Contacts of the helix formed by residues 140 - 163 (chain J) in PDB entry 6H25
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 ASN 140 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ASP* 5.4 8.8 - - - +
185E ASP* 4.4 12.8 + - - -
135J GLN* 4.9 0.4 - - - -
139J GLU* 1.3 82.4 - - - +
141J ALA* 1.3 65.2 + - - +
142J ASN* 3.3 7.6 - - + +
143J ASP* 3.3 21.1 + - - +
144J ARG* 3.2 18.0 + - - +
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Residues in contact with ALA 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J GLN* 4.9 9.4 - - - +
140J ASN* 1.3 72.5 - - - +
142J ASN* 1.3 61.1 + - - +
144J ARG* 3.2 12.5 + - - +
145J ASN* 2.9 39.6 + - - +
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Residues in contact with ASN 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J GLU* 4.3 17.3 + - - +
140J ASN* 3.3 5.5 - - + +
141J ALA* 1.3 79.9 - - - +
143J ASP* 1.3 58.9 + - - +
145J ASN* 3.3 9.9 + - - +
146J ASN* 2.9 47.7 + - - +
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Residues in contact with ASP 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J GLU* 3.6 17.2 - - + +
140J ASN* 3.3 30.1 + - - +
141J ALA 3.3 0.4 - - - -
142J ASN* 1.3 78.5 - - - +
144J ARG* 1.3 58.9 + - - +
146J ASN* 3.4 10.7 + - - +
147J ARG* 2.9 30.3 + - - +
150J ARG* 4.1 4.2 + - - +
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Residues in contact with ARG 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LYS* 4.2 21.8 - - - +
93J THR* 5.4 0.6 - - - +
126J GLU* 4.3 24.7 + - - -
132J TYR* 5.3 2.2 + - - -
133J VAL* 3.8 35.3 + - + +
134J GLU 4.7 2.5 - - - +
135J GLN* 3.7 43.7 + - + +
139J GLU* 3.4 15.6 + - - +
140J ASN 3.2 13.3 + - - +
141J ALA* 3.2 13.5 + - - +
143J ASP* 1.3 77.5 - - - +
145J ASN* 1.3 78.3 + - - +
147J ARG* 3.4 5.0 + - - +
148J ALA* 2.9 30.9 + - - +
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Residues in contact with ASN 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J THR* 3.4 26.4 - - + +
97J GLU* 4.5 23.5 + - - +
141J ALA* 2.9 30.2 + - - +
142J ASN* 3.7 11.2 - - - +
143J ASP 3.3 0.2 - - - -
144J ARG* 1.3 98.5 + - - +
146J ASN* 1.3 58.5 + - - +
148J ALA* 3.3 5.7 + - - +
149J ILE* 3.0 37.9 + - + +
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Residues in contact with ASN 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J ASP* 4.3 18.6 + - - -
70J THR* 5.6 2.0 + - - -
97J GLU* 6.0 0.4 + - - -
142J ASN* 2.9 40.9 + - - +
143J ASP* 3.8 10.2 - - - +
144J ARG 3.3 0.2 - - - -
145J ASN* 1.3 76.4 - - - +
147J ARG* 1.3 57.0 + - - +
149J ILE* 3.4 9.9 + - - +
150J ARG* 3.0 48.3 + - - +
180J ASN* 5.2 12.3 + - - +
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Residues in contact with ARG 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J VAL* 5.1 12.6 - - + +
134J GLU 3.5 21.6 + - - -
136J GLU* 3.3 33.6 + - - +
139J GLU* 2.8 36.9 + - - -
143J ASP 2.9 18.0 + - - +
144J ARG* 3.9 8.0 + - - +
146J ASN* 1.3 76.7 - - - +
148J ALA* 1.3 56.5 + - - +
150J ARG* 3.3 22.6 + - + +
151J VAL* 2.9 44.5 + - + +
187J GLU* 5.4 4.5 - - - +
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Residues in contact with ALA 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J THR* 5.2 4.5 - - + +
125J ASN* 5.4 4.7 + - - +
126J GLU* 4.9 12.6 - - - +
131J THR 5.0 6.3 - - - +
133J VAL* 3.7 28.7 - - + +
144J ARG* 2.9 20.5 + - - +
145J ASN* 3.3 8.3 + - - +
147J ARG* 1.3 77.6 - - - +
