Contacts of the strand formed by residues 989 - 993 (chain B) in PDB entry 3KQ4
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 TYR 989 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979B LEU* 3.4 17.1 - - - +
985B CYS 3.3 24.0 - - - +
986B THR* 3.4 23.1 - - + -
988B ASP* 1.3 76.6 + - - +
990B LEU* 1.3 65.2 + - - +
991B GLU* 4.5 21.8 + - + -
1003B ARG* 3.6 31.4 - - + -
1004B TYR 3.7 6.1 - - - +
1005B CYS* 4.4 5.4 - - + -
1023B VAL* 5.0 4.6 - - + +
1024B PHE* 3.2 14.8 - - - -
1025B VAL* 3.0 50.9 + - + +
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Residues in contact with LEU 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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974B PHE* 5.2 12.8 - - + -
977B PHE* 4.0 16.2 - - + -
979B LEU* 4.4 2.7 - - + -
989B TYR* 1.3 78.6 - - - +
991B GLU* 1.3 78.8 + - - +
992B VAL* 5.0 2.0 - - + -
1003B ARG 3.4 0.3 - - - -
1004B TYR* 2.6 47.9 + - + +
1009B ILE* 5.9 1.6 - - + -
1022B LEU* 3.6 22.0 - - + -
1023B VAL 3.4 13.0 - - - +
1024B PHE* 4.4 7.6 - - + -
1035B PHE* 3.2 41.1 - - + -
1037B ILE* 5.7 2.7 - - + -
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Residues in contact with GLU 991 (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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989B TYR* 4.2 16.4 + - + -
990B LEU* 1.3 88.9 - - - +
992B VAL* 1.3 63.6 + - - +
993B TYR* 5.2 5.6 + - + +
1000B SER* 3.9 17.5 + - - -
1002B GLY 3.1 13.8 - - - +
1003B ARG* 3.7 24.1 + - + +
1021B MET* 6.2 1.3 - - - -
1022B LEU* 3.6 0.3 - - - +
1023B VAL* 3.2 48.8 + - + +
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Residues in contact with VAL 992 (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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972B LEU* 4.7 9.6 - - + -
974B PHE* 6.4 1.3 - - + -
990B LEU* 5.0 1.3 - - + -
991B GLU* 1.3 75.9 - - - +
993B TYR* 1.3 58.3 + - - +
1000B SER* 3.2 4.1 + - - -
1001B LEU* 3.0 56.5 + - + +
1002B GLY 3.1 13.6 + - - +
1004B TYR* 4.1 14.8 - - + -
1013B LEU* 4.2 8.3 - - + -
1020B LEU* 3.8 13.9 - - + -
1021B MET 3.4 15.9 - - - +
1022B LEU* 3.6 17.3 - - + -
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Residues in contact with TYR 993 (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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991B GLU* 4.2 7.8 + - + +
992B VAL* 1.3 75.2 - - - +
994B ASP* 1.3 66.8 + - - +
995B THR* 3.1 11.5 + - - -
997B SER 3.2 23.0 + - - -
998B GLU* 3.4 18.8 + - - +
999B THR* 2.9 28.7 + - - -
1000B SER* 3.3 19.5 - - - -
1020B LEU* 3.5 6.4 - - - +
1021B MET* 2.9 59.2 + - + +
1023B VAL* 6.1 0.2 - - - +
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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