Contacts of the helix formed by residues 757 - 768 (chain A) in PDB entry 3KG2
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 GLY 757 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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754A SER 3.0 17.0 + - - -
755A GLU 3.0 2.8 + - - -
756A GLN* 1.3 77.8 - - - +
758A LEU* 1.3 57.8 + - - +
759A LEU 3.3 2.5 - - - -
760A ASP* 3.6 14.7 + - - +
761A LYS* 3.0 28.3 + - - +
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Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLU* 3.4 42.8 - - + +
435A HIS* 5.1 0.9 - - - +
753A LEU* 2.9 32.8 + - + +
756A GLN* 3.0 18.4 - - + +
757A GLY* 1.3 76.2 - - - +
759A LEU* 1.3 61.4 + - - +
761A LYS* 3.4 14.8 + - + +
762A LEU* 3.0 51.1 + - + +
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Residues in contact with LEU 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TYR* 3.7 23.2 + - + +
428A LEU* 3.7 30.1 - - + -
494A PRO 5.0 0.4 - - - +
495A PHE* 3.6 36.8 - - + +
750A VAL* 3.9 8.7 - - + +
753A LEU* 3.4 12.7 + - + -
754A SER* 3.5 41.1 - - - +
757A GLY 3.3 0.2 - - - -
758A LEU* 1.3 75.8 - - - +
760A ASP* 1.3 69.9 + - - +
762A LEU* 3.2 9.2 + - + +
763A LYS* 3.1 20.8 + - - +
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Residues in contact with ASP 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A SER* 5.2 4.4 - - - +
757A GLY* 3.6 15.9 + - - +
758A LEU 3.4 0.2 - - - -
759A LEU* 1.3 80.0 - - - +
761A LYS* 1.3 62.8 + - - +
763A LYS* 3.4 8.2 + - - +
764A ASN* 3.1 34.4 + - - +
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Residues in contact with LYS 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A GLY 3.0 19.7 + - - +
758A LEU* 3.4 17.0 - - + +
759A LEU 3.1 0.2 - - - -
760A ASP* 1.3 77.0 - - - +
762A LEU* 1.3 66.7 + - + +
764A ASN* 3.3 10.0 + - - +
765A LYS* 3.0 24.2 + - + +
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Residues in contact with LEU 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TYR* 3.5 24.2 - - + +
427A ASP* 3.7 31.4 - - + +
428A LEU* 4.1 36.8 - - + +
431A GLU* 4.7 2.5 - - + +
758A LEU* 3.0 38.9 + - + +
759A LEU* 3.2 6.0 + - + +
761A LYS* 1.3 81.4 - - + +
763A LYS* 1.3 61.1 + - - +
765A LYS* 3.0 15.6 + - + +
766A TRP* 3.0 28.4 - - + +
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Residues in contact with LYS 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TYR* 3.5 10.0 - - + -
496A MET* 4.2 23.3 - - + +
497A SER 5.4 4.4 + - - -
707A THR* 5.8 3.4 - - - +
710A GLU* 3.1 34.0 + - - -
759A LEU 3.1 11.9 + - - +
760A ASP* 3.7 11.4 - - - +
762A LEU* 1.3 74.8 - - - +
764A ASN* 1.3 63.7 + - - +
766A TRP 3.2 0.5 + - - -
767A TRP* 2.8 70.6 + - + +
768A TYR* 5.1 9.7 + - + -
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Residues in contact with ASN 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760A ASP* 3.1 20.7 + - - +
761A LYS* 3.6 10.6 - - - +
763A LYS* 1.3 79.9 - - - +
765A LYS* 1.3 55.4 + - - +
768A TYR* 3.3 29.3 + - + -
769A ASP* 2.7 45.2 + - - +
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Residues in contact with LYS 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ASP* 2.9 23.5 + - - +
761A LYS* 3.0 16.4 + - + +
762A LEU* 3.0 17.4 + - + +
764A ASN* 1.3 78.7 - - - +
766A TRP* 1.3 85.3 + - + +
769A ASP* 3.7 14.0 + - + +
770A LYS* 3.0 39.2 + - + +
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Residues in contact with TRP 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A PRO* 4.3 10.4 - - + +
407A MET* 4.0 20.4 - - + -
422A GLU* 4.0 22.0 - - + -
423A GLY* 3.3 42.9 + - - -
424A TYR* 3.7 18.9 - + + +
427A ASP* 3.4 30.5 + - - -
711A TYR* 4.1 18.0 - - - -
762A LEU* 3.0 27.0 + - - +
763A LYS 3.2 1.8 + - - -
765A LYS* 1.3 101.5 - - + +
767A TRP* 1.3 80.6 + - + +
770A LYS* 4.0 33.9 - - + +
771A GLY* 4.7 1.2 + - - -
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Residues in contact with TRP 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A PRO* 3.8 23.8 - - + -
405A TYR* 3.5 44.6 - + - -
424A TYR* 3.7 30.5 - + + -
496A MET* 4.2 10.1 - - + -
707A THR* 3.1 26.5 + - - +
710A GLU* 3.9 19.3 + - + +
711A TYR* 3.6 31.6 - - + +
714A GLN* 3.3 25.9 - - - +
763A LYS* 2.8 50.3 + - + +
766A TRP* 1.3 86.3 - - + +
768A TYR* 1.3 75.7 + + + +
771A GLY* 3.6 9.4 - - - -
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Residues in contact with TYR 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710A GLU* 4.1 27.0 + - + +
714A GLN* 3.5 35.7 - - + +
763A LYS* 5.1 10.0 + - + -
764A ASN* 3.3 32.2 + - + +
767A TRP* 1.3 91.2 - + + +
769A ASP* 1.3 73.5 + - - +
770A LYS 3.4 1.1 - - - -
771A GLY* 3.1 14.5 + - - +
773A CYS 6.1 1.0 - - - -
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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