Contacts of the helix formed by residues 724 - 737 (chain B) in PDB entry 2KV9
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 ARG 724 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720B THR* 3.1 26.2 + - + +
721B ILE* 3.1 25.5 + - - +
722B HIS 3.9 3.9 - - - +
723B ASP* 1.3 76.2 - - + +
725B LYS* 1.3 65.2 + - - +
726B GLU* 3.0 37.0 + - + +
727B PHE* 3.2 16.3 + - + +
728B ALA* 3.9 2.8 + - - +
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Residues in contact with LYS 725 (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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722B HIS 5.4 0.4 - - - -
723B ASP 3.2 9.5 + - - +
724B ARG* 1.3 69.9 - - - +
726B GLU* 1.3 66.8 + - + +
728B ALA* 3.1 10.9 + - - +
729B LYS* 3.0 44.6 + - - +
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Residues in contact with GLU 726 (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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724B ARG* 3.0 33.8 + - + +
725B LYS* 1.3 80.8 - - + +
727B PHE* 1.3 61.8 + - - +
729B LYS* 3.2 18.8 + - + +
730B PHE* 2.9 23.9 + - - +
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Residues in contact with PHE 727 (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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721B ILE* 3.2 44.2 - - + +
722B HIS* 5.0 5.6 - + - -
724B ARG* 3.2 18.9 + - + +
725B LYS 3.1 0.2 - - - -
726B GLU* 1.3 79.1 - - - +
728B ALA* 1.3 63.7 + - + +
730B PHE* 3.3 16.1 + + + +
731B GLU* 2.6 55.6 + - + +
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Residues in contact with ALA 728 (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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724B ARG 3.9 1.5 + - - +
725B LYS* 3.1 13.9 + - - +
727B PHE* 1.3 78.3 - - + +
729B LYS* 1.3 68.1 + - + +
731B GLU* 3.1 26.3 + - - +
732B GLU* 3.3 15.8 + - - +
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Residues in contact with LYS 729 (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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725B LYS* 3.0 35.0 + - - +
726B GLU* 3.5 20.6 - - + +
728B ALA* 1.3 77.5 - - + +
730B PHE* 1.3 59.3 + - - +
732B GLU* 2.7 36.7 - - - +
733B GLU* 3.1 15.6 - - + +
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Residues in contact with PHE 730 (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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726B GLU 2.9 12.5 + - - +
727B PHE* 3.5 19.3 - + + +
729B LYS* 1.3 73.8 - - - +
731B GLU* 1.3 73.0 + - + +
733B GLU* 3.2 12.7 + - + +
734B ARG* 3.0 65.6 + - + -
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Residues in contact with GLU 731 (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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727B PHE* 2.6 53.6 + - + +
728B ALA* 3.1 17.0 + - - +
730B PHE* 1.3 82.3 - - + +
732B GLU* 1.3 61.2 + - - +
734B ARG* 3.2 15.6 + - - +
735B ALA* 3.4 11.8 + - - +
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Residues in contact with GLU 732 (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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728B ALA 3.3 5.2 + - - +
729B LYS* 2.7 45.3 - - - +
731B GLU* 1.3 76.6 - - - +
733B GLU* 1.3 70.7 + - + +
735B ALA* 3.2 8.0 + - - +
736B ARG* 3.0 33.3 + - - +
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Residues in contact with GLU 733 (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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729B LYS* 3.1 17.5 - - + +
730B PHE* 3.2 17.9 + - + +
732B GLU* 1.3 86.5 - - + +
734B ARG* 1.3 61.1 + - - +
736B ARG* 3.2 22.8 + - - +
737B ALA* 2.9 25.7 + - - +
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Residues in contact with ARG 734 (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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730B PHE* 3.0 50.5 + - + +
731B GLU* 3.2 11.4 + - - +
733B GLU* 1.3 76.6 - - - +
735B ALA* 1.3 63.3 + - - +
737B ALA* 3.3 15.9 + - - +
738B LYS* 3.3 12.1 + - - +
743B ASN* 5.4 10.1 - - + +
748B LYS* 5.7 5.1 - - - +
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Residues in contact with ALA 735 (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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731B GLU 3.4 7.8 + - - +
732B GLU* 3.2 11.8 + - - +
733B GLU 3.2 0.6 - - - -
734B ARG* 1.3 79.7 - - - +
736B ARG* 1.3 59.2 + - + +
738B LYS* 2.9 33.1 - - + +
739B TRP* 4.7 2.3 + - - -
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Residues in contact with ARG 736 (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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732B GLU* 3.0 24.3 + - + +
733B GLU* 3.2 27.5 + - - +
735B ALA* 1.3 71.6 - - + +
737B ALA* 1.3 58.3 + - - +
738B LYS 2.9 5.2 - - - -
739B TRP* 2.9 33.3 + - - +
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Residues in contact with ALA 737 (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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733B GLU 2.9 15.9 + - - +
734B ARG* 3.3 9.1 + - - +
736B ARG* 1.3 72.6 - - - +
738B LYS* 1.3 54.8 + - - +
739B TRP* 3.0 10.8 + - - +
740B ASP* 4.0 8.2 + - - +
743B ASN* 3.1 27.1 - - - +
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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