65.2 + - - +
143S ILE* 3.2 8.8 + - - +
144S TRP* 3.1 18.7 + - - +
154S PRO* 5.8 0.2 - - - +
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Residues in contact with LYS 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N GLU* 4.2 18.6 - - + +
66N ALA* 4.7 5.5 - - - +
45S LYS* 5.7 1.0 - - - +
137S ALA 3.4 12.6 + - - +
138S SER* 3.6 12.1 - - - +
139S ILE 3.3 0.4 - - - -
140S ASP* 1.3 76.5 - - - +
142S HIS* 1.3 79.6 + - - +
144S TRP* 3.0 34.2 + - + +
145S MET* 3.1 45.6 + - + +
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Residues in contact with HIS 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S LYS* 4.3 10.5 - - - -
49S LEU* 3.4 31.0 - - + +
52S GLU* 2.7 29.5 + - - -
53S PHE* 4.2 11.4 - + - -
106S LEU* 3.9 19.3 - - + -
138S SER* 3.1 32.2 + - - -
139S ILE* 3.0 9.7 + - - +
141S LYS* 1.3 83.7 - - - +
143S ILE* 1.3 63.0 + - - +
145S MET* 3.2 18.3 + - + +
146S PHE* 3.0 38.1 + - + +
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Residues in contact with ILE 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103S VAL* 4.7 5.8 - - + +
106S LEU* 3.9 28.9 - - + +
107S GLU* 4.0 12.3 - - + +
110S ARG* 3.6 34.3 - - - +
139S ILE* 2.8 37.7 + - + +
140S ASP* 3.2 7.8 + - - +
142S HIS* 1.3 71.9 - - - +
144S TRP* 1.3 63.5 + - - +
146S PHE* 5.3 1.3 - - - -
147S LYS* 3.0 41.2 + - + +
154S PRO* 3.6 28.5 - - + +
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Residues in contact with TRP 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N GLU* 3.7 47.1 - - + -
65N LEU* 3.7 42.7 - - + +
66N ALA* 4.1 17.5 - - + -
31P HIS* 4.7 15.5 - + - -
32P TRP* 4.5 9.4 + + - -
39P PHE* 3.9 24.5 - + - -
140S ASP 3.1 9.7 + - - +
141S LYS* 3.0 20.5 + - + +
143S ILE* 1.3 76.2 - - - +
145S MET* 1.3 81.1 + - + +
147S LYS* 3.7 1.8 - - - +
148S ALA* 2.9 35.4 + - + +
154S PRO* 4.1 25.8 - - + +
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Residues in contact with MET 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P PHE* 3.6 33.6 - - + -
40P PHE* 4.0 17.4 - - + -
45S LYS* 4.1 11.7 - - - +
141S LYS* 3.1 53.2 + - + +
142S HIS* 3.2 20.6 + - - +
144S TRP* 1.3 102.1 - - + +
146S PHE* 1.3 62.9 + - + +
148S ALA* 3.3 3.5 + - - +
149S PHE* 3.0 26.7 + - - +
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Residues in contact with PHE 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P PHE* 3.7 21.8 - + - -
42S LEU* 5.0 2.7 - - + -
45S LYS* 3.7 35.2 - - + -
46S MET* 3.8 30.7 - - + -
49S LEU* 4.3 9.0 - - + -
99S MET* 3.8 25.1 - - + -
102S LEU* 4.2 16.2 - - + -
103S VAL* 3.7 23.8 - - + -
106S LEU* 4.6 2.0 - - + -
142S HIS* 3.0 44.4 + + + +
145S MET* 1.3 72.0 - - + +
147S LYS* 1.3 66.1 + - - +
149S PHE* 3.0 9.9 + + + +
150S LEU* 3.0 23.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 147 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103S VAL* 3.6 26.2 - - + +
107S GLU* 2.6 29.9 + - - -
143S ILE* 3.0 22.3 + - + +
144S TRP 3.7 3.1 - - - +
146S PHE* 1.3 75.2 - - - +
148S ALA* 1.3 60.1 + - - +
150S LEU* 3.0 19.2 + - + +
152S LYS* 2.9 43.3 + - + +
153S ALA 3.0 25.6 - - - +
154S PRO* 3.0 26.1 + - + +
155S LEU* 5.0 0.4 - - - +
156S GLU 3.8 21.8 + - - -
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Residues in contact with ALA 148 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P MET 4.0 7.9 - - - +
35P ARG* 3.3 10.4 - - + +
36P GLY 2.8 25.2 + - - -
39P PHE* 3.7 27.8 - - + -
144S TRP* 2.9 29.2 + - + +
145S MET 3.3 5.1 + - - +
147S LYS* 1.3 72.4 - - - +
149S PHE* 1.3 59.9 + - - +
151S GLY 3.1 5.2 + - - -
152S LYS 3.6 12.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 149 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P GLY* 3.3 24.4 - - - -
37P HIS* 3.1 70.3 + + - -
39P PHE* 4.2 3.9 - - + +
40P PHE* 3.8 28.5 - + + -
38S ASN* 3.8 13.5 - - - -
42S LEU* 3.6 23.6 - - + -
95S MET* 4.1 6.7 - - + -
96S ASP* 4.4 5.8 - - - -
99S MET* 3.8 30.1 - - + -
145S MET 3.0 13.0 + - - +
146S PHE* 3.2 13.7 - + - +
148S ALA* 1.3 76.3 - - - +
150S LEU* 1.3 63.6 + - + +
151S GLY 3.2 4.0 + - - -
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Residues in contact with LEU 150 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P HIS* 5.7 0.4 - - - -
96S ASP* 3.6 51.2 - - + +
99S MET* 4.1 9.0 - - + -
100S GLU* 4.2 27.4 - - + +
103S VAL* 4.2 23.1 - - + -
146S PHE 3.0 17.5 + - - +
147S LYS* 3.0 14.5 + - + +
149S PHE* 1.3 80.5 - - + +
151S GLY* 1.3 61.2 + - - -
152S LYS* 3.2 23.2 + - + +
----------------------------------------------------------
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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