Contacts of the helix formed by residues 259 - 263 (chain A) in PDB entry 3Q7I
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 GLY 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A HIS* 5.5 2.4 + - - -
199A LYS* 4.1 6.3 - - - -
256A ASP 4.8 0.4 + - - -
257A TRP 3.8 4.8 + - - -
258A VAL* 1.3 74.1 - - - +
260A GLY* 1.3 68.5 + - - -
261A ARG* 3.2 4.5 - - - -
262A TYR* 2.9 30.3 + - - +
263A SER* 3.1 10.7 + - - -
496A TYR* 5.8 4.3 - - - -
498A GLN* 6.1 0.4 - - - -
601A 6PG 4.6 1.3 - - - -
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY* 3.2 17.4 - - - +
148A SER* 5.8 1.1 - - - -
199A LYS* 4.7 9.0 - - - +
254A MET* 5.2 3.6 - - - -
258A VAL 3.6 2.8 + - - -
259A GLY* 1.3 69.3 - - - -
261A ARG* 1.3 55.4 + - - -
262A TYR 3.1 4.2 + - - -
263A SER* 2.7 30.0 + - - -
601A 6PG 2.9 32.9 + - - -
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY* 4.4 1.8 - - - -
259A GLY* 5.1 1.5 - - - -
260A GLY* 1.3 73.9 - - - +
262A TYR* 1.3 81.0 + - + +
263A SER 3.6 0.7 - - - -
339A TYR* 3.2 25.6 + - + -
342A GLN* 3.9 27.4 - - + +
343A ALA* 3.9 17.8 - - - +
346A GLU* 3.2 37.7 + - - +
347A SER* 2.9 23.6 + - - +
495A SER 2.9 23.6 + - - -
496A TYR* 3.5 9.4 - - - +
497A ASP 3.0 20.6 + - - -
498A GLN* 2.7 23.0 + - - -
601A 6PG 2.9 24.2 + - - +
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Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 3.4 39.6 - - + +
91A LEU* 4.1 0.9 - - - +
258A VAL* 4.0 3.8 - - - +
259A GLY* 2.9 21.3 + - - +
261A ARG* 1.3 107.8 - - + +
263A SER* 1.3 56.2 + - - +
264A LEU 3.7 2.2 - - - -
265A TRP* 3.3 19.5 - - - -
339A TYR* 4.6 1.3 - - - -
343A ALA* 3.7 10.1 + - + -
347A SER* 2.8 20.9 + - - -
481A GLU* 3.6 47.5 + - + -
484A ILE* 3.5 18.0 - - - +
496A TYR* 3.5 36.0 + + - -
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY 3.0 16.5 + - - -
148A SER* 5.2 0.3 + - - -
254A MET* 3.9 14.8 - - - -
258A VAL* 3.6 17.7 - - - -
259A GLY 3.4 9.4 - - - -
260A GLY* 2.7 23.7 + - - -
261A ARG 3.6 1.0 - - - -
262A TYR* 1.3 74.6 - - - +
264A LEU* 1.3 65.9 + - - +
265A TRP 3.0 3.1 - - - -
266A SER* 2.7 25.3 + - - +
268A ILE* 3.4 14.1 - - - +
339A TYR* 5.1 0.4 + - - -
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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
------------------------------------------------------------
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