Contacts of the helix formed by residues 744 - 758 (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 ASN 744 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738B LYS* 3.2 23.9 + - - +
739B TRP 5.1 1.6 + - - -
740B ASP 2.4 28.2 + - - +
741B THR* 3.0 25.4 + - + +
743B ASN* 1.3 82.6 - - - +
745B PRO* 1.3 64.2 - - + +
746B LEU* 4.2 10.3 - - + +
747B TYR* 2.7 32.4 + - - +
748B LYS* 3.7 3.7 + - - +
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Residues in contact with PRO 745 (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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738B LYS* 3.9 24.9 - - - +
743B ASN 3.9 2.0 - - - +
744B ASN* 1.3 88.0 - - + +
746B LEU* 1.3 62.5 + - - +
748B LYS* 3.0 16.6 + - + +
749B GLU* 2.9 37.9 + - + +
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Residues in contact with LEU 746 (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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741B THR* 5.3 1.8 - - - +
744B ASN* 2.9 10.2 + - + +
745B PRO* 1.3 79.1 - - - +
747B TYR* 1.3 63.6 + - - +
749B GLU* 3.3 20.2 + - + +
750B ALA* 3.0 25.2 + - + +
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Residues in contact with TYR 747 (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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741B THR 3.3 10.4 + - - +
742B ALA* 3.0 45.3 - - + +
744B ASN 2.7 15.3 + - - +
746B LEU* 1.3 74.2 - - - +
748B LYS* 1.3 69.0 + - + +
750B ALA* 3.3 9.9 + - + +
751B THR* 2.9 40.8 + - + +
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Residues in contact with LYS 748 (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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734B ARG* 5.7 5.0 - - - +
742B ALA 5.6 0.9 - - - +
743B ASN* 5.1 11.4 - - - +
744B ASN 4.6 4.3 - - - +
745B PRO* 3.0 15.8 + - + +
747B TYR* 1.3 82.8 - - + +
749B GLU* 1.3 67.4 + - + +
751B THR* 3.0 9.6 + - - -
752B SER* 3.0 23.0 + - - -
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Residues in contact with GLU 749 (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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745B PRO* 2.9 28.0 + - + +
746B LEU* 3.5 25.1 - - + +
748B LYS* 1.3 77.1 - - + +
750B ALA* 1.3 62.1 + - - +
752B SER* 2.5 24.7 + - - -
753B THR* 3.0 13.0 + - - -
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Residues in contact with ALA 750 (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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746B LEU* 3.0 19.5 + - + +
747B TYR* 3.5 13.5 - - + +
748B LYS 3.2 0.2 - - - -
749B GLU* 1.3 76.2 - - - +
751B THR* 1.3 62.5 + - - +
753B THR* 3.2 17.4 + - - -
754B PHE* 3.2 13.5 + - - +
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Residues in contact with THR 751 (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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747B TYR* 2.9 35.4 + - + +
748B LYS* 3.0 10.3 + - - -
750B ALA* 1.3 77.2 - - - +
752B SER* 1.3 61.1 + - - +
754B PHE* 3.2 9.5 + - + +
755B THR* 2.9 29.9 + - - +
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Residues in contact with SER 752 (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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748B LYS 3.0 10.8 + - - -
749B GLU* 2.5 28.2 + - - -
751B THR* 1.3 76.6 - - - +
753B THR* 1.3 63.0 + - - +
755B THR* 3.3 11.2 + - - -
756B ASN* 3.3 19.4 + - - +
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Residues in contact with THR 753 (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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749B GLU 3.0 14.1 + - - -
750B ALA* 3.3 12.3 - - - -
751B THR 3.1 0.6 - - - -
752B SER* 1.3 80.3 + - - +
754B PHE* 1.3 64.1 + - - +
756B ASN* 3.1 17.0 + - + +
757B ILE* 3.2 25.8 + - + +
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Residues in contact with PHE 754 (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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750B ALA 3.2 7.6 + - - +
751B THR* 3.2 13.3 + - + +
753B THR* 1.3 79.4 - - - +
755B THR* 1.3 58.3 + - - +
757B ILE* 3.1 13.6 + - + +
758B THR* 2.7 70.3 + - + -
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Residues in contact with THR 755 (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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751B THR* 2.9 21.9 + - - +
752B SER* 3.4 11.8 + - - -
753B THR 3.2 0.2 - - - -
754B PHE* 1.3 79.0 - - - +
756B ASN* 1.3 57.7 - - - +
758B THR* 3.7 10.5 - - + -
759B TYR* 3.0 39.6 + - + +
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Residues in contact with ASN 756 (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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752B SER 3.3 7.8 + - - +
753B THR* 3.1 12.8 + - + +
755B THR* 1.3 80.8 - - - +
757B ILE* 1.3 59.3 + - - +
759B TYR 2.8 29.5 + - - +
760B ARG* 2.8 51.5 + - - +
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Residues in contact with ILE 757 (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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753B THR* 3.4 27.8 - - + +
754B PHE* 3.1 15.1 + - + +
756B ASN* 1.3 78.1 - - - +
758B THR* 1.3 60.6 + - - +
759B TYR 2.9 9.7 + - - -
760B ARG* 3.7 33.5 + - - +
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Residues in contact with THR 758 (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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754B PHE* 2.7 50.3 + - + +
755B THR* 3.4 21.3 - - + +
757B ILE* 1.3 73.5 - - - +
759B TYR* 1.3 67.4 + - + +
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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