Contacts of the strand formed by residues 634 - 637 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633B GLY* 1.3 70.8 - - - -
635B TRP* 1.3 60.9 + - - +
636B THR* 4.0 0.9 + - - -
643B GLU* 3.0 53.7 + - + +
644B LEU* 3.3 8.2 + - - +
645B ASP* 3.0 40.8 + - - +
665B ASP* 3.3 25.8 + - + +
692B ASN* 3.1 29.6 - - + +
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Residues in contact with TRP 635 (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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595B PHE* 3.7 23.6 - + - -
609B MET* 4.2 10.5 - - + -
615B MET* 3.9 12.8 - - + -
630B LEU* 3.4 33.0 - - + +
631B PRO* 2.7 48.0 + - + -
632B GLU 3.8 6.4 + - - -
633B GLY* 3.3 16.6 + - - -
634B ARG* 1.3 73.7 - - - +
636B THR* 1.3 60.7 + - - +
642B ASP 3.8 0.2 - - - +
643B GLU* 3.2 5.9 - - - +
644B LEU 2.7 34.8 + - - +
646B GLY* 4.3 0.7 - - - -
662B TYR* 3.5 42.7 - - + -
663B VAL 3.2 15.7 - - - -
664B ARG* 3.3 33.9 - - + -
665B ASP 5.0 0.7 - - - +
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Residues in contact with THR 636 (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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634B ARG 4.4 0.3 + - - -
635B TRP* 1.3 74.4 - - - +
637B HIS* 1.3 74.4 + - - +
641B ASN* 3.7 14.1 - - - +
642B ASP 3.4 8.7 - - - +
643B GLU* 3.7 9.0 + - + -
662B TYR* 3.5 3.1 - - - -
663B VAL* 2.7 38.1 + - - +
691B PHE* 3.4 28.3 - - + +
692B ASN* 3.6 21.1 + - - -
739B ARG* 5.2 0.2 - - - +
740B ASN* 3.6 22.4 + - - +
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Residues in contact with HIS 637 (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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636B THR* 1.3 77.6 - - - +
638B LEU* 1.3 77.5 + - - +
639B TRP* 3.0 44.1 + + - -
640B HIS* 3.0 42.9 + + + -
641B ASN* 3.1 16.4 + - - +
642B ASP* 2.8 34.4 + - - +
654B HIS* 4.8 3.6 - + - -
659B LEU 3.3 20.9 + - - -
660B PRO* 4.6 1.1 - - + -
661B VAL* 3.5 22.5 + - + -
662B TYR* 3.3 21.5 - + + -
663B VAL* 4.5 0.2 - - - -
691B PHE* 4.6 0.3 - - - -
739B ARG* 4.3 1.7 + - - -
2001B MPO 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