Contacts of the strand formed by residues 634 - 637 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633F GLY* 1.3 72.5 - - - -
635F TRP* 1.3 61.4 + - - +
636F THR* 4.2 1.0 + - - -
643F GLU* 2.8 62.7 + - + +
644F LEU* 3.3 6.2 - - - +
645F ASP* 2.8 37.2 + - - +
663F VAL 4.3 0.3 - - - +
665F ASP* 3.0 32.5 + - + +
692F ASN* 3.0 29.9 - - + +
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Residues in contact with TRP 635 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595F PHE* 3.9 16.6 - + - -
609F MET* 4.2 7.2 - - + -
613F ASN 4.3 0.2 - - - -
615F MET* 3.9 13.9 - - + -
630F LEU* 3.5 25.5 - - + +
631F PRO* 2.8 52.1 + - + -
632F GLU 4.0 7.2 + - - -
633F GLY 3.4 15.0 + - - -
634F ARG* 1.3 75.0 - - - +
636F THR* 1.3 61.5 + - - +
642F ASP 3.9 0.2 - - - +
643F GLU* 3.0 7.4 - - - +
644F LEU 2.7 41.7 + - - +
646F GLY* 4.1 2.0 - - - -
662F TYR* 3.5 37.8 - - + -
663F VAL 3.5 7.4 - - - -
664F ARG* 3.2 53.4 - - + -
665F ASP 5.9 0.2 - - - -
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Residues in contact with THR 636 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634F ARG 4.6 0.5 + - - -
635F TRP* 1.3 75.9 - - - +
637F HIS* 1.3 71.4 - - - +
638F LEU 3.2 0.7 + - - -
641F ASN* 3.7 22.4 - - - +
642F ASP 3.3 3.6 - - - +
643F GLU* 3.5 16.9 + - + +
662F TYR* 3.4 4.5 - - - -
663F VAL* 2.9 33.3 + - - +
691F PHE* 3.6 27.8 - - + +
692F ASN* 3.8 13.5 + - - -
739F ARG* 4.3 0.2 - - + -
740F ASN* 3.7 23.1 - - - +
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Residues in contact with HIS 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636F THR* 1.3 72.8 - - - +
638F LEU* 1.3 65.8 + - - +
639F TRP* 2.9 46.3 + + - -
640F HIS* 3.1 38.6 + + + -
641F ASN* 3.1 16.9 + - - +
642F ASP* 2.9 31.9 + - - +
654F HIS* 4.9 3.8 - + - -
658F SER* 4.4 0.2 + - - -
659F LEU 3.1 21.3 + - - -
660F PRO* 4.5 1.1 - - + -
661F VAL* 3.4 21.2 + - + -
662F TYR* 3.2 26.6 - + + -
739F ARG* 3.7 4.2 + - - -
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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