Contacts of the strand formed by residues 762 - 766 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682B PRO* 4.1 9.0 - - + -
683B GLN 3.4 4.0 - - - +
684B TRP* 3.9 24.5 - - + +
695B CYS* 3.5 33.0 - - + -
704B ILE* 4.6 1.8 - - + -
738B ILE* 4.6 1.3 - - + -
740B ILE* 4.1 20.6 - - + -
751B CYS* 3.8 26.2 - - + +
752B ALA* 3.7 27.7 - - + +
755B CYS* 4.0 3.7 - - + -
760B LYS* 3.3 13.7 - - - +
761B ALA* 1.3 87.2 - - - +
763B VAL* 1.3 67.0 - - - +
3233B SF4 3.6 14.6 - - - -
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Residues in contact with VAL 763 (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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1225A ASP* 5.1 1.6 - - - +
1229A ARG* 3.3 37.9 - - - +
682B PRO* 4.2 1.6 - - - -
683B GLN* 2.8 39.6 + - + +
685B VAL* 4.3 17.5 - - + -
752B ALA* 4.9 0.7 - - - -
760B LYS* 4.4 14.8 - - + +
762B LEU* 1.3 81.1 - - - +
764B MET* 1.3 59.5 + - - +
765B GLN* 3.6 13.2 - - - +
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Residues in contact with MET 764 (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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1217A ALA 5.5 1.1 - - - +
1218A GLY* 4.5 3.6 - - - -
1222A GLN* 3.5 43.1 - - + +
1225A ASP* 5.4 1.5 + - - +
1226A LEU* 4.0 6.9 - - + +
1229A ARG* 2.9 30.0 + - - +
680B ASN* 3.6 42.8 - - + +
681B VAL* 3.4 8.1 - - - -
682B PRO* 3.8 18.4 - - - -
747B GLY 4.0 14.6 - - - +
749B GLY* 3.9 22.0 - - - -
752B ALA* 4.1 11.9 - - + +
763B VAL* 1.3 72.1 - - - +
765B GLN* 1.3 60.6 + - - +
3234B SF4 4.1 5.2 - - - -
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Residues in contact with GLN 765 (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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1226A LEU* 3.9 3.7 - - - +
1229A ARG* 3.0 30.3 + - - +
1230A THR* 5.9 0.6 - - - +
680B ASN* 3.1 7.4 - - - -
681B VAL* 2.8 33.0 + - - +
683B GLN* 3.7 30.8 + - + +
763B VAL* 3.6 20.9 - - - +
764B MET* 1.3 78.2 + - - +
766B PRO* 1.3 79.3 - - + +
769B THR* 3.7 13.0 + - - +
770B GLN* 3.8 11.0 - - - +
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Residues in contact with PRO 766 (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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1226A LEU* 4.1 16.8 - - + -
1230A THR* 5.7 4.0 - - + -
679B ILE* 3.6 2.2 - - + +
680B ASN* 3.3 16.6 - - - +
765B GLN* 1.3 98.6 - - + +
767B LEU* 1.3 65.3 + - - +
768B ASP* 3.1 24.2 - - - +
769B THR* 2.7 38.1 + - + +
770B GLN* 3.7 4.0 + - - +
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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