Contacts of the strand formed by residues 582 - 589 (chain B) in PDB entry 2QKT
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 LYS 582 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580B LEU* 3.4 40.6 + - + +
581B GLU* 1.3 78.7 - - - +
583B PHE* 1.3 61.9 + - - +
660B VAL 3.2 8.7 - - - +
661B THR* 3.9 17.3 - - - +
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Residues in contact with PHE 583 (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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581B GLU* 4.0 28.3 - - + -
582B LYS* 1.3 77.9 - - - +
584B ASN* 1.3 76.7 + - - +
585B VAL* 3.9 8.7 - - + -
622B LYS* 3.9 24.2 - - + +
623B LEU* 3.8 22.4 - - + -
627B ASP* 4.1 1.8 - - - -
659B GLU* 3.7 0.3 - - - +
660B VAL* 2.7 58.5 + - + +
662B ARG* 3.8 38.4 - - + -
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Residues in contact with ASN 584 (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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583B PHE* 1.3 82.2 + - - +
585B VAL* 1.3 67.1 + - - +
586B ASP* 3.7 15.3 - - - +
622B LYS* 3.0 27.4 + - - +
657B SER* 5.9 0.4 - - - +
658B MET 3.2 5.6 + - - +
659B GLU* 3.3 32.5 - - - +
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Residues in contact with VAL 585 (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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583B PHE* 3.9 11.0 - - + -
584B ASN* 1.3 80.1 - - - +
586B ASP* 1.3 62.4 + - - +
587B LEU* 4.3 3.8 - - + -
618B GLU* 4.0 26.9 - - + +
619B ILE* 4.6 3.8 - - + -
622B LYS* 4.0 9.6 - - + +
623B LEU* 3.7 35.7 - - + -
656B VAL 3.6 1.9 - - - +
657B SER* 3.5 2.3 - - - -
658B MET* 2.8 64.5 + - + +
660B VAL* 4.1 6.3 - - + -
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Residues in contact with ASP 586 (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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584B ASN* 3.7 20.1 - - - +
585B VAL* 1.3 80.1 - - - +
587B LEU* 1.3 63.5 + - - +
618B GLU* 3.4 18.1 - - - +
622B LYS* 5.4 2.4 - - - +
655B LYS* 5.0 2.4 - - - +
656B VAL 3.3 2.9 - - - +
657B SER* 2.7 33.4 + - - -
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Residues in contact with LEU 587 (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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585B VAL* 4.7 6.1 - - + -
586B ASP* 1.3 75.6 - - - +
588B MET* 1.3 68.2 + - - +
589B LYS* 3.8 16.2 - - - +
595B LEU* 4.1 11.2 - - + -
616B TYR* 3.8 33.2 - - + -
618B GLU* 3.7 26.0 - - + +
619B ILE* 3.9 23.6 - - + -
655B LYS* 4.0 1.7 - - - +
656B VAL* 3.0 60.3 + - + +
658B MET* 5.0 0.9 - - + -
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Residues in contact with MET 588 (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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587B LEU* 1.3 78.4 - - - +
589B LYS* 1.3 67.6 + - - +
590B LYS* 3.5 23.8 + - - +
616B TYR* 3.5 13.2 - - - -
618B GLU* 5.0 2.0 + - - -
654B GLY* 3.6 26.2 - - - +
655B LYS* 4.2 7.4 - - + +
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Residues in contact with LYS 589 (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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587B LEU* 3.8 6.9 - - + +
588B MET* 1.3 76.1 - - - +
590B LYS* 1.3 93.2 + - - +
591B ALA* 3.7 13.3 + - - +
593B LYS 3.0 21.4 + - - -
594B GLU* 4.1 9.8 - - - +
595B LEU* 4.2 15.5 - - + +
616B TYR* 3.4 11.2 - - + +
649B PHE* 5.6 2.0 - - - -
652B ALA* 3.6 36.3 + - + +
653B ASN* 4.5 1.6 - - - -
654B GLY* 2.7 38.4 + - - +
656B VAL* 3.9 13.2 - - + -
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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