Contacts of the helix formed by residues 162 - 174 (chain B) in PDB entry 6QNW
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 ARG 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A TRP 5.9 0.2 - - - -
189A ASP* 3.1 37.3 - - - +
192A ARG* 3.9 22.3 - - - +
193A GLN* 5.1 0.2 - - - -
203A GLU* 3.0 34.6 + - - +
114B VAL 4.5 0.8 + - - -
115B GLN* 3.2 24.8 + - - +
117B THR 4.1 6.7 - - - +
118B ARG* 4.6 9.0 - - - +
119B VAL* 4.0 6.5 - - - +
158B ASN 4.6 2.9 - - - +
160B SER* 3.3 9.7 + - - +
161B GLY* 1.3 79.4 - - - +
163B LEU* 1.3 63.8 + - - +
164B ILE* 3.2 35.4 - - + +
165B ASP* 3.3 33.2 + - - +
166B PHE* 3.4 8.7 + - - +
168B LYS* 6.1 0.4 - - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B THR* 3.3 30.4 + - + +
118B ARG 3.3 16.7 - - - +
119B VAL* 4.4 7.0 - - + -
121B ARG* 5.6 2.0 - - + -
122B LEU* 3.9 39.5 - - + +
161B GLY 3.7 1.6 + - - -
162B ARG* 1.3 70.0 - - - +
164B ILE* 1.3 60.3 + - - +
166B PHE* 3.1 16.4 + - + +
167B LEU* 2.9 36.6 + - + +
250B GLY* 4.4 12.8 - - - -
253B TYR* 4.6 6.5 - - + -
254B PHE* 3.6 30.3 - - + -
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 5.3 9.2 - - + -
205A PHE* 3.5 29.4 - - + -
114B VAL* 4.5 16.6 + - + +
117B THR 5.0 0.4 + - - +
162B ARG* 3.2 46.9 - - + +
163B LEU* 1.3 78.9 - - - +
165B ASP* 1.3 62.4 + - - +
167B LEU* 3.2 16.6 + - + +
168B LYS* 2.9 40.2 + - - +
254B PHE* 5.3 5.1 - - + -
332B TRP* 6.3 1.3 - - + -
336B VAL* 3.9 19.3 - - + -
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.4 15.8 + - - -
157B ALA* 3.2 31.6 - - + +
160B SER* 2.2 31.2 + - - +
162B ARG* 3.3 29.9 + - - +
163B LEU 3.2 0.6 - - - -
164B ILE* 1.3 76.6 - - - +
166B PHE* 1.3 60.1 + - - +
168B LYS* 3.2 32.7 + - - +
169B ASP* 2.9 26.3 + - - +
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 5.1 9.0 - - + -
122B LEU* 3.7 30.3 - - + -
143B LEU* 5.6 2.7 - - + -
146B THR* 4.2 19.5 - - + -
147B ILE* 4.6 11.0 - - + -
150B PHE* 4.2 20.2 - + - -
158B ASN* 4.1 35.3 - - + +
162B ARG 3.4 5.7 + - - +
163B LEU* 3.1 20.1 + - + +
165B ASP* 1.3 78.1 - - - +
167B LEU* 1.3 67.0 + - + +
169B ASP* 3.2 5.5 + - + +
170B VAL* 2.9 46.1 + - + +
246B MET* 4.3 21.1 - - + -
247B GLN* 5.0 1.6 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PHE* 4.0 9.6 - - + -
163B LEU* 2.9 22.8 + - + +
164B ILE* 3.4 17.0 - - + +
166B PHE* 1.3 88.5 - - + +
168B LYS* 1.3 60.1 + - - +
170B VAL* 3.3 6.6 + - + +
171B MET* 2.9 32.6 + - - +
247B GLN 4.3 4.7 - - - +
250B GLY* 4.2 19.1 - - - -
251B PHE* 3.5 47.3 - - + -
254B PHE* 3.8 31.6 - - + -
336B VAL* 4.9 2.0 - - + -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.1 19.5 - - - +
196A ARG* 5.5 3.2 - - - +
203A GLU* 4.7 15.9 - - - +
204A ARG 4.1 20.6 + - - -
205A PHE* 3.6 19.1 - - + -
206A GLU* 5.0 13.5 - - - +
157B ALA* 5.2 5.6 - - + -
