Contacts of the strand formed by residues 637 - 641 (chain A) in PDB entry 1WKB
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 GLY 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A MET* 4.0 3.4 - - - +
486A LYS* 3.2 11.7 - - - -
604A LEU 5.3 0.3 - - - +
605A ASP 3.3 11.4 + - - -
606A TRP* 3.5 16.0 - - - -
607A ARG* 2.9 24.3 + - - +
621A PHE* 4.9 2.3 - - - -
635A PRO* 3.6 2.1 - - - +
636A LYS* 1.3 81.5 - - - +
638A ILE* 1.3 67.8 + - - +
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Residues in contact with ILE 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A MET* 3.3 27.6 - - + -
486A LYS 2.9 5.7 + - - -
487A ILE* 3.4 13.7 - - + -
488A LEU 2.9 24.5 + - - +
496A PHE* 3.9 35.2 - - + -
606A TRP* 3.6 5.8 - - - -
607A ARG* 3.3 12.8 - - + +
618A LEU* 4.1 13.2 - - + +
621A PHE* 3.9 22.9 - - + -
622A ILE* 4.0 8.5 - - + -
637A GLY* 1.3 76.7 - - - +
639A ALA* 1.3 62.3 + - - +
640A VAL* 3.8 23.6 - - + -
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Residues in contact with ALA 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 6.0 0.2 - - + -
488A LEU* 3.5 15.5 - - + -
606A TRP* 4.0 10.0 - - + -
607A ARG 3.0 7.3 + - - +
608A CYS* 3.3 28.2 - - - +
609A SER 3.4 3.1 + - - -
638A ILE* 1.3 74.5 - - - +
640A VAL* 1.3 63.7 + - - +
641A ASN* 5.2 0.3 - - - +
747A PHE* 3.6 38.8 - - + -
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Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 5.5 1.1 - - - +
487A ILE* 6.3 0.7 - - + -
488A LEU 3.0 19.0 + - - +
489A PRO* 3.9 12.1 - - + -
492A ARG* 4.5 5.2 - - + -
496A PHE* 4.9 2.0 - - + -
609A SER* 3.1 10.3 - - - +
610A GLY 4.5 0.9 - - - +
611A LYS* 4.0 14.8 - - + -
614A ILE* 4.1 25.6 - - + -
618A LEU* 3.4 32.1 - - + -
638A ILE* 3.8 9.9 - - + -
639A ALA* 1.3 79.4 - - - +
641A ASN* 1.3 63.5 + - - +
683A HIS* 3.6 18.7 + - - -
684A ASP* 4.8 3.8 - - + -
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Residues in contact with ASN 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 5.1 0.2 + - - -
55A ARG* 3.9 10.4 - - - +
56A THR* 3.2 40.9 + - - +
59A ILE* 3.3 33.3 - - + +
608A CYS* 5.6 1.4 - - - +
609A SER* 3.1 20.3 + - - +
610A GLY* 3.4 4.8 - - - -
611A LYS* 2.9 25.1 + - - +
639A ALA 5.2 0.5 - - - +
640A VAL* 1.3 74.5 - - - +
642A GLY* 1.3 83.2 + - - +
683A HIS* 3.2 9.9 - - - +
684A ASP* 4.2 3.8 - - - -
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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