Contacts of the helix formed by residues 162 - 174 (chain B) in PDB entry 1OH7
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 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B PHE* 3.9 7.9 - - - -
160B PRO 4.2 0.2 - - - -
161B ALA* 1.3 83.1 + - - +
163B ARG* 1.3 62.3 + - - +
164B GLU* 4.0 13.1 - - - +
165B THR* 2.5 53.1 + - - +
166B MET* 3.6 5.5 + - - +
263B GLU* 5.4 2.1 - - - +
652B ARG* 5.6 2.9 + - - -
683B ASN* 4.3 13.5 - - - +
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Residues in contact with ARG 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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143B PHE* 3.6 27.0 - - + -
162B ASP* 1.3 73.5 - - - +
164B GLU* 1.3 78.9 + - - +
166B MET* 3.1 3.9 + - - +
167B ALA* 2.9 31.4 + - - +
186B GLU* 3.5 33.1 + - - +
188B SER* 3.3 32.5 + - - -
189B LEU* 3.6 38.2 - - + +
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Residues in contact with GLU 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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162B ASP* 3.4 12.7 + - - +
163B ARG* 1.3 94.3 + - + +
165B THR* 1.3 58.8 + - + +
167B ALA* 3.5 9.7 + - + +
168B ALA* 3.0 24.6 + - - +
270B ASP* 5.7 3.7 - - + +
679B ASN* 3.6 30.7 + - - +
683B ASN* 5.2 11.1 + - - +
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Residues in contact with THR 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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160B PRO* 3.9 13.3 - - - +
161B ALA 4.0 2.9 + - - -
162B ASP* 2.5 40.9 + - - +
164B GLU* 1.3 74.0 - - + +
166B MET* 1.3 58.9 + - - +
168B ALA* 3.6 8.3 - - - +
169B GLU* 3.2 33.0 + - - +
263B GLU* 4.1 21.0 + - + +
268B ILE* 4.4 24.0 - - + -
652B ARG* 4.9 10.8 - - - +
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Residues in contact with MET 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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136B ILE* 3.8 19.7 - - + -
143B PHE* 3.5 47.1 - - + -
144B GLY 4.7 0.2 - - - +
145B TYR* 3.6 43.7 - - + -
160B PRO* 3.8 12.1 - - + +
162B ASP 3.6 1.8 + - - +
163B ARG* 3.1 11.4 + - - +
165B THR* 1.3 79.0 + - - +
167B ALA* 1.3 65.4 + - - +
169B GLU* 3.2 16.5 + - + -
170B LEU* 3.2 18.1 + - + +
189B LEU* 3.8 21.8 - - + -
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Residues in contact with ALA 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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163B ARG* 2.9 16.0 + - - +
164B GLU* 3.6 13.5 - - + +
166B MET* 1.3 74.9 - - - +
168B ALA* 1.3 63.5 + - - +
170B LEU* 3.2 18.0 + - - +
171B GLN* 3.2 14.4 + - - +
189B LEU* 3.9 19.2 - - + +
271B ALA* 5.1 6.8 - - + +
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Residues in contact with ALA 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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164B GLU 3.0 18.4 + - - +
165B THR* 3.6 13.0 - - - +
167B ALA* 1.3 76.9 - - - +
169B GLU* 1.3 60.8 + - + +
171B GLN* 3.6 3.0 + - - +
172B ARG* 3.4 23.1 + - - +
268B ILE* 5.1 8.5 - - + -
269B MET 4.0 18.3 - - - +
270B ASP* 4.4 8.1 - - - -
271B ALA 4.6 11.7 - - - +
274B ARG* 4.3 7.8 + - - +
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Residues in contact with GLU 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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145B TYR* 4.2 12.2 - - + -
158B SER* 3.5 22.1 + - - -
160B PRO* 4.3 12.6 - - + -
165B THR* 3.2 21.4 + - - +
166B MET* 3.2 16.8 + - + +
168B ALA* 1.3 77.1 - - + +
170B LEU* 1.3 54.0 + - - +
172B ARG* 3.4 37.4 + - - +
173B THR* 2.6 42.3 + - - +
261B GLU* 4.2 6.3 - - - +
313B MET* 5.3 1.9 - - - +
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Residues in contact with LEU 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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136B ILE* 4.8 5.8 - - + -
145B TYR* 3.4 32.1 - - + +
166B MET* 3.2 21.4 + - + +
167B ALA* 3.2 11.4 + - - +
169B GLU* 1.3 76.5 - - - +
171B GLN* 1.3 61.2 + - - +
173B THR* 3.9 2.2 - - - -
174B ASN* 3.0 26.5 + - - -
175B PRO* 3.9 6.9 - - + +
178B LEU* 4.7 9.2 - - + -
189B LEU* 3.8 30.5 - - + +
190B ILE* 4.1 15.7 - - + -
193B ARG* 3.7 31.7 + - - +
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Residues in contact with GLN 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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167B ALA 3.2 9.5 + - - +
168B ALA 3.6 4.0 + - - +
169B GLU 3.5 0.2 - - - -
170B LEU* 1.3 78.1 - - - +
172B ARG* 1.3 64.7 + - - +
173B THR 3.5 0.3 + - - -
174B ASN* 3.6 13.2 - - - +
193B ARG* 5.1 8.3 + - - +
271B ALA* 3.5 35.2 + - + +
274B ARG* 4.5 11.6 - - + -
275B ARG* 3.5 37.8 - - - +
281B GLN* 6.0 3.8 - - - -
312B HIS* 5.9 1.2 - - - -
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Residues in contact with ARG 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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154B ARG* 5.2 7.3 - - - +
168B ALA 3.4 15.0 + - - +
169B GLU* 3.4 29.7 + - - +
171B GLN* 1.3 82.1 - - - +
173B THR* 1.3 82.7 + - - +
174B ASN* 4.4 1.9 - - - +
261B GLU* 3.1 31.9 + - - -
274B ARG* 3.8 34.9 - - - +
309B ARG* 5.5 2.4 + - - +
312B HIS* 3.7 38.7 + - + +
313B MET* 3.4 30.3 - - - +
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 6.0 0.5 - - - +
132B LEU* 3.4 32.5 - - + +
145B TYR* 3.1 30.9 + - + -
147B THR* 4.4 9.0 - - + -
169B GLU* 2.6 24.4 + - - +
170B LEU* 3.9 0.2 - - - -
172B ARG* 1.3 111.5 - - - +
174B ASN* 1.3 74.2 + - - +
175B PRO* 3.3 2.4 - - - +
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Residues in contact with ASN 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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129B GLN* 5.4 5.9 + - - -
130B ASP 5.7 0.3 - - - +
132B LEU* 5.4 1.4 + - - +
170B LEU 3.0 12.4 + - - -
171B GLN* 3.6 16.2 - - - +
172B ARG 4.4 2.5 - - - +
173B THR* 1.3 78.9 - - - +
175B PRO* 1.3 76.3 - - - +
176B ALA 3.6 0.7 + - - -
193B ARG* 3.0 18.4 + - - +
194B ARG* 3.0 22.6 + - - +
281B GLN* 6.2 0.6 - - - +
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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