Contacts of the strand formed by residues 762 - 766 (chain A) in PDB entry 1KEK
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 LEU 762 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682A PRO* 4.0 18.2 - - + -
683A GLN 3.3 1.3 - - - -
684A TRP* 3.9 24.5 - - + -
695A CYS* 3.5 32.3 - - + -
704A ILE* 4.6 0.9 - - + -
738A ILE* 4.5 2.2 - - + -
740A ILE* 4.0 14.1 - - + -
751A CYS* 3.8 26.5 - - + +
752A ALA* 3.5 26.2 - - + +
755A CYS* 3.9 3.6 - - + -
760A LYS* 3.6 12.5 - - - +
761A ALA* 1.4 88.6 - - - +
763A VAL* 1.3 67.4 + - - +
2233A SF4 3.7 15.3 - - - -
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Residues in contact with VAL 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A PRO* 4.1 1.8 - - - -
683A GLN* 2.8 35.5 + - + +
685A VAL* 4.3 16.4 - - + -
752A ALA* 4.8 0.9 - - - -
760A LYS* 4.4 14.4 - - + +
762A LEU* 1.3 80.6 - - - +
764A MET* 1.3 65.2 + - - +
765A GLN* 3.2 22.9 - - - +
1225B ASP* 5.1 2.7 - - - +
1229B ARG* 3.5 31.0 - - - +
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Residues in contact with MET 764 (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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680A ASN* 3.5 37.9 - - + +
681A VAL* 3.4 14.4 - - - -
682A PRO* 3.7 17.5 - - - -
747A GLY 4.0 11.2 - - - +
749A GLY* 4.0 15.0 - - - -
751A CYS* 5.1 0.4 - - - -
752A ALA* 4.2 12.9 - - + +
763A VAL* 1.3 71.7 - - - +
765A GLN* 1.3 60.6 + - - +
2234A SF4 3.8 16.6 - - - -
1217B ALA 5.4 0.7 - - - +
1218B GLY* 4.7 2.9 - - - -
1222B GLN* 3.7 42.6 - - + +
1225B ASP* 5.9 0.2 + - - -
1226B LEU* 4.2 5.1 - - + +
1229B ARG* 2.8 32.5 + - - +
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Residues in contact with GLN 765 (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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680A ASN* 3.1 6.5 - - - -
681A VAL* 2.7 33.9 + - - +
683A GLN* 3.7 33.6 + - + +
763A VAL* 3.2 25.6 - - - +
764A MET* 1.3 78.9 + - - +
766A PRO* 1.3 79.0 - - + +
769A THR* 3.8 0.9 - - - +
770A GLN* 3.6 20.4 - - - +
1226B LEU* 4.1 3.1 - - - +
1229B ARG* 2.7 30.9 + - - +
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Residues in contact with PRO 766 (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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679A ILE 3.5 2.7 - - - +
680A ASN* 3.1 16.4 - - - +
765A GLN* 1.3 96.8 - - + +
767A LEU* 1.3 65.6 + - - +
768A ASP* 3.4 23.1 - - - +
769A THR* 2.8 36.4 + - + +
770A GLN* 3.6 4.0 - - - +
1226B LEU* 4.3 15.7 - - + -
1230B THR* 5.9 2.9 - - + -
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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