Contacts of the helix formed by residues 764 - 779 (chain A) in PDB entry 2X5Y
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 764 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A LYS* 3.2 24.2 + - - +
728A TYR* 4.0 1.6 - - + -
762A ILE* 4.8 3.6 - - + -
763A GLU* 1.3 75.4 - - - +
765A SER* 1.3 58.2 + - - +
766A GLU* 3.1 11.3 + - - +
767A LEU* 3.0 32.0 + - + +
768A LEU* 2.9 28.9 + - - +
798A CYS 2.8 28.4 + - - +
799A SER* 3.1 24.0 + - - +
886A TYR* 3.0 13.0 + - + -
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Residues in contact with SER 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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727A LYS 4.2 4.8 + - - -
763A GLU* 4.2 7.3 - - - +
764A ASN* 1.3 73.3 + - - +
766A GLU* 1.3 65.8 + - - +
768A LEU* 4.3 7.4 - - - -
769A ASP* 2.9 43.7 + - - -
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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
----------------------------------------------------------
727A LYS* 4.0 39.2 + - - +
764A ASN* 3.1 7.4 + - - +
765A SER* 1.3 85.1 + - - +
767A LEU* 1.3 64.8 + - + +
769A ASP* 3.8 6.6 - - - +
770A LYS* 3.2 38.9 + - - +
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Residues in contact with LEU 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LYS* 5.4 3.6 - - - +
762A ILE* 6.4 0.2 - - + -
764A ASN* 3.0 39.1 + - + +
766A GLU* 1.3 78.6 - - + +
768A LEU* 1.3 62.2 + - - +
770A LYS* 3.4 20.2 + - + +
771A PHE* 3.0 24.3 + - - +
797A ILE 4.2 0.7 - - - +
798A CYS 3.9 7.0 - - - +
799A SER 4.1 3.8 - - - +
800A ASN* 4.4 8.1 - - - +
801A ASN* 3.8 43.2 + - + +
882A LYS* 6.3 0.4 - - + -
885A VAL 4.8 2.4 - - - +
886A TYR* 3.8 12.2 - - + -
887A PRO* 3.9 21.5 - - + -
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Residues in contact with LEU 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A GLU* 6.3 2.2 - - + -
764A ASN 2.9 17.0 + - - +
765A SER* 3.8 8.1 - - - +
766A GLU 3.3 0.2 - - - -
767A LEU* 1.3 78.0 - - - +
769A ASP* 1.3 62.5 + - - +
771A PHE* 3.2 11.8 + - + +
772A THR* 2.8 47.0 + - - +
844A GLN* 5.3 4.7 - - - +
886A TYR* 3.5 40.5 - - + +
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Residues in contact with ASP 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A SER* 2.9 29.0 + - - +
766A GLU* 3.8 6.8 - - - +
767A LEU 3.3 0.2 - - - -
768A LEU* 1.3 84.1 - - - +
770A LYS* 1.3 62.8 + - + +
772A THR* 3.9 5.9 + - - -
773A TRP* 3.1 24.1 + - - +
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Residues in contact with LYS 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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727A LYS* 6.2 0.2 - - - +
766A GLU* 3.2 24.8 + - - +
767A LEU* 3.7 19.9 - - + +
768A LEU 3.3 0.2 - - - -
769A ASP* 1.3 79.4 - - + +
771A PHE* 1.3 56.5 + - - +
773A TRP* 3.5 7.0 + - - +
774A LYS* 3.0 28.8 + - - +
883A ASP* 3.6 38.7 + - + +
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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 LEU 3.0 17.1 + - - +
768A LEU* 3.5 13.9 - - + +
770A LYS* 1.3 74.3 - - - +
772A THR* 1.3 62.8 + - - +
774A LYS* 3.2 2.3 + - - +
775A LYS* 2.9 50.1 + - - +
782A GLY* 4.2 2.5 - - - -
844A GLN* 3.4 55.6 - - + -
846A LEU* 3.5 32.5 - - + +
883A ASP* 3.5 16.5 + - - +
884A GLN 3.6 5.2 - - - -
885A VAL 3.6 20.9 - - - +
886A TYR* 3.7 14.8 - - + -
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Residues in contact with THR 772 (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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768A LEU* 2.8 38.4 + - - +
769A ASP* 3.9 7.1 + - - -
771A PHE* 1.3 75.7 - - - +
773A TRP* 1.3 62.8 + - - +
775A LYS* 3.4 14.0 + - + +
776A SER* 3.2 22.3 + - - -
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Residues in contact with TRP 773 (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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769A ASP 3.1 17.1 + - - +
770A LYS* 3.7 6.3 - - - +
772A THR* 1.3 78.4 - - - +
774A LYS* 1.3 66.7 + - + +
776A SER* 3.2 9.3 + - - -
777A GLN* 3.0 59.6 + - + +
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Residues in contact with LYS 774 (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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770A LYS 3.0 13.4 + - - +
771A PHE 3.2 1.8 + - - +
773A TRP* 1.3 81.3 - - + +
775A LYS* 1.3 57.3 + - - +
777A GLN* 3.3 10.3 + - + +
778A MET* 2.8 65.6 + - + +
846A LEU* 3.9 3.6 - - + -
865A ASP* 5.8 1.2 + - - -
881A GLN* 3.4 32.0 + - - +
883A ASP* 3.4 35.9 - - + +
884A GLN* 3.8 10.0 + - + -
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Residues in contact with LYS 775 (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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771A PHE* 2.9 43.4 + - - +
772A THR* 3.6 11.9 + - + +
773A TRP 3.2 0.2 - - - -
774A LYS* 1.3 76.1 - - - +
776A SER* 1.3 62.5 + - - +
778A MET* 3.5 2.4 + - - -
779A LYS* 3.0 19.2 + - - -
780A GLU 2.9 36.1 + - - +
781A GLU* 2.8 32.0 + - - +
782A GLY 4.0 4.5 - - - +
844A GLN* 4.9 3.4 + - - -
846A LEU* 3.5 17.2 - - + +
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Residues in contact with SER 776 (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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772A THR 3.2 11.0 + - - -
773A TRP* 3.5 12.5 - - - -
775A LYS* 1.3 81.9 - - - +
777A GLN* 1.3 67.8 + - - +
779A LYS* 3.4 17.7 + - - +
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Residues in contact with GLN 777 (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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773A TRP* 3.0 60.3 + - + +
774A LYS* 3.6 13.5 - - + +
776A SER* 1.3 82.5 + - - +
778A MET* 1.3 60.7 + - + +
779A LYS* 3.5 12.8 + - - +
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Residues in contact with MET 778 (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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774A LYS* 2.8 56.1 + - + +
775A LYS 4.0 0.2 - - - +
777A GLN* 1.3 73.6 - - + +
779A LYS* 1.3 70.2 + - - +
780A GLU* 4.0 12.4 - - + +
846A LEU* 3.7 30.5 - - + +
848A GLY* 3.7 33.9 - - - +
865A ASP* 3.7 26.2 - - + +
884A GLN* 3.9 6.5 - - - +
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Residues in contact with LYS 779 (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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775A LYS 3.0 8.3 + - - -
776A SER 3.4 12.5 + - - +
777A GLN* 3.3 10.7 + - - +
778A MET* 1.3 82.5 - - - +
780A GLU* 1.3 60.0 + - - +
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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