149J ILE* 1.3 58.5 + - + +
151J VAL* 3.3 2.5 + - - +
152J ALA* 3.0 30.7 + - - +
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Residues in contact with ILE 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LEU* 5.6 1.1 - - + -
68J PRO 4.8 6.5 - - - +
69J ASP* 4.0 17.3 - - - +
70J THR* 4.1 7.2 - - - +
91J LEU* 4.1 23.7 - - + +
93J THR* 5.0 11.7 - - + -
94J VAL* 3.7 27.8 - - + -
97J GLU* 5.5 0.7 - - - +
125J ASN* 5.3 0.7 - - - +
145J ASN* 3.0 29.3 + - + +
146J ASN* 3.7 10.5 - - - +
148J ALA* 1.3 75.3 - - - +
150J ARG* 1.3 62.4 + - + +
152J ALA* 3.4 1.9 + - - +
153J ALA* 3.0 22.9 + - - +
173J PHE* 3.6 31.4 - - + -
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Residues in contact with ARG 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J ASP* 4.1 4.6 + - - +
146J ASN* 3.0 33.0 + - - +
147J ARG* 3.3 34.7 - - - +
148J ALA 3.3 0.2 - - - -
149J ILE* 1.3 77.8 - - + +
151J VAL* 1.3 56.7 + - + +
153J ALA* 3.3 7.0 + - - +
154J LYS* 3.0 28.1 + - - +
173J PHE* 5.2 13.5 - - + -
180J ASN* 5.4 4.9 + - - -
183J LYS* 3.9 25.3 - - - +
184J ALA* 5.0 14.4 - - + +
187J GLU* 3.2 41.5 + - - +
189J ILE* 5.0 7.3 - - + +
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Residues in contact with VAL 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J GLU 4.8 4.9 - - - +
131J THR* 4.5 21.8 - - + +
133J VAL* 4.6 15.5 - - + -
147J ARG* 2.9 30.9 + - + +
148J ALA 3.9 4.0 - - - +
150J ARG* 1.3 77.0 - - + +
152J ALA* 1.3 58.3 + - - +
154J LYS* 3.3 8.2 + - + +
155J TRP* 2.9 27.4 + - + +
187J GLU* 5.8 2.0 - - - +
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Residues in contact with ALA 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LEU* 5.1 1.6 - - - -
91J LEU* 4.2 26.5 - - + -
123J PHE* 5.3 3.1 - - + -
125J ASN* 4.5 9.0 - - + +
131J THR* 4.2 19.0 - - + -
148J ALA 3.0 18.4 + - - +
149J ILE 3.9 4.0 - - - +
151J VAL* 1.3 75.6 - - - +
153J ALA* 1.3 58.4 + - - +
155J TRP* 3.2 9.9 + - - +
156J TYR* 2.9 30.2 + - - +
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Residues in contact with ALA 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LEU* 3.7 26.4 - - + +
149J ILE 3.0 17.9 + - - +
150J ARG* 3.6 5.4 - - - +
151J VAL 3.3 0.2 - - - -
152J ALA* 1.3 74.5 - - - +
154J LYS* 1.3 64.2 + - - +
156J TYR* 3.3 5.0 + - - +
157J ASN* 3.0 22.7 + - - +
171J VAL* 4.1 5.9 - - + +
173J PHE* 4.6 5.2 - - + -
189J ILE* 3.7 28.9 - - + +
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Residues in contact with LYS 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J ARG 3.0 13.5 + - - +
151J VAL* 3.7 11.2 - - + +
153J ALA* 1.3 76.7 - - - +
155J TRP* 1.3 58.3 + - - +
157J ASN* 3.3 4.8 + - + +
158J GLU* 3.0 32.7 + - + +
187J GLU* 4.2 21.8 + - + +
188J GLY* 5.2 7.0 - - - -
189J ILE* 3.8 16.7 - - + +
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Residues in contact with TRP 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ILE 5.5 1.3 - - - -
31J CYS* 5.0 4.5 - - + -
123J PHE* 3.7 24.9 - + - -
128J HIS* 3.4 32.3 - + - -
130J GLU* 3.4 34.5 + - + +
131J THR* 3.7 25.1 - - + -
151J VAL* 2.9 15.6 + - + +
152J ALA 3.5 8.5 - - - +
153J ALA 3.2 0.4 - - - -
154J LYS* 1.3 78.1 - - - +
156J TYR* 1.3 81.4 + + - +
158J GLU* 3.4 7.2 + - + +
159J HIS* 2.8 68.3 + + + +
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Residues in contact with TYR 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J CYS* 2.7 39.8 + - + -
