Contacts of the strand formed by residues 167 - 172 (chain B) in PDB entry 1OPL
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 SER 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 3.5 11.0 - - - +
163B GLY* 2.8 26.8 - - - -
164B ILE* 2.8 33.5 + - - +
165B ASN 3.4 0.6 + - - -
166B GLY* 1.3 77.4 - - - +
168B PHE* 1.3 62.3 + - - +
184B LEU* 3.4 0.3 - - - +
185B ARG* 3.0 26.4 + - - -
234B TYR* 3.1 18.8 - - - +
236B ALA* 5.6 3.6 - - - -
329B PRO* 4.5 5.0 - - - +
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Residues in contact with PHE 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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146B TRP* 3.5 41.6 - + + +
160B LEU* 3.9 4.3 - - - +
166B GLY 3.6 13.5 - - - -
167B SER* 1.3 76.9 - - - +
169B LEU* 1.3 72.7 + - - +
170B VAL* 4.8 5.2 - - + -
182B ILE* 4.7 2.7 - - + -
183B SER 3.1 14.1 - - - +
184B LEU* 3.9 13.0 - - + -
218B VAL* 3.9 17.3 - - + -
222B SER* 4.7 1.1 - - - -
232B LEU* 3.7 48.0 - - + -
233B HIS 3.8 1.3 - - - -
234B TYR 3.0 12.1 + - - -
235B PRO* 3.6 24.1 - - + +
236B ALA* 2.9 26.8 + - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TRP 3.4 12.3 - - - +
148B HIS* 3.7 19.5 - - + +
151B VAL* 5.1 0.9 - - + -
156B ALA* 4.1 11.4 - - + -
159B LEU* 3.7 36.1 - - + -
160B LEU* 4.0 16.6 - - + -
168B PHE* 1.3 82.1 - - - +
170B VAL* 1.3 76.1 + - - +
171B ARG* 4.0 15.3 - - + -
182B ILE* 3.4 5.0 - - - +
183B SER* 2.9 42.5 + - - +
236B ALA* 4.0 15.0 - - + -
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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
----------------------------------------------------------
146B TRP* 2.8 38.0 + - + +
147B TYR* 3.7 20.9 - - + -
148B HIS* 2.9 27.2 + - - +
149B GLY 3.9 1.0 + - - -
168B PHE* 4.8 5.8 - - + -
169B LEU* 1.3 78.2 - - - +
171B ARG* 1.3 67.9 + - - +
180B ARG* 4.5 2.5 - - + -
181B SER 3.3 10.8 - - - +
182B ILE* 4.2 13.9 - - + -
195B ILE* 4.1 12.3 - - + -
214B LEU* 4.0 14.4 - - + -
218B VAL* 4.0 15.3 - - + -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 5.1 1.6 - - - -
148B HIS* 5.4 0.2 - - + -
149B GLY* 3.3 14.1 - - - +
151B VAL* 3.5 23.7 + - + +
152B SER* 4.0 1.5 - - - +
153B ARG* 3.7 32.1 - - - +
156B ALA* 3.8 19.5 - - - +
169B LEU* 4.0 9.0 - - + -
170B VAL* 1.3 75.9 - - - +
172B GLU* 1.3 64.4 + - - +
173B SER* 6.2 1.0 - - - +
180B ARG* 3.2 9.4 - - - +
181B SER* 2.9 58.1 + - - +
183B SER* 2.9 19.6 + - - -
192B HIS* 3.0 35.2 + - - +
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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
----------------------------------------------------------
147B TYR* 3.7 23.9 + - - +
149B GLY* 2.8 19.0 + - - +
150B PRO* 3.7 15.2 - - + +
151B VAL 3.7 6.8 - - - +
171B ARG* 1.3 78.0 + - - +
173B SER* 1.3 78.1 + - - +
174B GLU* 3.3 10.2 - - - +
177B PRO* 3.6 8.8 - - - +
178B GLY* 2.7 30.3 + - - +
179B GLN 3.5 10.3 - - - +
180B ARG* 3.9 15.3 + - + -
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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