Contacts of the helix formed by residues 756 - 771 (chain A) in PDB entry 4KHQ
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 756 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A LYS* 3.2 24.7 + - - -
698A ILE* 5.4 1.1 - - - -
751A ARG 2.6 19.7 + - - +
752A MET* 3.8 12.0 + - - -
755A GLU* 1.3 75.7 - - - +
757A GLU* 1.3 65.5 + - - -
758A GLU 3.4 2.7 - - - -
759A SER* 3.4 3.5 + - - -
760A LEU* 3.3 18.7 + - - +
889A LEU* 5.3 0.9 - - - -
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Residues in contact with GLU 757 (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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696A LYS* 5.4 0.6 - - - +
698A ILE* 5.9 0.2 - - - +
756A GLY* 1.3 71.0 - - - -
758A GLU* 1.3 63.2 + - - +
760A LEU* 3.1 9.4 + - - +
761A GLN* 3.0 48.8 + - - +
889A LEU* 3.5 36.0 - - + +
890A ASP* 3.0 36.9 + - - +
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Residues in contact with GLU 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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756A GLY 3.4 0.6 - - - -
757A GLU* 1.3 78.6 - - - +
759A SER* 1.3 62.2 + - - +
761A GLN* 3.4 13.9 + - - +
762A GLU* 3.2 45.0 + - + +
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Residues in contact with SER 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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751A ARG* 2.8 47.5 + - - +
755A GLU* 2.5 43.7 + - - -
756A GLY 3.4 10.1 + - - -
757A GLU 3.2 0.4 - - - -
758A GLU* 1.3 78.6 - - - +
760A LEU* 1.3 62.5 + - - +
762A GLU* 3.4 8.6 + - - +
763A TYR 3.2 10.2 + - - -
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Residues in contact with LEU 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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748A CYS* 3.9 42.6 - - + +
751A ARG* 4.1 10.9 - - + +
752A MET* 3.8 18.8 - - + -
756A GLY 3.3 9.8 + - - +
757A GLU* 3.1 9.8 + - - +
759A SER* 1.3 79.6 - - - +
761A GLN* 1.3 57.7 + - - +
763A TYR* 3.4 2.0 + - + +
764A PHE* 3.0 26.7 + - + +
880A LEU* 4.4 8.3 - - + -
884A THR* 3.8 27.4 - - + -
889A LEU* 4.9 7.9 - - + -
890A ASP 3.8 17.9 - - - +
891A TYR* 4.0 11.0 - - + -
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Residues in contact with GLN 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 GLU* 3.0 36.5 + - - +
758A GLU* 3.8 11.5 - - - +
759A SER 3.3 0.4 - - - -
760A LEU* 1.3 74.1 - - - +
762A GLU* 1.3 64.3 + - + +
764A PHE* 4.0 1.4 - - - +
765A LYS* 3.2 23.7 + - - +
890A ASP* 3.0 27.2 + - - +
891A TYR 3.6 19.8 - - - +
892A GLU* 3.8 14.6 + - - -
893A LYS* 4.1 21.8 + - - +
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Residues in contact with GLU 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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751A ARG* 4.4 8.9 + - - +
758A GLU* 3.2 35.7 + - + +
759A SER* 3.6 11.4 - - - +
760A LEU 3.3 0.2 - - - -
761A GLN* 1.3 78.5 - - + +
763A TYR* 1.3 63.8 + - - +
765A LYS* 3.4 5.1 + - - +
766A GLU* 3.2 22.3 + - - +
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Residues in contact with TYR 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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743A LYS* 4.5 5.9 + - - +
744A ALA* 3.5 43.5 - - + +
747A GLU* 3.6 24.1 - - + +
748A CYS* 3.9 21.1 - - - -
751A ARG* 3.4 45.7 - - - +
759A SER 3.2 4.1 + - - +
760A LEU* 3.9 2.7 - - - +
762A GLU* 1.3 79.4 - - - +
764A PHE* 1.3 58.1 + - - +
766A GLU* 3.3 8.8 + - + +
767A PHE* 2.9 41.0 + + + +
876A PHE* 5.4 0.2 - + - -
