Contacts of the helix formed by residues 760 - 768 (chain B) in PDB entry 3KZ1
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 PHE 760 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755B VAL* 4.2 5.2 - - + -
756B LEU* 3.3 19.1 + - + +
759B ILE* 1.3 83.3 - - + +
761B TYR* 1.3 70.0 + - - +
762B GLN 3.3 1.8 - - - -
763B ARG* 3.1 4.0 + - - +
764B MET* 2.8 44.7 + - + +
779B PHE* 4.2 9.4 - - + -
856B PHE* 4.3 1.7 - + - -
857B MET* 4.1 9.9 - - - -
860B ALA* 3.7 23.8 - - + -
861B GLU* 4.0 18.2 - - + -
866B CYS* 3.7 29.2 - - - -
870B GLN 5.1 0.2 - - - -
871B LEU* 3.7 44.4 - - + -
874B LEU* 4.2 14.1 - - + -
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Residues in contact with TYR 761 (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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756B LEU 3.0 12.2 + - - +
757B ASP* 3.6 12.8 - - - +
760B PHE* 1.3 77.0 - - - +
762B GLN* 1.3 94.0 + - - +
764B MET* 3.2 4.4 + - - +
765B LYS* 3.0 50.4 + - + +
772B ARG* 5.5 4.5 - - - -
775B LEU* 3.9 25.1 - - + +
776B ALA* 5.8 0.9 - - - -
779B PHE* 3.5 51.2 + + + -
782B LEU* 4.1 14.8 - - + -
783B PRO* 5.5 10.1 - - + -
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Residues in contact with GLN 762 (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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757B ASP* 3.0 52.5 + - - +
758B LEU* 3.9 15.9 - - + +
761B TYR* 1.3 93.6 - - - +
763B ARG* 1.3 58.1 + - - +
765B LYS* 3.5 17.3 + - - +
766B LYS* 3.0 29.0 + - - +
783B PRO* 5.6 3.8 - - - +
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Residues in contact with ARG 763 (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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758B LEU 4.2 8.1 + - - +
759B ILE* 3.7 31.7 + - - +
760B PHE 3.1 2.6 + - - -
762B GLN* 1.3 78.3 - - + +
764B MET* 1.3 62.7 + - - +
766B LYS* 4.4 9.2 - - + -
767B GLU* 3.1 48.6 + - - +
856B PHE* 3.6 34.0 + - + +
859B GLU* 3.7 35.8 + - - +
860B ALA* 3.5 23.6 - - - +
863B HIS* 5.5 5.3 + - - +
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Residues in contact with MET 764 (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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760B PHE* 2.8 41.2 + - + +
761B TYR 3.6 3.4 - - - +
763B ARG* 1.3 73.8 - - - +
765B LYS* 1.3 67.3 + - - +
768B ASN* 2.9 21.5 + - - -
769B LEU* 3.4 25.5 + - + -
770B MET* 3.8 11.8 + - + +
775B LEU* 3.8 19.0 - - + +
778B LEU* 3.7 24.5 - - + -
779B PHE* 4.0 7.0 - - + -
856B PHE* 3.6 20.6 - - + -
857B MET* 3.6 31.0 - - + -
871B LEU* 4.0 9.4 - - + -
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Residues in contact with LYS 765 (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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761B TYR* 3.0 47.1 + - + +
762B GLN* 3.7 16.5 + - - +
764B MET* 1.3 79.4 - - - +
766B LYS* 1.3 60.5 + - - +
768B ASN* 3.7 12.4 + - - +
772B ARG* 3.5 49.1 + - - +
775B LEU* 3.7 13.8 - - + +
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Residues in contact with LYS 766 (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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762B GLN 3.0 19.1 + - - +
763B ARG* 4.0 10.5 - - + +
764B MET 3.2 0.2 - - - -
765B LYS* 1.3 79.5 - - - +
767B GLU* 1.3 64.2 + - + +
768B ASN* 3.2 7.2 + - - -
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Residues in contact with GLU 767 (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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763B ARG* 3.1 42.6 + - - +
764B MET 4.7 0.2 - - - +
766B LYS* 1.3 80.7 - - + +
768B ASN* 1.3 71.2 + - - +
769B LEU* 3.4 2.3 - - - +
852B ARG* 4.5 8.5 + - - -
856B PHE* 3.6 29.9 - - + -
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Residues in contact with ASN 768 (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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764B MET 2.9 9.9 + - - -
765B LYS* 3.7 12.8 + - - +
766B LYS 3.2 7.9 + - - -
767B GLU* 1.3 81.9 - - - +
769B LEU* 1.3 67.2 + - - +
770B MET 3.3 13.0 + - - +
771B PRO* 5.7 0.9 - - - +
772B ARG* 4.3 13.0 + - - +
852B ARG* 4.2 7.8 + - - -
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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