Contacts of the strand formed by residues 634 - 637 (chain E) in PDB entry 1XSK
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 ARG 634 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633E GLY* 1.3 71.6 - - - -
635E TRP* 1.3 60.6 + - - +
636E THR* 4.2 0.5 + - - -
643E GLU* 3.2 41.9 + - + +
644E LEU* 3.1 15.8 - - - +
645E ASP* 3.0 35.7 + - - +
663E VAL 4.3 0.3 - - - +
665E ASP* 3.4 25.3 + - + +
692E ASN* 3.3 36.0 + - + +
694E GLN* 6.0 0.2 - - - +
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Residues in contact with TRP 635 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595E PHE* 3.8 20.0 - + - -
609E MET* 4.3 7.0 - - + -
613E ASN 4.3 1.8 - - - -
615E MET* 4.0 12.3 - - + -
630E LEU* 3.6 30.6 - - + +
631E PRO* 2.9 46.3 + - + -
632E GLU 3.8 8.2 + - - -
633E GLY* 3.3 16.8 + - - -
634E ARG* 1.3 73.4 - - - +
636E THR* 1.3 64.9 + - - +
642E ASP 3.9 0.2 - - - +
643E GLU* 3.1 7.3 - - - +
644E LEU 2.7 38.5 + - - +
646E GLY* 4.4 0.4 - - - -
662E TYR* 3.6 36.6 - - + -
663E VAL 3.4 22.0 - - - -
664E ARG* 3.2 38.4 - - + -
665E ASP 5.6 0.7 - - - -
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Residues in contact with THR 636 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634E ARG 4.5 0.5 + - - -
635E TRP* 1.3 74.9 + - - +
637E HIS* 1.3 75.2 + - - +
638E LEU 3.2 0.7 + - - -
641E ASN* 3.4 33.7 - - - +
642E ASP 3.4 2.9 - - - +
643E GLU* 3.5 17.0 + - + -
662E TYR* 3.5 4.5 - - - -
663E VAL* 2.8 33.7 + - - +
691E PHE* 3.6 28.6 - - + +
692E ASN* 3.7 9.7 + - - -
739E ARG* 5.3 0.4 - - + -
740E ASN* 3.5 13.3 + - - +
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Residues in contact with HIS 637 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636E THR* 1.3 76.0 - - - +
638E LEU* 1.3 77.0 + - - +
639E TRP* 3.2 43.7 + + - -
640E HIS* 3.1 43.6 + + + -
641E ASN* 3.2 18.1 + - - +
642E ASP* 3.0 31.1 + - - +
654E HIS* 4.7 3.8 - + - -
659E LEU 3.0 21.3 + - - -
660E PRO* 4.5 1.1 - - + -
661E VAL* 3.3 23.0 + - + -
662E TYR* 3.1 24.0 - + + -
739E ARG* 3.7 1.6 + - - -
2004E MPO 5.7 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