Contacts of the strand formed by residues 672 - 677 (chain B) in PDB entry 2XTA
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 ILE 672 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B VAL* 4.2 20.0 - - + -
525B CYS* 5.7 0.2 - - - -
638B VAL* 4.2 20.2 - - + -
639B PRO 3.0 8.3 + - - +
640B LEU* 3.5 23.9 - - + +
641B MET 2.9 26.2 + - - -
671B THR* 1.3 71.4 - - - +
673B HIS* 1.3 61.7 + - - +
674B ILE* 4.7 1.3 - - + -
724B ALA* 3.5 37.5 - - + +
725B VAL* 3.9 13.7 - - + +
728B ARG* 3.7 20.4 - - + -
735B VAL* 3.8 8.5 - - + +
737B ILE* 4.4 17.9 - - + -
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Residues in contact with HIS 673 (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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614B GLU* 5.2 1.1 - - - -
641B MET* 3.2 29.2 - - + +
643B HIS* 3.0 28.0 + - + +
648B PHE* 4.3 6.7 - + + -
657B THR* 6.1 2.0 - - + -
658B LEU* 3.8 15.9 - - + +
671B THR* 3.5 27.2 - - + +
672B ILE* 1.3 72.7 - - - +
674B ILE* 1.3 64.6 + - - +
675B VAL* 4.1 0.7 - - + -
734B ASP* 2.8 27.6 + - + -
735B VAL 2.9 15.3 + - - +
736B VAL* 3.7 28.7 - - + -
737B ILE* 2.8 28.9 + - - +
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Residues in contact with ILE 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 3.9 22.7 - - + -
517B MET* 3.9 35.0 - - + -
518B MET* 4.0 22.0 - - + -
521B VAL* 4.2 11.2 - - + -
640B LEU* 3.8 24.0 - - + -
641B MET 2.9 8.5 + - - +
642B LEU* 3.4 12.4 - - + +
643B HIS* 2.9 24.7 + - - +
672B ILE* 4.7 1.1 - - + -
673B HIS* 1.3 76.8 - - - +
675B VAL* 1.3 72.6 + - - +
676B VAL* 3.8 2.8 + - + +
737B ILE* 3.4 15.9 - - + +
739B MET* 4.8 3.1 - - + -
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Residues in contact with VAL 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B HIS* 3.5 12.3 - - + +
644B GLY 3.8 7.2 - - - +
645B ASP* 3.8 22.7 - - - +
648B PHE* 4.0 22.2 - - + -
674B ILE* 1.3 74.2 - - - +
676B VAL* 1.3 59.7 + - - +
677B ASN* 3.1 7.0 + - + +
695B CYS* 3.7 22.9 - - - -
696B THR* 3.8 23.1 - - + -
736B VAL* 4.3 5.2 - - + -
737B ILE 2.8 16.1 + - - +
738B ASP* 4.4 6.3 - - - -
739B MET* 2.8 32.1 + - - +
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Residues in contact with VAL 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 5.0 4.9 - - + -
511B ALA* 3.8 17.9 - - + -
514B VAL* 4.0 29.2 - - + -
540B ARG* 4.9 14.1 - - - +
642B LEU* 4.4 14.1 - - + -
643B HIS 2.7 18.8 + - - +
644B GLY* 3.9 5.1 - - - -
645B ASP* 3.8 14.9 + - - +
674B ILE* 4.6 3.6 - - + +
675B VAL* 1.3 69.8 - - - +
677B ASN* 1.3 57.6 + - - +
678B ASN* 3.3 13.2 + - - +
739B MET* 4.2 7.0 - - + -
741B CYS* 3.8 19.7 - - - -
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Residues in contact with ASN 677 (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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645B ASP* 3.3 25.5 - - + +
675B VAL* 3.1 4.0 + - + +
676B VAL* 1.3 69.2 - - - +
678B ASN* 1.4 57.0 + - - +
679B GLN* 3.3 24.7 + - - +
690B ARG* 5.1 8.7 + - - +
694B TYR* 6.2 0.2 - - - +
695B CYS* 3.7 9.9 - - - +
738B ASP* 2.8 37.9 + - - +
739B MET 2.9 15.4 + - - +
740B LEU* 3.4 14.5 - - - +
741B CYS* 2.9 24.8 + - - +
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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