Contacts of the strand formed by residues 728 - 732 (chain I) in PDB entry 2VKZ
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 728 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695I ILE* 5.4 5.4 - - + -
703I LEU* 3.3 17.7 - - + +
705I LEU* 4.0 28.3 - - + -
716I VAL* 4.3 11.7 - - + +
719I ILE* 4.1 9.4 - - + +
720I ALA* 3.3 41.3 - - + +
723I HIS 5.1 1.8 - - - +
726I PHE* 3.5 14.6 - - + +
727I PRO* 1.3 78.1 - - - +
729I ALA* 1.3 61.5 + - - +
730I LEU* 3.3 4.1 + - + +
762I ASN* 2.8 25.4 + - - +
763I ILE* 3.4 7.0 - - + +
764I MET* 2.9 28.3 + - - -
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Residues in contact with ALA 729 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702I TYR* 3.5 31.8 - - + -
703I LEU 2.9 11.1 + - - +
704I GLY* 3.6 5.5 - - - -
705I LEU 3.1 21.2 + - - +
728I ILE* 1.3 69.7 - - - +
730I LEU* 1.3 58.8 + - - +
731I GLN* 2.9 17.3 + - + +
764I MET* 3.6 19.3 - - + +
766I ILE* 4.4 14.6 - - + -
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Residues in contact with LEU 730 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705I LEU 3.8 4.0 - - - +
707I PRO* 3.3 36.6 - - + -
713I ILE* 4.2 14.4 - - + +
716I VAL* 4.5 20.6 - - + -
717I ILE* 5.5 0.4 - - + -
728I ILE* 3.3 4.8 + - - +
729I ALA* 1.3 69.5 - - - +
731I GLN* 1.3 57.3 + - - +
732I TRP* 3.1 18.3 + - + +
757I ILE* 3.9 36.1 - - + -
763I ILE* 3.7 20.2 - - + -
764I MET 3.2 6.2 + - - +
765I LEU* 3.7 14.3 - - + +
766I ILE 3.1 23.2 + - - -
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Residues in contact with GLN 731 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593I LEU* 3.7 18.9 - - - +
595I PRO* 4.7 0.7 - - - +
618I GLU* 2.8 28.5 + - - +
678I PHE* 5.0 2.2 - - - -
680I THR* 3.4 11.2 + - - -
702I TYR* 5.8 0.4 + - - -
704I GLY* 4.9 0.4 - - - -
705I LEU 2.9 14.1 + - - +
706I LYS* 3.1 52.0 + - + +
729I ALA* 2.9 21.7 + - + +
730I LEU* 1.3 70.7 - - - +
732I TRP* 1.3 60.4 + - - +
733I THR* 3.1 10.4 + - - -
766I ILE* 3.5 22.6 - - + +
800I LEU* 3.9 21.5 - - + +
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Residues in contact with TRP 732 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707I PRO* 3.8 10.5 - - + -
708I GLY* 3.8 32.5 - - - -
709I SER 4.4 0.4 - - - -
713I ILE* 4.1 12.8 - - + -
730I LEU* 3.1 16.8 + - + +
731I GLN* 1.3 68.4 - - - +
733I THR* 1.3 82.0 + - - +
734I GLY* 4.4 1.3 - - - -
744I GLU* 4.7 4.7 - - + -
745I ASP 3.4 14.6 - - - -
746I ALA* 3.0 23.0 + - - +
749I PRO* 3.3 39.7 - - + -
750I MET* 2.7 47.0 - - + +
765I LEU* 5.2 1.8 - - + -
766I ILE 3.0 11.5 + - - +
767I PHE* 3.9 19.8 - + - -
768I GLY* 3.1 22.0 + - - +
796I PHE* 5.3 0.4 - - + -
800I LEU* 5.6 0.2 - - - -
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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