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Residues in contact with PHE 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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748A CYS* 5.3 2.7 - - - -
760A LEU* 3.0 19.9 + - + +
761A GLN 4.0 0.7 - - - +
762A GLU 3.3 0.2 - - - -
763A TYR* 1.3 79.1 - - - +
765A LYS* 1.3 67.8 + - + +
767A PHE* 3.2 6.8 + - - +
768A GLU* 2.9 54.3 + - + +
872A LEU* 6.0 0.4 - - + -
876A PHE* 3.6 25.1 - + - -
877A ILE* 4.2 19.5 - - + -
880A LEU* 3.5 23.1 - - + -
891A TYR* 3.4 54.5 - + + +
892A GLU* 3.7 18.2 - - + -
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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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761A GLN 3.2 16.2 + - - +
762A GLU* 3.7 5.8 - - - +
764A PHE* 1.3 85.2 - - + +
766A GLU* 1.3 62.3 + - - +
768A GLU* 3.5 9.1 + - - +
769A LYS* 3.2 40.4 + - + +
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Residues in contact with GLU 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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762A GLU 3.2 12.0 + - - +
763A TYR* 3.6 13.2 - - + +
764A PHE 3.2 0.4 - - - -
765A LYS* 1.3 77.4 - - - +
767A PHE* 1.3 64.1 + - - +
769A LYS* 3.3 14.3 + - - +
770A GLU* 3.2 50.1 + - + +
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Residues in contact with PHE 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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740A ALA* 4.4 8.5 - - + -
741A VAL* 5.2 6.3 - - + -
744A ALA* 3.4 28.5 - - + -
763A TYR* 2.9 34.8 + + + +
764A PHE* 3.7 6.1 - - - +
766A GLU* 1.3 77.1 - - - +
768A GLU* 1.3 63.6 + - - +
770A GLU* 5.2 1.6 - - - -
771A PHE* 3.1 51.6 + + + +
774A LEU* 4.0 25.4 - - + -
779A ILE* 6.0 0.4 - - + -
872A LEU* 4.0 9.2 - - + -
876A PHE* 3.6 44.2 - + + -
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Residues in contact with GLU 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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764A PHE* 2.9 45.9 + - + +
765A LYS* 3.8 9.3 - - - +
766A GLU 3.2 0.2 - - - -
767A PHE* 1.3 80.7 - - - +
769A LYS* 1.3 62.4 + - + +
771A PHE* 3.3 23.6 - - + -
872A LEU* 4.0 23.5 - - + +
876A PHE* 6.2 0.2 - - - -
877A ILE* 4.9 4.5 - - - +
892A GLU* 4.3 9.1 - - - +
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Residues in contact with LYS 769 (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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765A LYS* 3.2 27.5 + - + +
766A GLU* 3.7 19.7 - - - +
767A PHE 3.3 0.4 - - - -
768A GLU* 1.3 80.9 - - + +
770A GLU* 1.3 73.1 + - + +
771A PHE 3.6 0.2 - - - -
772A ARG* 5.0 6.6 + - - +
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Residues in contact with GLU 770 (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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766A GLU* 3.2 37.6 + - + +
767A PHE* 4.6 1.8 - - - +
769A LYS* 1.3 87.7 - - + +
771A PHE* 1.3 64.8 + - - +
772A ARG 3.1 4.7 + - - -
773A GLN* 3.1 29.5 + - - +
774A LEU* 4.4 2.1 + - - +
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Residues in contact with PHE 771 (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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767A PHE* 3.1 39.7 + + + +
768A GLU 3.3 23.6 - - - -
770A GLU* 1.3 77.2 - - - +
772A ARG* 1.3 78.2 + - + +
773A GLN 3.0 2.7 + - - -
774A LEU* 3.1 32.0 + - + +
779A ILE* 4.7 10.1 - - + +
868A TYR* 3.2 52.9 - + + -
869A THR* 5.0 1.3 - - - -
871A LEU* 4.9 6.5 - - + -
872A LEU* 3.5 44.0 - - + -
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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