67J LEU* 4.9 13.7 - - + -
89J ILE* 3.6 40.6 - - + +
91J LEU* 5.4 3.4 - - + -
121J TYR* 3.9 5.7 - - - -
123J PHE* 3.2 30.4 - + - -
152J ALA 2.9 14.8 + - - +
153J ALA* 3.3 8.9 + - - +
155J TRP* 1.3 100.1 - + - +
157J ASN* 1.3 58.7 + - - +
159J HIS* 4.3 6.1 - + - -
160J LEU* 2.9 42.9 + - + +
171J VAL* 4.0 19.3 - - + -
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Residues in contact with ASN 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J ALA 3.0 13.3 + - - +
154J LYS* 3.5 10.3 - - + +
155J TRP 3.3 0.2 - - - -
156J TYR* 1.3 76.4 - - - +
158J GLU* 1.3 57.2 + - - +
160J LEU* 3.9 2.2 - - - +
161J LYS* 3.0 44.7 + - - +
169J LEU 5.5 1.9 - - - +
170J GLN* 4.1 15.7 + - - +
171J VAL* 3.9 20.3 + - + +
188J GLY 5.7 0.4 - - - -
189J ILE* 4.1 19.2 - - + +
190J PRO* 4.3 15.0 - - - +
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Residues in contact with GLU 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS* 3.0 21.6 + - + +
155J TRP* 4.0 8.1 - - + +
157J ASN* 1.3 77.7 - - - +
159J HIS* 1.3 61.0 + - - +
161J LYS* 4.6 16.0 + - - +
162J LYS* 3.3 34.8 + - + +
163J MET 4.4 0.2 + - - -
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Residues in contact with HIS 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J CYS* 3.7 29.5 - - + +
36J CYS* 3.5 33.2 - - + +
38J ALA* 5.3 3.4 - - + -
39J CYS* 3.8 7.5 - - - -
155J TRP* 2.8 53.3 + + + +
156J TYR* 4.0 7.4 - + - +
158J GLU* 1.3 78.3 - - - +
160J LEU* 1.3 70.7 + - + +
163J MET* 3.3 36.4 + - + +
164J SER 3.9 1.6 + - - -
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Residues in contact with LEU 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J CYS* 5.4 2.5 - - + -
33J ALA* 4.7 19.3 - - + -
35J GLY* 6.3 1.6 - - - -
36J CYS* 5.8 5.8 - - + +
65J TYR* 4.3 19.7 - - + -
89J ILE* 6.0 2.5 - - + -
156J TYR* 2.9 24.6 + - + +
157J ASN* 4.2 2.7 - - - +
159J HIS* 1.3 88.5 - - + +
161J LYS* 1.3 57.1 + - - +
164J SER* 2.5 33.5 + - - -
167J ASN* 4.3 5.2 - - - -
168J GLN 5.2 0.7 + - - -
169J LEU* 3.7 37.6 + - + +
171J VAL* 3.8 28.9 - - + -
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Residues in contact with LYS 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ASN* 3.0 36.4 + - - +
158J GLU* 3.9 18.6 + - - +
159J HIS 3.3 0.4 - - - -
160J LEU* 1.3 77.6 - - - +
162J LYS* 1.3 63.5 + - + +
164J SER* 2.8 21.1 + - - +
165J ALA 5.3 0.2 - - - -
167J ASN* 3.8 31.9 + - + +
169J LEU 5.8 2.5 - - - +
170J GLN* 5.6 7.4 - - - +
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Residues in contact with LYS 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J GLU* 3.3 24.0 + - + +
161J LYS* 1.3 78.1 - - + +
163J MET* 1.3 62.1 + - - +
164J SER 3.0 13.9 - - - +
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Residues in contact with MET 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J GLY 5.1 0.5 - - - +
36J CYS* 4.6 16.9 - - + -
37J ALA 5.1 2.4 + - - -
38J ALA* 5.5 5.8 - - + +
158J GLU 4.4 0.2 + - - -
159J HIS* 3.3 41.6 + - + +
162J LYS* 1.3 79.0 - - - +
164J SER* 1.3 59.8 + - - +
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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
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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) + - + + + + + -
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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