Contacts of the strand formed by residues 667 - 671 (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 THR 667 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B ASN* 3.6 37.3 + - + +
663B VAL* 3.7 16.2 - - + -
664B ARG* 2.4 40.6 + - - +
665B ASP 3.1 3.0 + - - -
666B ASN* 1.3 78.9 + - - +
668B LEU* 1.3 62.7 + - - +
669B LEU* 3.7 15.3 - - + +
689B HIS 3.4 1.4 - - - +
690B LEU* 3.4 4.9 - - - +
691B PHE* 2.7 35.4 + - + -
699B ALA* 4.1 2.0 - - - -
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ASN* 5.5 2.3 + - - +
667B THR* 1.3 75.8 - - - +
669B LEU* 1.3 58.4 + - - +
688B PHE* 4.5 6.3 - - + -
689B HIS 3.4 9.9 - - - +
690B LEU* 3.6 18.4 - - + -
699B ALA* 3.6 29.2 - - + +
700B VAL 4.0 6.2 + - - +
701B CYS* 3.0 33.3 - - + +
714B LEU* 3.2 48.2 - - + +
716B ALA* 4.1 7.6 - - + +
736B LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B MET* 5.9 3.6 - - + -
572B TYR* 3.3 50.7 - - + -
613B ASN* 4.6 3.6 - - + +
614B VAL* 5.9 4.7 - - + -
638B LEU* 3.7 31.2 - - + -
663B VAL* 4.3 11.2 - - + -
667B THR* 3.7 11.0 - - + -
668B LEU* 1.3 76.7 - - - +
670B ALA* 1.3 61.8 + - - +
671B LEU* 3.9 15.9 - - + -
687B ALA 4.0 0.2 - - - +
688B PHE* 3.2 6.2 - - - -
689B HIS* 2.8 34.9 + - + +
691B PHE* 3.9 22.9 - - + -
701B CYS* 4.1 0.4 - - - -
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Residues in contact with ALA 670 (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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568B ARG 4.4 0.2 - - - +
569B MET* 4.6 0.9 - - - +
571B PRO* 3.3 26.5 - - + +
572B TYR* 3.6 18.3 + - - +
669B LEU* 1.3 78.6 - - - +
671B LEU* 1.3 63.5 + - - +
686B THR* 4.1 8.5 - - + -
687B ALA 4.1 2.9 - - - -
688B PHE* 3.7 15.9 - - + -
701B CYS* 3.4 25.6 - - - -
703B VAL* 4.2 5.6 - - + -
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Residues in contact with LEU 671 (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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565B LEU* 6.3 2.9 - - + -
568B ARG* 3.4 32.3 - - + +
569B MET* 5.3 9.9 - - + -
571B PRO* 3.9 3.1 - - - -
638B LEU* 4.9 16.2 - - + +
669B LEU* 3.9 25.8 - - + -
670B ALA* 1.3 80.9 - - - +
672B GLY* 1.3 61.7 + - - +
686B THR* 3.4 5.2 - - - +
687B ALA* 3.0 36.3 + - - +
689B HIS* 3.4 34.8 - - + +
691B PHE* 6.0 0.2 - - + -
739B ARG* 5.3 3.1 - - - +
3010B SO4 4.2 8.3 - - - +
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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