Contacts of the helix formed by residues 589 - 597 (chain B) in PDB entry 3KUT
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 589 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559B LYS* 4.7 0.7 - - - +
587B GLU 5.3 0.5 - - - +
588B ILE* 1.3 77.4 - - - +
590B ASN* 1.3 64.9 + - - +
591B SER* 3.7 17.4 + - - +
592B GLU* 3.1 22.4 + - + +
593B LEU* 3.1 11.1 + - - +
114C ASN* 5.1 13.2 - - - +
109D SER* 5.6 4.5 - - - -
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Residues in contact with ASN 590 (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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550B LEU* 4.7 11.4 - - + +
558B GLN* 3.2 32.2 - - - +
559B LYS* 2.8 37.7 - - - +
562B LEU* 3.4 24.0 - - + +
589B ASP* 1.3 72.2 - - - +
591B SER* 1.3 57.4 + - - +
593B LEU* 3.2 7.9 + - - +
594B LEU* 2.9 35.6 + - + +
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Residues in contact with SER 591 (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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589B ASP* 3.7 14.4 + - - +
590B ASN* 1.3 77.0 - - - +
592B GLU* 1.3 62.5 + - - +
594B LEU* 3.4 12.0 + - - +
595B HIS* 3.1 23.2 + - - +
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Residues in contact with GLU 592 (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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588B ILE* 3.4 19.5 - - + +
589B ASP* 3.1 15.9 + - + +
591B SER* 1.3 81.9 + - - +
593B LEU* 1.3 57.5 + - - +
595B HIS* 3.2 11.7 + - - +
596B MET* 2.9 40.7 + - + +
606B LYS* 3.7 17.0 + - - -
109D SER* 2.7 34.6 + - - -
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Residues in contact with LEU 593 (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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559B LYS* 3.9 4.9 - - - +
562B LEU* 3.9 32.5 - - + -
566B LEU* 3.7 25.1 - - + +
585B LEU* 3.4 25.6 - - + +
586B LEU* 4.0 17.3 - - + +
588B ILE* 3.6 22.4 - - + +
589B ASP 3.1 8.0 + - - +
590B ASN* 3.5 13.0 - - - +
592B GLU* 1.3 73.9 - - - +
594B LEU* 1.3 64.3 + - - +
596B MET* 3.3 22.9 + - + +
597B LEU* 3.1 26.2 + - - +
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Residues in contact with LEU 594 (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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545B LEU* 4.1 27.6 - - + +
546B THR 5.7 1.3 - - - +
547B ALA* 6.4 1.6 - - - -
550B LEU* 3.8 25.1 - - + -
562B LEU* 3.8 21.3 - - + -
590B ASN* 2.9 27.1 + - + +
591B SER* 3.7 9.2 - - - +
593B LEU* 1.3 73.1 - - - +
595B HIS* 1.3 63.5 + - - +
597B LEU* 3.3 20.3 + - + +
598B GLU* 3.5 13.6 + - - +
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Residues in contact with HIS 595 (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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591B SER 3.1 14.3 + - - +
592B GLU* 3.2 15.6 + - - +
594B LEU* 1.3 77.7 - - - +
596B MET* 1.3 56.9 + - - +
598B GLU* 2.9 19.4 + - + +
599B SER* 2.9 38.8 + - - -
602B SER* 3.0 30.7 + - - -
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Residues in contact with MET 596 (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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566B LEU* 4.7 3.6 - - + -
569B LEU* 5.6 0.5 - - - +
585B LEU* 4.1 11.7 - - + -
588B ILE* 3.1 33.2 - - + -
592B GLU* 2.9 36.7 + - + +
593B LEU* 3.3 20.8 + - + +
595B HIS* 1.3 76.2 - - - +
597B LEU* 1.3 61.1 + - - +
598B GLU 3.1 1.1 + - - -
599B SER 3.3 21.3 + - - +
600B PRO* 4.3 0.7 - - - +
602B SER* 3.9 12.1 - - - +
603B LEU* 3.7 39.5 - - + +
606B LYS* 3.7 31.4 - - - -
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Residues in contact with LEU 597 (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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545B LEU* 4.4 11.0 - - + -
562B LEU* 4.1 26.5 - - + +
565B ARG* 3.7 47.8 - - + +
566B LEU* 3.9 17.5 - - + -
569B LEU* 4.3 15.0 - - + +
593B LEU 3.1 16.9 + - - +
594B LEU* 3.5 14.8 - - + +
595B HIS 3.1 0.4 - - - -
596B MET* 1.3 76.8 - - - +
598B GLU* 1.3 59.1 + - - +
600B PRO* 5.9 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