Contacts of the strand formed by residues 985 - 990 (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 ASN 985 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956B SER* 3.7 10.1 + - - +
957B VAL 2.9 25.2 + - - +
958B TRP* 3.2 47.0 - - + +
959B ILE 2.8 26.3 + - - +
983B ASP* 4.3 6.7 + - - -
984B VAL* 1.3 77.8 - - - +
986B VAL* 1.3 63.0 + - - +
1056B ALA* 3.2 12.9 - - + +
1057B GLU* 3.4 10.5 + - - +
1063B SER* 3.7 8.4 - - - -
3238B CA 2.7 24.7 - - - -
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Residues in contact with VAL 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B TRP* 4.8 2.0 - - - -
959B ILE* 3.4 27.8 - - + +
965B TRP* 3.9 17.3 - - + -
974B LEU* 3.6 31.2 - - + -
977B VAL* 5.5 0.7 - - + -
978B LEU* 4.0 11.2 - - + -
984B VAL* 4.8 3.1 - - + -
985B ASN* 1.3 75.3 - - - +
987B PHE* 1.3 56.1 + - - +
988B VAL* 3.9 7.2 - - + -
1063B SER 2.6 22.1 + - - +
1064B LEU* 3.5 21.7 - - + -
1065B VAL* 2.8 35.5 + - - +
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Residues in contact with PHE 987 (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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820B TYR* 3.5 28.5 - + + -
821B VAL* 4.8 1.3 - - + -
824B ILE* 3.8 25.1 - - + -
958B TRP* 4.0 13.9 - + + -
959B ILE 2.9 8.3 + - - +
960B PHE* 3.4 24.0 - + + -
961B GLY 3.2 23.2 + - - +
985B ASN 4.0 0.4 + - - -
986B VAL* 1.3 73.3 - - - +
988B VAL* 1.3 61.0 + - - +
989B MET* 3.4 34.8 + - + +
1040B VAL* 4.6 0.2 - - + -
1049B PHE* 4.3 11.0 - + - -
1053B LEU* 5.0 1.6 - - + -
1065B VAL* 3.5 30.5 - - + -
1067B ALA* 3.5 30.3 - - + -
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Residues in contact with VAL 988 (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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961B GLY 3.4 2.9 - - - -
962B GLY 4.0 15.3 - - - +
963B ASP* 4.2 5.6 - - - +
965B TRP* 4.1 4.0 - - + -
966B ALA* 3.8 32.8 - - + -
967B TYR* 4.3 6.5 - - + -
986B VAL* 3.9 8.7 - - + -
987B PHE* 1.3 73.9 - - - +
989B MET* 1.3 66.1 + - - +
990B ASP* 3.4 4.3 + - - +
1025B LEU* 4.9 1.3 - - + -
1064B LEU* 3.7 28.0 - - + -
1065B VAL 2.9 11.9 + - - +
1066B ILE* 3.5 16.6 - - + -
1067B ALA* 2.8 32.6 + - - +
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Residues in contact with MET 989 (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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817B GLU* 2.7 72.8 - - + +
820B TYR* 4.5 1.1 - - + -
821B VAL* 3.0 30.3 - - + -
841B SER* 4.3 18.8 - - - -
844B TRP* 4.3 0.7 - - + -
960B PHE* 5.5 5.6 - - - -
961B GLY 3.0 12.4 + - - +
962B GLY* 3.2 21.0 - - - -
963B ASP* 3.4 0.9 + - - +
987B PHE* 3.4 29.6 - - + +
988B VAL* 1.3 70.2 - - - +
990B ASP* 1.3 64.2 + - - +
991B THR* 3.4 3.3 + - - +
1067B ALA* 4.0 5.2 - - + -
1069B ALA* 4.5 5.8 - - + -
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Residues in contact with ASP 990 (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* 3.2 23.3 - - + +
967B TYR* 2.9 19.1 + - - -
988B VAL* 3.4 2.8 + - + -
989B MET* 1.3 72.1 - - - +
991B THR* 1.3 57.7 + - - +
992B GLU* 3.0 31.0 + - - +
1004B ALA* 3.6 0.2 - - - +
1022B LYS* 2.6 29.3 + - - -
1066B ILE* 4.0 8.3 - - + -
1067B ALA 2.9 18.6 + - - +
1068B TYR* 4.2 2.9 - - - -
1069B ALA* 3.0 22.2 + - - +
1096B TRP* 3.4 16.7 - - + -
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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