Contacts of the strand formed by residues 167 - 172 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.7 17.1 - - - +
163A GLY* 3.5 10.6 - - - -
164A ILE* 2.9 38.4 + - - +
165A ASN 3.4 0.6 + - - -
166A GLY* 1.3 77.4 - - - +
168A PHE* 1.3 61.4 + - - +
184A LEU* 3.4 0.5 - - - +
185A ARG* 3.0 28.2 + - - -
234A TYR* 2.9 24.3 + - - +
236A ALA* 5.6 1.8 - - - -
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TRP* 3.5 41.1 - + + -
160A LEU* 3.6 6.5 - - - +
166A GLY 3.6 13.0 - - - -
167A SER* 1.3 75.8 - - - +
169A LEU* 1.3 70.0 + - - +
170A VAL* 4.8 4.7 - - + -
182A ILE* 4.7 2.0 - - + -
183A SER 3.1 13.9 - - - +
184A LEU* 3.9 13.0 - - + -
218A VAL* 3.9 17.3 - - + -
222A SER* 4.7 1.6 - - - -
232A LEU* 3.7 49.4 - - + -
233A HIS 4.1 0.4 - - - -
234A TYR 2.8 14.5 + - - -
235A PRO* 3.3 24.3 - - + +
236A ALA 2.8 25.5 + - - -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TRP 3.4 12.6 - - - +
148A HIS* 3.7 18.4 - - + -
151A VAL* 5.1 2.0 - - + -
156A ALA* 4.1 14.6 - - + -
159A LEU* 3.7 31.4 - - + -
160A LEU* 4.4 5.6 - - + -
168A PHE* 1.3 82.1 - - - +
170A VAL* 1.3 75.9 + - - +
171A ARG* 4.0 15.0 - - + -
182A ILE* 3.4 5.2 - - - +
183A SER* 2.9 49.0 + - - +
236A ALA* 3.6 20.9 - - + -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TRP* 2.8 37.4 + - + +
147A TYR* 3.7 22.0 - - + -
148A HIS* 2.9 27.5 + - - +
149A GLY 3.9 1.2 + - - -
168A PHE* 4.8 6.3 - - + -
169A LEU* 1.3 78.5 - - - +
171A ARG* 1.3 67.8 + - - +
180A ARG* 4.5 2.5 - - + -
181A SER 3.3 9.0 - - - +
182A ILE* 4.2 14.6 - - + -
195A ILE* 4.1 13.0 - - + -
214A LEU* 4.0 14.1 - - + -
218A VAL* 4.0 14.4 - - + -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 5.1 1.6 - - - -
148A HIS* 5.4 0.4 - - + -
149A GLY* 3.3 13.2 - - - +
151A VAL* 3.5 24.2 + - + +
152A SER* 4.0 1.5 - - - +
153A ARG* 3.7 32.6 - - - +
156A ALA* 3.8 18.9 - - - +
169A LEU* 4.0 8.7 - - + -
170A VAL* 1.3 77.0 - - - +
172A GLU* 1.3 63.7 + - - +
173A SER* 6.2 1.2 - - - +
180A ARG* 3.2 9.4 - - - +
181A SER* 2.9 59.5 + - - +
183A SER* 2.9 19.3 + - - +
192A HIS* 3.0 35.2 + - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 3.7 24.1 + - - +
149A GLY* 2.8 19.0 + - - +
150A PRO* 3.7 16.3 - - + +
151A VAL 3.7 6.8 - - - +
171A ARG* 1.3 77.8 + - - +
173A SER* 1.3 76.2 + - - +
174A GLU* 3.3 9.9 - - - +
177A PRO* 3.6 9.0 - - - +
178A GLY* 2.7 29.9 + - - +
179A GLN 3.5 10.1 - - - +
180A ARG* 3.9 14.6 + - + -
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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