Contacts of the helix formed by residues 174 - 181 (chain B) in PDB entry 1O94
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 TYR 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B TYR* 4.3 15.3 - + - -
69B ASP* 4.8 3.6 + - - -
105B TRP* 3.2 35.0 - + + +
106B TYR 3.7 6.5 - - - +
107B GLY* 3.7 14.1 - - - -
110B HIS* 3.9 24.7 - + + -
130B PHE* 5.5 2.6 - - - -
169B TYR* 3.3 48.9 - + - +
171B ALA 3.3 17.8 + - - +
172B HIS* 3.0 18.3 + - + -
173B SER* 1.3 77.1 - - - +
175B LEU* 1.3 67.2 + - - +
176B PRO* 3.5 4.5 - - - -
177B LEU* 3.0 7.6 + - - +
178B GLN* 2.9 21.5 + - - +
261B ILE* 3.7 20.0 - - + +
355B TRP* 4.7 7.6 - - - -
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Residues in contact with LEU 175 (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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106B TYR* 3.0 47.3 + - + +
108B GLY* 4.5 1.8 - - - +
121B ARG 3.7 21.1 - - - +
122B GLY* 4.0 2.0 - - - -
123B PRO* 3.9 15.9 - - + -
139B MET* 4.7 3.6 - - - -
147B VAL* 3.8 13.7 - - + -
151B TYR* 4.1 2.9 - - - +
174B TYR* 1.3 69.9 - - - +
176B PRO* 1.3 69.7 - - + +
178B GLN* 3.0 32.6 + - - +
179B PHE* 3.1 23.2 + - + -
201B PHE* 3.7 30.1 - - + -
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Residues in contact with PRO 176 (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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106B TYR 4.7 0.7 - - - +
151B TYR* 3.6 18.6 - - + +
168B VAL* 4.0 15.9 - - + -
169B TYR 3.3 23.6 - - - +
170B GLY* 4.2 2.7 - - - -
174B TYR 3.6 2.2 - - - -
175B LEU* 1.3 93.8 - - + +
177B LEU* 1.3 54.7 + - - +
179B PHE* 3.4 6.2 + - - +
180B LEU* 3.1 20.3 + - - +
198B ARG 5.0 0.3 - - - +
201B PHE* 4.4 16.8 - - + -
202B TRP* 3.5 48.6 - - + +
205B THR* 5.9 0.7 - - + -
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Residues in contact with LEU 177 (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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170B GLY* 3.6 30.0 - - - +
171B ALA* 5.1 0.9 - - - -
173B SER* 3.8 31.4 - - - +
174B TYR 3.0 9.1 + - - +
176B PRO* 1.3 75.6 - - - +
178B GLN* 1.3 60.9 + - - +
180B LEU* 2.9 7.5 + - + +
181B ASN* 2.8 58.2 + - + +
184B TYR* 4.8 1.3 - - + -
202B TRP* 4.1 5.3 - - + -
223B PHE* 3.8 24.7 - - + -
224B GLY* 4.0 11.2 - - - +
227B THR* 5.2 2.7 - - + +
234B ILE* 4.3 12.6 - - + -
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Residues in contact with GLN 178 (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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107B GLY 2.9 28.7 + - - -
108B GLY* 4.0 3.7 - - - -
110B HIS* 3.5 4.4 - - - -
122B GLY* 4.6 0.3 - - - -
123B PRO* 3.6 21.0 - - + +
126B TYR* 2.5 33.3 + - - -
173B SER 3.1 26.1 + - - +
174B TYR 2.9 16.1 + - - +
175B LEU* 3.0 17.9 + - - +
177B LEU* 1.3 76.6 - - - +
179B PHE* 1.3 60.5 + - - +
181B ASN 3.2 17.8 - - - +
184B TYR* 3.4 30.7 - - + +
185B ASN* 3.5 5.2 - - - +
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Residues in contact with PHE 179 (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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123B PRO* 3.7 38.1 - - + -
139B MET* 3.8 26.0 - - - -
144B ILE* 4.1 12.8 - - + -
175B LEU* 3.1 24.6 + - + -
176B PRO 3.6 8.5 - - - +
178B GLN* 1.3 76.2 - - - +
180B LEU* 1.3 62.5 - - - +
181B ASN 3.4 0.2 + - - -
185B ASN* 2.6 26.3 + - - +
187B ARG* 3.9 15.7 - - - -
191B TYR* 4.0 26.7 - + + -
198B ARG* 3.2 14.7 - - - +
201B PHE* 3.5 50.3 - + + -
202B TRP 5.4 0.2 - - - +
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Residues in contact with LEU 180 (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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176B PRO 3.1 13.5 + - - +
177B LEU* 2.9 13.2 + - + +
179B PHE* 1.3 79.2 - - - +
181B ASN* 1.3 56.6 - - - +
182B PRO* 3.5 0.7 - - - +
195B LEU* 3.8 27.1 - - + -
198B ARG* 2.9 34.8 + - - +
199B ALA* 3.8 24.2 - - - +
202B TRP* 4.2 9.0 - - + -
223B PHE* 3.6 38.1 - - + -
234B ILE* 3.7 17.7 - - + +
239B ASP* 5.3 2.7 - - + -
243B PHE* 4.0 19.5 - - + -
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Residues in contact with ASN 181 (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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173B SER* 5.1 0.2 + - - -
177B LEU* 2.8 35.3 + - + +
178B GLN 3.2 4.0 - - - +
179B PHE 3.3 1.0 - - - -
180B LEU* 1.3 77.0 - - - +
182B PRO* 1.4 64.8 - - - +
183B TYR* 3.0 22.3 + - - +
184B TYR* 2.9 30.1 + - + -
185B ASN* 2.9 12.0 + - - -
227B THR* 4.2 5.7 + - - +
233B GLN* 2.8 44.7 + - - +
234B ILE* 3.9 9.2 - - + -
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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
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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