Contacts of the helix formed by residues 963 - 968 (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 ASP 963 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A GLY* 1.3 69.7 - - - -
964A GLY* 1.3 62.7 + - - +
967A TYR* 2.7 48.7 + - + +
988A VAL* 4.2 3.4 - - - -
989A MET 3.4 3.6 + - - -
990A ASP* 3.1 29.2 - - - +
991A THR 3.0 12.0 + - - -
992A GLU* 3.5 3.2 - - - -
993A VAL 2.9 19.2 + - - +
1002A SER* 2.8 23.1 + - - -
1004A ALA* 3.6 11.9 - - + -
2237A MG 2.1 30.1 - - - -
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Residues in contact with GLY 964 (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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869A PHE* 4.1 0.7 - - - -
963A ASP* 1.3 72.1 - - - +
965A TRP* 1.3 63.8 + - - +
968A ASP* 3.1 26.8 + - - +
969A ILE* 3.4 4.3 + - - +
994A TYR* 3.5 32.8 - - - -
1002A SER* 4.1 9.6 - - - -
2236A HTL 2.8 20.6 + - - -
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Residues in contact with TRP 965 (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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837A ALA* 3.5 20.0 - - + -
869A PHE* 3.0 38.0 + - + -
870A GLU 4.1 0.8 + - - -
872A ALA* 3.7 17.3 - - + +
873A ALA* 3.7 27.5 - - + +
874A GLU* 5.4 0.2 + - - -
959A ILE* 3.6 20.4 - - + -
961A GLY* 3.7 21.1 - - - -
962A GLY 3.5 11.7 - - - +
964A GLY* 1.3 78.8 - - - +
966A ALA* 1.3 88.4 + - + +
968A ASP 3.7 0.3 + - - -
969A ILE* 4.0 2.7 - - - -
970A GLY* 2.8 46.4 + - - -
971A TYR 3.5 0.3 + - - -
974A LEU* 4.2 17.7 - - + -
986A VAL* 3.9 23.1 - - + -
987A PHE 5.1 0.2 - - - -
988A VAL* 4.1 5.2 - - + -
2236A HTL 2.9 14.0 + - - +
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Residues in contact with ALA 966 (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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962A GLY 3.0 14.5 + - - +
965A TRP* 1.3 97.0 - - + +
967A TYR* 1.3 63.7 + - + +
971A TYR* 3.3 29.4 - - - +
974A LEU* 3.7 15.9 - - + +
988A VAL* 3.7 29.4 - - + -
1025A LEU* 4.2 5.7 - - + +
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Residues in contact with TYR 967 (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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963A ASP* 2.7 36.5 + - + +
966A ALA* 1.3 78.1 - - + +
968A ASP* 1.3 70.8 + - - +
971A TYR* 3.8 3.8 - - - +
988A VAL* 4.3 8.1 - - + -
990A ASP* 2.9 21.6 + - - -
1003A LYS* 3.2 7.8 + - + +
1004A ALA* 3.4 40.4 - - + +
1022A LYS* 3.7 9.8 - - - -
1023A LYS* 2.8 68.0 + - + +
1025A LEU* 3.8 28.1 + - + +
1066A ILE* 4.0 16.3 - - + +
1096A TRP* 4.9 0.3 - - - -
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Residues in contact with ASP 968 (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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60A GLU* 5.8 1.0 - - - -
61A MET 5.1 1.4 - - - +
62A GLN* 3.7 22.4 - - - +
964A GLY 3.1 14.4 + - - +
966A ALA 3.5 0.6 - - - -
967A TYR* 1.3 82.7 - - - +
969A ILE* 1.3 67.9 + - - +
970A GLY 3.3 1.8 - - - -
971A TYR* 3.1 16.6 + - - +
972A GLY 4.7 0.5 + - - -
994A TYR* 2.6 34.6 + - - +
1001A SER 4.7 0.2 - - - +
1002A SER* 3.5 4.5 - - - -
1003A LYS* 2.9 57.1 + - - +
972B GLY* 5.3 3.5 - - - +
976B HIS* 4.9 2.3 + - - -
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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