Contacts of the strand formed by residues 535 - 539 (chain B) in PDB entry 1KWA
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 GLU 535 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A LYS* 4.6 2.9 + - - -
512B HIS* 2.8 48.4 + - + +
513B CYS 3.2 17.0 + - - +
514B ILE* 4.4 4.1 - - + +
533B GLY 3.5 0.8 + - - +
534B ASP* 1.3 73.4 - - - +
536B ILE* 1.3 66.2 + - - +
537B ARG* 3.3 27.7 + - - +
567B ILE* 3.2 6.4 - - - -
568B VAL* 2.8 44.1 + - + +
570B SER* 2.8 25.4 + - - +
571B TYR* 5.4 0.3 - - - -
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Residues in contact with ILE 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ILE* 5.6 0.4 - - + -
505B LEU* 4.1 33.7 - - + -
513B CYS* 2.7 27.0 + - - +
515B VAL* 4.4 13.9 - - + -
530B LEU* 5.4 0.2 - - + -
534B ASP 5.5 0.2 - - - -
535B GLU* 1.3 76.4 - - - +
537B ARG* 1.3 60.5 - - - +
538B GLU 3.7 19.3 - - - +
539B ILE* 3.9 19.5 - - + -
544B VAL* 3.7 22.5 - - + +
556B LEU* 5.3 1.1 - - + -
565B PHE* 3.7 41.3 - - + -
566B LYS 3.8 4.3 - - - +
567B ILE* 4.6 7.4 - - + -
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Residues in contact with ARG 537 (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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512B HIS* 4.3 12.5 + - - -
535B GLU* 3.3 34.4 + - - +
536B ILE* 1.3 75.0 - - - +
538B GLU* 1.3 62.8 + - + +
543B SER* 3.8 1.9 + - - -
544B VAL* 2.9 25.0 + - - +
545B ALA* 4.3 23.2 + - - +
566B LYS* 2.8 33.9 + - + +
568B VAL* 3.7 28.6 - - + +
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Residues in contact with GLU 538 (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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490B LEU* 5.8 0.5 - - - +
536B ILE* 3.7 3.5 - - - +
537B ARG* 1.3 87.3 - - + +
539B ILE* 1.3 68.1 + - - +
540B ASN 4.1 0.7 - - - -
541B GLY* 3.6 33.2 - - - +
542B ILE 3.2 12.3 - - - +
543B SER* 4.2 10.2 - - - -
544B VAL* 4.0 1.8 - - - -
565B PHE* 3.4 5.4 - - - -
566B LYS* 2.9 58.0 + - + +
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Residues in contact with ILE 539 (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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536B ILE* 3.9 11.4 - - + -
538B GLU* 1.3 78.5 - - - +
540B ASN* 1.3 66.3 + - + +
542B ILE* 2.8 39.3 + - + +
544B VAL* 4.0 11.4 - - + -
552B LEU* 4.4 5.2 - - + +
555B MET* 3.2 30.3 - - + -
556B LEU* 3.9 21.1 - - + -
559B MET* 3.6 35.2 - - + -
563B ILE* 4.4 0.7 - - + -
564B THR 3.5 3.6 - - - -
565B PHE* 3.8 25.1 - - + -
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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