Contacts of the strand formed by residues 661 - 663 (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 VAL 661 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E LEU* 4.1 18.2 - - + -
569E MET* 5.9 0.4 - - - -
614E VAL* 3.7 23.6 - - + -
615E MET 3.2 4.3 - - - +
616E VAL* 4.8 4.0 - - + -
637E HIS* 3.3 9.6 + - + -
638E LEU* 2.8 45.8 + - + +
639E TRP* 3.7 22.2 - - + -
659E LEU* 3.0 38.3 + - + +
660E PRO* 1.3 74.6 - - - +
662E TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 662 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614E VAL* 3.3 3.8 - - - -
615E MET* 2.8 58.7 + - + -
628E PHE* 3.8 21.5 - + - -
630E LEU* 4.6 1.8 - - + -
635E TRP* 3.6 29.0 - - + -
636E THR 3.5 9.4 - - - -
637E HIS* 3.1 45.2 - + + -
642E ASP* 2.7 30.6 + - - -
644E LEU* 3.4 20.3 - - + +
652E GLN* 2.6 28.3 + - - -
660E PRO* 4.1 4.0 - - + -
661E VAL* 1.3 78.4 - - - +
663E VAL* 1.3 61.9 + - - +
2004E MPO 4.7 1.0 + - - -
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Residues in contact with VAL 663 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613E ASN* 3.5 11.0 - - + +
614E VAL* 4.8 8.1 - - + -
634E ARG 4.3 0.3 - - - +
635E TRP* 3.4 11.3 - - - -
636E THR* 2.8 41.1 + - - +
638E LEU* 4.0 24.7 - - + -
662E TYR* 1.3 74.3 - - - +
664E ARG* 1.3 74.1 - - - +
667E THR* 4.0 13.2 - - + -
669E LEU* 4.6 7.6 - - + -
691E PHE* 3.8 42.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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