Contacts of the strand formed by residues 729 - 733 (chain D) in PDB entry 2OX8
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 729 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D TYR* 4.1 11.4 - - + -
620D TYR 3.2 15.0 - - - +
621D PHE* 3.3 39.5 - - + -
635D CYS* 4.5 0.7 - - - -
642D LEU* 3.3 7.8 - - - +
643D VAL* 2.7 52.9 + - + +
654D ILE* 4.1 12.6 - - + -
658D MET* 5.2 2.0 - - + -
664D HIS* 2.9 37.0 - - + +
665D TRP 4.0 5.1 + - - +
666D ILE* 5.8 0.2 - - + -
711D LEU* 5.2 6.3 - - + -
728D PHE* 1.3 75.4 - - - +
730D CYS* 1.3 69.9 + - - +
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Residues in contact with CYS 730 (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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611D TRP* 4.2 16.4 - - + -
618D CYS 4.4 0.2 - - - -
619D TYR* 3.1 24.0 - - - +
620D TYR* 3.2 12.6 + - + -
634D PHE* 4.0 17.9 - - - -
635D CYS* 2.0 52.9 - - - -
638D LYS* 5.5 0.4 - - - -
640D SER* 3.4 14.1 - - - +
641D HIS 3.3 5.6 - - - -
728D PHE* 4.2 6.3 - - - -
729D ILE* 1.3 81.1 - - - +
731D GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 731 (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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2D ZN 2.0 36.7 - - - -
5D CL 3.5 4.9 - - - +
617D LYS* 3.3 27.9 - - + +
618D CYS 3.3 7.4 - - - +
619D TYR* 3.0 26.4 + - + -
640D SER* 3.1 15.3 - - - -
641D HIS* 2.8 33.3 + - + +
643D VAL* 3.8 14.6 - - - -
644D PHE* 3.7 10.6 + - - +
650D GLU* 2.9 5.7 - - - +
730D CYS* 1.3 76.0 - - - +
732D LYS* 1.3 77.1 + - - +
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Residues in contact with LYS 732 (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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608D PRO* 3.7 25.6 - - - +
611D TRP* 3.6 31.8 - - + -
617D LYS* 4.0 3.8 - - - -
618D CYS* 2.7 46.9 + - + +
638D LYS* 4.2 14.4 + - - +
639D SER* 4.1 19.6 - - - +
640D SER* 4.0 6.5 - - - -
641D HIS* 5.0 6.1 - - + -
731D GLU* 1.3 83.3 - - - +
733D ASP* 1.3 66.5 + - - +
734D ARG 3.5 0.2 + - - -
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Residues in contact with ASP 733 (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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616D ASP* 2.3 37.5 - - - +
617D LYS* 3.6 24.2 + - + +
641D HIS* 5.9 0.2 + - - -
732D LYS* 1.3 76.4 - - - +
734D ARG* 1.3 90.2 + - - +
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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