Contacts of the helix formed by residues 131 - 154 (chain J) in PDB entry 2YW7
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 131 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 3.7 12.7 + - - +
13J LYS* 6.0 0.2 - - + -
17J VAL* 4.0 20.9 - - + +
71J ARG* 2.8 24.6 + - - -
75J LEU* 3.6 17.7 - - - +
127J LEU* 3.2 15.0 + - + +
130J LEU* 1.3 81.2 - - - +
132J LEU* 1.3 63.6 + - - +
133J VAL* 2.9 6.2 + - - +
134J SER* 2.6 41.2 + - - -
135J GLN* 3.3 17.7 + - - +
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Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 4.5 4.4 - - - +
124E ILE* 4.9 10.3 - - + -
125E GLU* 5.5 7.9 - - + -
128E GLU* 4.0 24.2 - - - +
135E GLN* 4.1 13.0 - - - +
139E ILE* 3.7 32.5 - - + +
127J LEU 4.9 0.2 - - - -
128J GLU* 3.9 29.8 - - - +
129J ASP 5.7 1.3 - - - -
130J LEU 5.5 1.8 - - - +
131J ASP* 1.3 73.0 - - - +
133J VAL* 1.3 61.2 + - + +
135J GLN* 3.6 22.6 - - - +
136J ASP* 2.9 30.8 + - - +
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Residues in contact with VAL 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 3.6 23.6 - - - +
124E ILE* 4.9 6.5 - - + -
139E ILE* 4.4 9.6 - - + +
142E ALA* 4.0 18.8 - - + -
143E GLY* 3.7 22.9 - - - -
146E GLU* 4.0 7.9 - - - +
71J ARG* 3.3 31.4 - - - +
131J ASP* 2.9 6.2 + - - +
132J LEU* 1.3 80.3 - - - +
134J SER* 1.3 64.1 - - - +
135J GLN 3.0 0.9 + - - -
136J ASP* 3.2 12.1 + - - +
137J LEU* 3.3 12.7 + - + +
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Residues in contact with SER 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J VAL* 4.6 0.2 - - - -
21J LEU* 3.5 28.5 - - - +
71J ARG* 3.0 31.2 + - - +
75J LEU* 3.8 0.5 - - - +
127J LEU* 4.2 11.2 - - - -
131J ASP* 2.6 31.4 + - - -
133J VAL* 1.3 72.2 - - - +
135J GLN* 1.3 56.5 + - - +
137J LEU* 3.2 12.6 - - - +
138J LEU* 3.1 27.7 + - - +
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Residues in contact with GLN 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 4.2 4.9 - - - +
124J ILE* 3.1 37.9 + - + +
127J LEU* 4.0 14.8 - - + +
128J GLU* 2.8 44.6 + - - +
131J ASP 3.3 12.4 + - - +
132J LEU* 3.6 22.3 - - - +
133J VAL 3.1 0.6 - - - -
134J SER* 1.3 73.8 - - - +
136J ASP* 1.3 53.8 + - - +
137J LEU 2.9 4.0 - - - -
138J LEU* 2.7 8.4 + - - +
139J ILE* 2.7 49.4 + - + +
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Residues in contact with ASP 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP* 3.4 23.9 - - - +
136E ASP* 4.6 2.2 - - - +
139E ILE* 3.5 31.1 - - + +
140E ALA* 4.6 8.5 - - - +
132J LEU 2.9 20.4 + - - +
133J VAL* 3.7 5.2 - - - +
135J GLN* 1.3 74.8 + - - +
137J LEU* 1.3 58.9 + - - +
139J ILE* 3.6 10.1 - - - +
140J ALA* 3.3 19.9 + - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LEU* 5.4 0.9 - - + -
67J GLU* 2.9 32.8 - - + +
68J VAL* 4.3 20.2 - - + +
71J ARG* 4.0 33.0 - - + -
133J VAL* 3.3 10.6 + - + +
134J SER* 3.2 12.3 - - - +
135J GLN 2.9 0.8 - - - -
136J ASP* 1.3 77.1 - - - +
138J LEU* 1.3 64.3 + - + +
140J ALA* 3.5 14.4 - - + +
141J HIS* 3.4 24.9 + - + +
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Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 6.1 0.2 - - + -
21J LEU* 4.6 7.6 - - + -
24J GLN* 3.7 32.8 - - + +
28J TYR* 4.2 2.0 - - - +
68J VAL* 4.5 12.3 - - + -
120J THR* 4.4 4.9 - - + +
123J SER* 3.5 36.8 - - - +
124J ILE* 3.7 16.8 - - + +
127J LEU* 3.9 17.9 - - + -
134J SER 3.1 14.3 + - - +
135J GLN* 2.7 12.9 + - - +
137J LEU* 1.3 69.7 - - + +
