Contacts of the strand formed by residues 667 - 671 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ASN* 3.4 40.6 + - + +
663D VAL* 4.1 9.4 - - + -
664D ARG* 2.7 36.1 + - - +
665D ASP 3.3 7.3 + - - -
666D ASN* 1.3 78.2 + - - +
668D LEU* 1.3 70.8 + - - +
669D LEU* 4.1 9.6 - - + +
689D HIS 3.5 2.3 - - - +
690D LEU* 3.5 3.0 - - - +
691D PHE* 2.8 33.8 + - - -
699D ALA* 3.9 4.0 - - - +
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Residues in contact with LEU 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ASN* 5.1 2.6 + - - -
667D THR* 1.3 78.9 - - - +
669D LEU* 1.3 58.2 + - - +
688D PHE* 4.1 9.2 - - + -
689D HIS 3.5 14.1 - - - +
690D LEU* 4.1 8.1 - - + -
699D ALA* 3.6 29.3 - - + +
700D VAL 3.9 7.1 + - - +
701D CYS* 3.2 28.9 - - + +
714D LEU* 3.2 49.1 - - + +
716D ALA* 4.4 7.2 - - + +
736D LEU* 3.7 28.9 - - + -
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Residues in contact with LEU 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569D MET* 6.5 0.7 - - + -
572D TYR* 3.4 46.7 - - + -
613D ASN* 4.3 5.6 - - + +
614D VAL* 5.6 4.3 - - + -
638D LEU* 3.7 30.5 - - + -
663D VAL* 4.3 8.5 - - + -
667D THR* 4.0 18.6 - - + -
668D LEU* 1.3 75.1 - - - +
670D ALA* 1.3 62.6 + - - +
671D LEU* 4.4 15.3 - - + -
687D ALA 3.7 0.9 - - - +
688D PHE* 3.2 5.1 - - - +
689D HIS* 2.8 43.4 + - + +
691D PHE* 4.0 16.4 - - + -
701D CYS* 4.2 1.8 - - - -
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Residues in contact with ALA 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D ARG 4.4 0.2 - - - +
569D MET 4.8 0.3 - - - +
571D PRO* 3.6 19.5 - - + +
572D TYR* 3.6 28.1 + - - +
669D LEU* 1.3 75.3 - - - +
671D LEU* 1.3 67.2 + - - +
686D THR* 4.1 3.1 - - + -
687D ALA 3.9 2.5 - - - -
688D PHE* 3.7 16.4 - - + -
701D CYS* 3.4 26.1 - - - -
703D VAL* 4.0 8.1 - - + -
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Residues in contact with LEU 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D LEU* 6.5 1.6 - - + -
568D ARG* 3.5 42.2 - - + +
569D MET* 4.8 15.3 - - + -
571D PRO* 4.0 3.1 - - - -
572D TYR* 5.5 1.1 - - + -
638D LEU* 5.1 8.7 - - + -
669D LEU* 4.4 24.9 - - + -
670D ALA* 1.3 80.7 - - - +
672D GLY* 1.3 61.8 + - - +
686D THR* 3.7 5.0 - - - +
687D ALA* 2.8 45.4 + - + +
689D HIS* 3.8 26.9 - - + +
739D ARG* 4.6 7.6 - - - +
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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