162B ARG* 6.1 0.4 - - - +
164B ILE* 2.9 29.2 + - - +
165B ASP* 3.2 31.8 + - - +
167B LEU* 1.3 74.5 - - - +
169B ASP* 1.3 59.6 + - - +
171B MET* 3.2 5.5 + - - +
172B GLU* 2.9 39.6 + - - +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE* 4.4 16.5 - - + -
155B LEU* 3.2 37.8 - - + +
156B THR 3.8 1.0 + - - -
157B ALA* 2.8 43.0 + - - +
158B ASN* 3.0 21.8 + - - +
165B ASP 2.9 7.7 + - - +
166B PHE* 3.2 11.6 + - + +
168B LYS* 1.3 77.0 - - - +
170B VAL* 1.3 55.9 + - - +
172B GLU* 3.3 7.7 + - - +
173B SER* 2.9 25.3 + - - -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE* 4.1 9.4 - - + -
166B PHE* 2.9 42.0 + - + +
167B LEU* 3.5 11.7 - - + +
169B ASP* 1.3 74.6 - - - +
171B MET* 1.3 65.1 + - + +
173B SER* 2.5 26.2 + - - +
174B MET* 3.6 18.9 + - + +
247B GLN* 3.6 42.8 - - + +
251B PHE* 4.5 15.0 - - + -
343B MET* 5.5 0.4 - - + -
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Residues in contact with MET 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PHE* 3.4 25.8 - - + -
206A GLU* 4.5 21.5 - - + +
207A ILE* 5.6 0.2 - - - -
208A THR 6.3 0.4 - - - +
211A MET* 3.8 33.9 - - + +
167B LEU 2.9 16.7 + - - +
168B LYS* 3.2 8.9 + - - +
170B VAL* 1.3 81.5 - - + +
172B GLU* 1.3 62.7 + - + +
173B SER 3.3 0.7 + - - -
174B MET* 3.4 14.3 + - - +
175B ASP* 3.4 14.7 - - - +
251B PHE* 3.5 29.8 - - + -
339B ILE* 3.6 34.1 - - + -
343B MET* 5.9 0.2 - - - -
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLU* 3.8 19.9 - - - +
208A THR* 6.1 0.4 - - - +
155B LEU* 4.4 7.3 - - + +
168B LYS* 2.9 25.4 + - - +
169B ASP* 4.1 8.9 - - - +
171B MET* 1.3 73.6 - - - +
173B SER* 1.3 64.5 + - - +
175B ASP* 3.2 26.7 + - + +
176B LYS* 3.6 13.3 + - + +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE* 4.2 5.2 - - - -
155B LEU* 3.5 18.8 - - - +
169B ASP 2.9 14.2 + - - -
170B VAL* 2.5 23.2 + - - -
172B GLU* 1.3 77.6 - - - +
174B MET* 1.3 60.9 + - - +
175B ASP 3.2 1.0 + - - -
176B LYS* 3.2 21.8 + - - +
179B MET* 3.8 15.4 - - - +
217B TYR* 2.5 36.8 + - - -
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Residues in contact with MET 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 2.8 33.8 + - - +
211A MET* 3.9 27.4 - - + +
214A LEU* 5.2 4.3 - - - -
170B VAL* 3.9 25.1 - - + +
171B MET* 3.4 9.1 + - - +
172B GLU 3.3 0.4 - - - -
173B SER* 1.3 80.4 + - - +
175B ASP* 1.3 61.7 + - - +
176B LYS 3.4 1.3 - - - -
214B LYS* 3.7 15.0 - - - +
217B TYR* 3.8 20.2 - - + +
218B LEU* 4.2 18.3 - - + +
221B ALA* 3.9 21.3 - - + -
222B LEU* 5.1 5.8 - - + -
343B MET* 3.9 28.3 - - + -
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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
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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