139J ILE* 1.3 55.6 + - - +
140J ALA 2.8 3.1 + - - -
141J HIS* 2.9 18.7 + - + +
142J ALA* 2.7 33.6 + - - +
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Residues in contact with ILE 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.8 19.5 - - + +
133C VAL* 3.7 37.3 - - + +
136C ASP* 3.9 33.9 - - + +
124J ILE* 3.5 23.4 - - + +
135J GLN* 2.7 38.5 + - + +
136J ASP* 3.6 12.8 - - - +
138J LEU* 1.3 71.3 - - - +
140J ALA* 1.3 63.4 + - - +
142J ALA* 3.4 1.7 - - - +
143J GLY* 3.3 14.9 + - - -
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Residues in contact with ALA 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J TYR* 5.7 0.2 - - - -
136J ASP 3.3 12.0 + - - +
137J LEU* 3.5 15.3 - - + +
138J LEU 2.8 1.4 + - - -
139J ILE* 1.3 80.6 - - - +
141J HIS* 1.3 71.8 + - + +
142J ALA 3.1 1.4 + - - -
143J GLY* 3.2 1.2 + - - -
144J GLU* 3.2 23.3 + - - +
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Residues in contact with HIS 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 3.2 31.3 + + + +
64J TYR* 3.0 73.1 - + + +
67J GLU* 3.4 20.3 + - + -
68J VAL* 4.9 2.5 - - + -
137J LEU* 3.4 33.9 + - + +
138J LEU* 2.9 13.9 + - + +
140J ALA* 1.3 77.0 - - + +
142J ALA* 1.3 68.6 - - - +
144J GLU* 3.3 1.1 + - - +
145J LEU* 2.7 28.3 + - + +
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Residues in contact with ALA 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 3.7 13.0 - - + -
117J ILE* 6.2 0.7 - - - +
120J THR* 4.4 14.4 - - + +
121J ARG* 5.5 2.2 - - + +
124J ILE* 3.7 22.0 - - + -
138J LEU 2.7 20.3 + - - +
139J ILE 3.4 7.9 - - - +
140J ALA 3.1 0.2 - - - -
141J HIS* 1.3 78.3 - - - +
143J GLY* 1.3 56.8 + - - +
145J LEU* 2.7 22.3 + - - +
146J GLU* 3.0 22.2 + - - +
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Residues in contact with GLY 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG* 4.5 11.8 + - - -
133C VAL* 3.4 22.7 - - - +
139J ILE 3.3 4.0 + - - -
140J ALA 3.2 5.8 + - - -
142J ALA* 1.3 78.3 - - - +
144J GLU* 1.3 59.3 + - - +
146J GLU* 3.9 4.8 + - - +
147J LYS* 3.3 30.5 + - - +
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Residues in contact with GLU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J GLN* 5.0 3.5 - - - +
60J LEU* 4.6 19.4 - - + +
64J TYR* 3.2 28.1 + - + +
140J ALA 3.2 12.3 + - - +
141J HIS 3.7 6.1 - - - +
142J ALA 2.8 5.1 + - - -
143J GLY* 1.3 72.3 - - - +
145J LEU* 1.3 65.2 + - - +
147J LYS* 3.1 51.6 + - - +
148J PHE* 3.3 5.4 + - - +
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Residues in contact with LEU 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 4.3 14.8 - - + +
31J LEU* 5.1 1.8 - - + -
57J GLN* 4.0 21.1 - - - +
61J VAL* 4.8 6.1 - - + -
64J TYR* 3.7 28.7 - - + -
113J TYR* 4.1 11.7 - - + -
116J VAL* 3.8 28.5 - - + -
117J ILE* 4.1 17.7 - - + +
120J THR* 3.9 16.6 - - + +
141J HIS 2.7 27.9 + - - +
142J ALA* 2.7 10.0 + - - +
144J GLU* 1.3 71.1 - - - +
146J GLU* 1.3 58.4 + - - +
148J PHE* 2.8 22.7 + - - +
149J GLN 3.0 8.8 + - - -
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Residues in contact with GLU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG* 3.0 24.0 + - - +
74C THR* 3.2 22.7 - - + +
75C LEU* 4.1 3.5 - - - +
133C VAL* 4.3 10.7 - - - +
117J ILE* 3.7 19.7 - - + -
121J ARG* 2.7 54.4 + - - +
142J ALA* 3.0 18.1 + - - +
143J GLY* 4.0 5.6 - - - +
145J LEU* 1.3 75.6 - - - +
147J LYS* 1.3 62.0 + - - +
149J GLN* 3.0 25.1 + - + +
150J TRP 3.1 5.4 + - - -
