Contacts of the strand formed by residues 180 - 186 (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 ARG 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.7 20.0 - - - +
147B TYR* 3.0 38.0 + - - -
170B VAL* 4.5 1.6 - - + -
171B ARG 3.2 12.1 - - - +
172B GLU* 3.9 21.7 + - + -
178B GLY* 3.5 22.8 + - - +
179B GLN* 1.3 78.4 + - - +
181B SER* 1.3 66.4 + - - +
194B ARG* 3.9 4.3 + - - +
195B ILE* 2.9 47.4 + - + +
203B LEU* 5.8 5.6 - - - +
214B LEU* 4.2 16.7 - - - +
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Residues in contact with SER 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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170B VAL* 3.3 4.9 - - - +
171B ARG* 2.9 67.1 + - - +
179B GLN 5.3 0.7 + - - -
180B ARG* 1.3 78.5 + - - +
182B ILE* 1.3 65.3 + - - +
192B HIS* 5.6 0.7 - - - -
193B TYR 3.1 16.2 + - - -
194B ARG* 4.0 16.1 + - - +
195B ILE* 4.2 2.9 - - - +
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Residues in contact with ILE 182 (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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168B PHE* 4.7 2.7 - - + -
169B LEU 3.4 9.4 - - - +
170B VAL* 4.2 11.7 - - + -
181B SER* 1.3 75.8 - - - +
183B SER* 1.3 70.3 + - - +
184B LEU* 4.2 3.8 - - + -
191B TYR 3.6 0.9 - - - +
192B HIS* 3.3 4.3 - - - +
193B TYR* 2.8 44.2 + - + +
195B ILE* 3.9 20.2 - - + -
205B VAL* 3.9 28.3 - - + -
217B LEU* 5.1 8.1 - - + -
218B VAL* 5.5 2.9 - - + -
221B HIS* 5.4 1.6 - - + -
228B LEU* 4.7 8.5 - - + -
232B LEU* 3.9 41.5 - - + -
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Residues in contact with SER 183 (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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156B ALA* 3.7 9.4 - - - +
160B LEU* 3.3 20.8 - - - +
168B PHE* 3.1 6.8 - - - +
169B LEU* 2.9 38.0 + - - -
171B ARG* 2.9 20.4 + - - -
181B SER 4.2 0.6 + - - -
182B ILE* 1.3 70.2 - - - +
184B LEU* 1.3 60.1 + - - +
190B VAL* 4.2 0.4 - - - -
191B TYR 3.3 4.3 - - - -
192B HIS* 2.7 32.1 + - - -
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Residues in contact with LEU 184 (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 LEU* 4.0 1.3 - - - +
166B GLY* 3.8 14.1 - - - -
167B SER 3.4 17.0 - - - +
168B PHE* 3.9 10.5 - - + -
182B ILE* 4.6 1.8 - - + -
183B SER* 1.3 74.4 - - - +
185B ARG* 1.3 65.3 + - - +
189B ARG 3.7 0.3 - - - +
190B VAL* 3.3 5.3 - - - +
191B TYR* 2.7 45.1 + - - +
193B TYR* 4.2 16.8 - - + -
228B LEU* 4.3 4.3 - - + -
229B ILE* 3.9 21.1 - - + -
230B THR* 3.5 27.6 - - + +
231B THR 3.7 18.4 - - - +
232B LEU* 3.9 15.3 - - + -
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Residues in contact with ARG 185 (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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157B GLU* 3.7 5.1 + - - +
160B LEU* 3.3 18.4 + - + +
161B SER* 3.2 40.2 + - - +
163B GLY 3.6 17.2 + - - +
164B ILE 3.6 15.5 - - - +
165B ASN* 3.6 0.2 - - - -
166B GLY 3.0 26.7 + - - -
167B SER 3.0 13.1 + - - +
184B LEU* 1.3 76.3 - - - +
186B TYR* 1.3 67.2 + - - +
187B GLU 5.3 0.2 - - - +
188B GLY* 3.2 37.2 + - - +
189B ARG 3.3 7.2 - - - +
190B VAL* 2.8 43.2 - - - +
230B THR* 4.3 0.2 - - - +
262B THR* 4.8 6.9 - - - +
263B MET* 4.6 8.5 + - - +
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Residues in contact with TYR 186 (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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165B ASN* 3.6 29.2 - - + -
184B LEU 4.0 0.4 + - - -
185B ARG* 1.3 76.2 - - - +
187B GLU* 1.3 91.6 - - + +
188B GLY 3.3 0.7 - - - -
189B ARG* 2.8 20.9 + - - +
191B TYR* 3.7 16.9 + - + -
229B ILE* 3.6 48.0 - - + -
230B THR* 3.9 25.6 - - + -
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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