Contacts of the helix formed by residues 709 - 724 (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 SER 709 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710B PRO* 1.3 78.9 - - - +
711B GLU* 3.1 16.0 + - - +
712B CYS* 2.7 47.9 + - - +
713B LEU* 3.6 3.8 + - - +
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Residues in contact with PRO 710 (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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709B SER* 1.3 88.4 - - - +
711B GLU* 1.3 63.0 + - + +
713B LEU* 3.2 11.9 + - + +
714B ILE* 3.1 32.5 + - + +
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Residues in contact with GLU 711 (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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709B SER* 3.2 18.6 + - - +
710B PRO* 1.3 81.5 - - + +
712B CYS* 1.3 70.9 + - - +
714B ILE* 3.4 13.0 + - - +
715B TRP* 3.0 23.6 + - - +
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Residues in contact with CYS 712 (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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709B SER* 2.7 36.1 + - - +
711B GLU* 1.3 91.2 - - - +
713B LEU* 1.3 62.5 + - - +
715B TRP* 3.3 12.4 + - + +
716B LYS* 3.2 32.6 + - - +
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Residues in contact with LEU 713 (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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709B SER 3.6 2.9 + - - +
710B PRO* 3.2 15.5 + - + +
712B CYS* 1.3 79.8 - - - +
714B ILE* 1.3 64.6 + - + +
716B LYS* 3.1 30.3 + - + +
717B LEU* 3.3 27.1 - - + +
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Residues in contact with ILE 714 (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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710B PRO* 3.1 22.1 + - + +
711B GLU* 3.6 10.5 - - - +
712B CYS 3.3 0.2 - - - -
713B LEU* 1.3 78.9 - - + +
715B TRP* 1.3 63.8 + - - +
717B LEU* 2.9 19.8 + - + +
718B LEU* 3.1 31.9 + - + +
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Residues in contact with TRP 715 (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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711B GLU 3.0 13.6 + - - +
712B CYS* 3.4 15.5 - - + +
713B LEU 3.2 0.2 - - - -
714B ILE* 1.3 77.0 - - - +
716B LYS* 1.3 76.6 + - + +
718B LEU* 3.1 30.5 + - + +
719B ILE* 3.2 45.3 + - + +
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Residues in contact with LYS 716 (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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712B CYS* 3.4 22.4 - - - +
713B LEU* 3.3 23.6 - - + +
714B ILE 3.1 0.6 - - - -
715B TRP* 1.3 90.2 - - + +
717B LEU* 1.3 66.8 + - + +
719B ILE* 3.1 24.4 + - + +
720B THR* 3.2 15.3 + - - -
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Residues in contact with LEU 717 (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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713B LEU* 3.3 28.9 - - + +
714B ILE* 2.9 13.3 + - + +
716B LYS* 1.3 80.6 - - + +
718B LEU* 1.3 62.2 + - + +
720B THR* 3.2 13.0 + - + +
721B ILE* 2.9 46.1 + - + +
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Residues in contact with LEU 718 (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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714B ILE* 3.1 32.1 - - + +
715B TRP* 3.1 23.3 + - + +
717B LEU* 1.3 81.4 - - + +
719B ILE* 1.3 53.6 + - + +
721B ILE* 3.7 11.0 - - + +
722B HIS* 2.7 37.7 + - - +
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Residues in contact with ILE 719 (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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715B TRP* 3.3 61.9 - - + +
716B LYS* 3.1 14.1 + - + +
718B LEU* 1.3 78.4 - - + +
720B THR* 1.3 58.7 + - - +
722B HIS* 3.7 6.3 + - - +
723B ASP* 3.0 29.8 + - + +
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Residues in contact with THR 720 (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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716B LYS 3.2 11.0 + - - -
717B LEU* 3.2 15.9 + - + +
719B ILE* 1.3 79.7 - - - +
721B ILE* 1.3 65.1 + - + +
723B ASP* 3.2 9.1 + - + +
724B ARG* 3.1 34.9 + - + +
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Residues in contact with ILE 721 (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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717B LEU* 2.9 36.5 + - + +
718B LEU* 3.7 12.1 - - + +
720B THR* 1.3 78.6 - - + +
722B HIS* 1.3 64.2 + - - +
724B ARG* 3.1 29.8 + - - +
727B PHE* 3.2 53.3 - - + +
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Residues in contact with HIS 722 (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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718B LEU 2.7 23.2 + - - +
719B ILE* 3.7 6.1 - - - +
721B ILE* 1.3 75.1 - - - +
723B ASP* 1.3 63.8 + - - +
724B ARG 3.5 5.4 + - - +
725B LYS* 5.4 0.5 - - - -
727B PHE* 5.0 7.0 - + - -
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Residues in contact with ASP 723 (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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719B ILE* 3.0 16.1 + - + +
720B THR* 3.4 12.6 - - + +
721B ILE 3.1 0.2 - - - -
722B HIS* 1.3 80.6 + - - +
724B ARG* 1.3 62.4 + - + +
725B LYS* 3.2 11.6 + - - +
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Residues in contact with ARG 724 (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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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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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