Contacts of the helix formed by residues 261 - 265 (chain A) in PDB entry 3OP5
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 TRP 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLU* 2.8 26.5 + - + +
249A TYR* 3.7 34.1 - + - -
259A LEU* 3.9 22.7 - - + +
260A PRO* 1.3 91.8 - - + +
262A GLU* 1.3 63.7 + - - +
263A ASP 3.2 4.4 + - - -
264A ASN* 3.2 16.4 + - - +
265A LEU* 3.5 19.5 - - + +
270A TYR* 4.0 16.4 - - + -
271A VAL* 3.8 26.6 - - + +
274A SER* 3.7 31.4 - - - -
275A LYS* 3.7 29.2 - - + +
278A TYR* 3.8 18.8 - + + -
285A LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 262 (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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226A GLU* 5.7 2.7 - - + -
253A GLN* 4.3 7.3 + - - +
257A GLY 4.2 2.4 - - - +
258A HIS* 2.7 36.6 + - - +
259A LEU* 3.2 34.9 + - + +
260A PRO 3.4 1.3 - - - +
261A TRP* 1.3 77.7 - - - +
263A ASP* 1.3 63.7 + - + +
264A ASN 3.3 1.2 + - - -
265A LEU* 3.5 30.5 + - + +
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Residues in contact with ASP 263 (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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260A PRO 4.8 4.0 + - - +
261A TRP 3.2 1.6 + - - -
262A GLU* 1.3 81.6 - - + +
264A ASN* 1.4 71.8 + - - +
265A LEU 3.9 0.9 - - - -
101B ARG* 4.9 18.4 - - - +
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Residues in contact with ASN 264 (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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260A PRO 5.9 0.4 + - - -
261A TRP 3.2 7.1 + - - -
263A ASP* 1.4 94.6 + - - +
265A LEU* 1.3 62.4 + - - +
266A LYS* 3.3 4.0 - - - +
267A ASP* 3.3 27.2 + - + +
270A TYR* 3.4 47.9 + - + -
271A VAL* 3.5 4.7 - - - +
97B GLN* 3.3 35.1 + - - +
101B ARG* 5.3 2.2 - - - +
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Residues in contact with LEU 265 (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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225A ILE* 3.8 29.7 - - + +
226A GLU* 3.7 52.7 - - + +
261A TRP* 3.5 20.9 - - + +
262A GLU* 3.5 26.0 + - + +
263A ASP 3.9 1.2 - - - -
264A ASN* 1.3 71.4 - - - +
266A LYS* 1.3 61.6 + - - +
267A ASP* 3.2 4.4 + - - -
268A PRO* 4.6 1.6 - - - +
271A VAL* 4.0 13.0 - - + -
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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