Contacts of the helix formed by residues 963 - 968 (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 ASP 963 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962B GLY* 1.3 69.4 - - - -
964B GLY* 1.3 61.2 + - - +
967B TYR* 2.7 49.5 + - + +
988B VAL* 4.3 2.5 - - - -
989B MET 3.4 3.0 + - - -
990B ASP* 3.2 28.5 - - - +
991B THR 3.0 12.3 + - - -
992B GLU 3.7 2.5 - - - -
993B VAL 3.1 16.2 + - - +
1002B SER* 2.8 25.4 + - - -
1004B ALA* 3.5 12.8 - - + +
3237B MG 2.0 29.6 - - - -
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Residues in contact with GLY 964 (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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869B PHE* 4.0 7.0 - - - -
963B ASP* 1.3 80.6 - - - +
965B TRP* 1.3 63.9 + - - +
968B ASP* 3.1 26.7 + - - +
969B ILE* 3.3 5.0 + - - +
994B TYR* 3.5 26.6 + - - -
1002B SER* 4.3 4.9 - - - -
3236B HTL 2.8 19.1 + - - -
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Residues in contact with TRP 965 (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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837B ALA* 3.5 16.8 - - + -
869B PHE* 3.1 42.7 - - + -
870B GLU 4.3 0.8 + - - -
872B ALA* 3.7 17.8 - - + +
873B ALA* 3.7 27.9 - - + +
874B GLU* 5.4 0.4 + - - -
959B ILE* 3.6 20.6 - - + -
961B GLY* 3.5 28.5 - - - -
962B GLY 3.5 9.6 - - - +
964B GLY* 1.3 78.8 - - - +
966B ALA* 1.3 85.0 + - + +
968B ASP 3.7 0.3 + - - -
969B ILE* 4.1 2.5 - - - -
970B GLY* 2.7 48.0 + - - -
971B TYR 3.5 0.3 + - - -
974B LEU* 4.2 15.7 - - + -
986B VAL* 3.9 23.8 - - + -
988B VAL* 4.1 4.0 - - + -
3236B HTL 3.0 9.0 + - - +
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Residues in contact with ALA 966 (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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962B GLY 3.0 16.7 + - - +
965B TRP* 1.3 97.4 - - + +
967B TYR* 1.3 65.1 + - + +
971B TYR* 3.3 29.2 - - - +
974B LEU* 3.9 16.2 - - + +
988B VAL* 3.8 26.9 - - + -
1025B LEU* 4.2 5.7 - - + +
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Residues in contact with TYR 967 (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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963B ASP* 2.7 36.4 + - + +
966B ALA* 1.3 76.7 - - + +
968B ASP* 1.4 67.9 + - - +
971B TYR* 3.7 3.1 - - - +
988B VAL* 4.3 8.5 - - + -
990B ASP* 2.9 29.2 + - - -
1003B LYS* 3.1 14.2 + - + +
1004B ALA* 3.5 32.1 - - + +
1022B LYS* 3.4 9.4 - - - -
1023B LYS* 2.7 66.7 + - + +
1025B LEU* 3.8 31.4 + - + +
1066B ILE* 4.0 13.8 - - + +
1096B TRP* 4.8 0.3 - - - -
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Residues in contact with ASP 968 (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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972A GLY* 5.3 3.8 - - - +
976A HIS* 4.8 2.1 + - - -
60B GLU* 5.7 1.2 - - - -
61B MET 5.0 2.3 - - - +
62B GLN* 3.6 24.3 - - - +
964B GLY 3.1 13.2 + - - +
966B ALA 3.4 1.0 - - - -
967B TYR* 1.4 80.1 - - - +
969B ILE* 1.3 68.6 + - - +
970B GLY 3.3 0.9 - - - -
971B TYR* 3.2 17.4 + - - +
972B GLY 4.7 0.9 + - - -
994B TYR* 2.5 32.7 + - - +
1002B SER* 3.5 3.6 - - - -
1003B LYS* 2.8 64.7 + - - +
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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