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Residues in contact with LYS 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 4.2 26.5 + - + +
71C ARG* 5.9 1.1 - - - +
74C THR* 4.1 15.7 - - + +
143J GLY 3.3 17.7 + - - +
144J GLU* 3.1 38.5 + - - +
146J GLU* 1.3 76.6 - - - +
148J PHE* 1.3 52.6 + - - +
149J GLN 3.0 0.9 + - - -
150J TRP* 3.1 7.8 + - + +
151J PHE* 2.7 37.9 + - + +
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Residues in contact with PHE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 4.4 8.7 - - + -
53J MET* 3.2 52.9 - - + -
54J ILE* 4.5 12.1 - - + -
57J GLN* 3.4 39.5 - - + +
109J LEU* 5.1 2.9 - - + -
113J TYR* 3.2 39.6 - + + -
144J GLU 3.3 3.4 + - - +
145J LEU 2.8 13.9 + - - +
147J LYS* 1.3 71.3 - - - +
149J GLN* 1.3 66.4 + - - +
151J PHE* 3.7 18.8 - + + -
152J VAL* 3.0 39.6 + - + +
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Residues in contact with GLN 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 5.3 1.1 - - + -
110J ASP* 2.7 30.6 + - - +
113J TYR* 3.9 13.4 - - + -
114J ASN* 2.9 25.4 + - - +
117J ILE* 3.7 31.8 - - + +
145J LEU 3.0 5.7 + - - -
146J GLU* 3.0 15.5 - - + +
148J PHE* 1.3 73.2 - - - +
150J TRP* 1.3 68.8 + - - +
152J VAL* 2.8 8.3 + - - +
153J ARG* 2.7 59.7 + - - +
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Residues in contact with TRP 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 5.8 1.1 - - + -
73C ALA* 3.3 22.8 + - + +
74C THR* 3.9 28.6 - - + +
40F TRP 4.4 16.6 - - - -
42F VAL 4.6 3.6 - - - -
43F VAL* 3.9 18.4 - - + +
47F PHE* 3.9 31.2 - + - -
51F HIS* 4.8 9.4 - + - -
99F ARG* 3.0 46.4 - - + +
146J GLU 3.1 2.0 + - - -
147J LYS* 3.5 9.0 - - + +
149J GLN* 1.3 77.8 - - - +
151J PHE* 1.3 83.0 + + + +
153J ARG* 3.2 14.8 + - + +
154J ALA* 2.6 46.0 + - + +
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Residues in contact with PHE 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F PHE* 3.8 27.6 - + - -
48F ILE* 4.5 12.8 - - + -
53J MET* 4.0 22.2 - - + -
147J LYS* 2.7 21.3 + - + +
148J PHE* 3.6 26.9 - + + +
149J GLN 2.9 0.2 + - - -
150J TRP* 1.3 86.1 - + + +
152J VAL* 1.3 56.3 - - - +
154J ALA* 2.9 14.6 + - - +
155J HIS* 2.7 52.0 + + + -
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J MET* 4.2 4.3 - - - -
106J LEU* 3.2 44.3 - - + +
109J LEU* 4.9 8.5 - - + -
110J ASP* 4.4 15.3 - - + +
113J TYR* 6.1 1.1 - - + -
148J PHE* 3.0 47.0 + - + +
149J GLN* 2.8 9.1 + - - +
151J PHE* 1.3 74.3 - - - +
153J ARG* 1.3 64.9 - - - +
155J HIS* 2.8 34.7 + - + +
156J LEU* 4.1 2.1 + - - +
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Residues in contact with ARG 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR 4.9 10.9 + - - -
76C GLY* 6.0 2.6 - - - +
99F ARG* 6.0 3.6 - - - +
110J ASP* 3.6 25.8 + - - +
114J ASN* 3.1 22.2 + - - +
149J GLN* 2.7 54.4 + - - +
150J TRP* 3.4 15.7 - - + +
152J VAL* 1.3 74.9 - - - +
154J ALA* 1.3 57.8 + - + +
155J HIS 3.6 0.7 + - - -
156J LEU* 3.6 17.3 + - - +
157J GLU 5.0 0.9 - - - +
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F VAL* 4.0 28.9 - - + -
44F GLY* 2.8 35.3 + - - +
47F PHE* 4.1 6.3 - - + -
99F ARG* 5.4 2.7 - - - +
150J TRP* 2.6 39.4 + - + +
151J PHE* 2.9 6.7 + - - +
152J VAL 2.9 0.2 + - - -
153J ARG* 1.3 72.4 - - + +
155J HIS* 1.3 52.0 + - - +
156J LEU 3.3 2.0 - - - -
157J GLU 4.1 4.1 - - - +
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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