Contacts of the helix formed by residues 764 - 779 (chain D) in PDB entry 4X52
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727D LYS* 3.4 24.5 + - - +
728D TYR* 3.9 1.1 - - + +
762D ILE* 4.7 3.1 - - + -
763D GLU* 1.3 76.2 - - - +
765D SER* 1.3 58.4 + - - +
766D GLU* 3.3 14.2 + - - +
767D LEU* 3.2 29.9 + - + +
768D LEU* 2.9 25.5 + - - +
798D CYS 2.8 29.8 + - - +
799D SER* 3.2 24.2 + - - +
886D TYR* 3.2 16.4 + - + -
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Residues in contact with SER 765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727D LYS 4.7 3.1 + - - -
763D GLU* 4.1 5.8 - - - +
764D ASN* 1.3 68.9 + - - +
766D GLU* 1.3 57.7 + - - +
768D LEU* 3.3 9.0 + - - +
769D ASP* 2.8 49.1 + - - +
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Residues in contact with GLU 766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727D LYS* 3.8 33.3 + - + +
764D ASN* 3.3 9.1 + - - +
765D SER* 1.3 79.0 + - - +
767D LEU* 1.3 68.3 + - + +
769D ASP* 3.9 5.7 - - - +
770D LYS* 3.2 50.3 + - - +
799D SER 4.7 4.0 - - - +
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Residues in contact with LEU 767 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764D ASN* 3.2 35.2 + - + +
766D GLU* 1.3 85.9 - - - +
768D LEU* 1.3 58.1 + - - +
770D LYS* 3.5 15.5 + - + +
771D PHE* 3.1 28.4 + - - +
798D CYS 3.8 8.3 - - - +
799D SER 4.2 4.7 - - - +
800D ASN* 4.2 5.8 - - - +
801D ASN* 3.7 46.3 + - + +
882D LYS* 6.0 0.9 - - + -
885D VAL 4.7 2.6 - - - +
886D TYR* 3.8 12.8 - - + -
887D PRO* 3.9 24.2 - - + -
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Residues in contact with LEU 768 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763D GLU* 6.5 0.4 - - + -
764D ASN 2.9 17.7 + - - +
765D SER* 3.7 9.4 - - - +
767D LEU* 1.3 77.0 - - - +
769D ASP* 1.4 56.2 + - - +
771D PHE* 3.3 11.6 + - + +
772D THR* 2.8 50.7 + - - +
886D TYR* 3.6 34.9 - - + +
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Residues in contact with ASP 769 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D SER* 2.8 32.6 + - - +
766D GLU* 3.9 6.1 + - - +
767D LEU 3.4 0.2 - - - -
768D LEU* 1.4 77.5 - - - +
770D LYS* 1.4 57.2 + - + +
772D THR* 4.0 5.6 - - - -
773D TRP* 3.0 31.0 + - - +
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Residues in contact with LYS 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766D GLU* 3.2 40.1 + - + +
767D LEU* 3.8 15.2 - - + +
769D ASP* 1.4 76.2 - - + +
771D PHE* 1.4 57.5 + - - +
773D TRP* 3.5 7.1 + - - +
774D LYS* 3.0 28.2 + - - +
883D ASP* 3.6 39.0 + - + +
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Residues in contact with PHE 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767D LEU 3.1 18.1 + - - +
768D LEU* 3.6 11.9 - - + +
770D LYS* 1.4 72.8 - - - +
772D THR* 1.4 61.1 + - - +
774D LYS* 3.1 4.2 + - - +
775D LYS* 2.8 54.5 + - + +
782D GLY* 4.6 5.8 - - - -
844D GLN* 3.3 45.3 - - + -
845D VAL 4.5 0.7 - - - -
846D LEU* 3.6 23.0 - - + +
883D ASP* 3.4 14.5 + - - +
884D GLN 3.5 12.6 - - - -
885D VAL 3.5 25.6 - - - +
886D TYR* 3.7 15.9 - - + -
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Residues in contact with THR 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768D LEU* 2.8 39.1 + - - +
769D ASP* 4.0 5.4 - - - -
771D PHE* 1.4 74.8 - - - +
773D TRP* 1.3 62.1 + - - +
775D LYS* 3.4 11.9 + - + +
776D SER* 3.1 24.1 + - - -
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Residues in contact with TRP 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769D ASP 3.0 18.8 + - - +
770D LYS* 3.7 7.2 - - - +
772D THR* 1.3 77.5 - - - +
774D LYS* 1.3 56.3 + - + +
776D SER* 3.2 16.9 + - - -
777D GLN* 3.0 70.4 + - + +
883D ASP* 5.9 2.2 - - - -
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Residues in contact with LYS 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770D LYS 3.0 10.6 + - - +
771D PHE 3.6 2.0 - - - +
773D TRP* 1.3 75.2 - - + +
775D LYS* 1.4 56.5 + - - +
777D GLN* 3.3 23.3 + - + +
778D MET* 2.9 55.4 + - + +
846D LEU* 3.8 11.4 - - + -
881D GLN* 3.1 36.0 + - - +
883D ASP* 3.3 34.8 - - + +
884D GLN* 3.8 15.0 - - + -
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Residues in contact with LYS 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771D PHE* 2.8 37.2 + - + +
772D THR* 3.6 12.6 - - + +
774D LYS* 1.4 70.3 - - - +
776D SER* 1.4 53.5 + - - +
778D MET* 4.6 0.4 - - - -
779D LYS* 2.8 32.1 + - - -
780D GLU 3.4 15.3 + - - +
781D GLU* 3.8 34.9 + - - +
782D GLY 4.7 3.6 - - - +
846D LEU* 3.5 21.7 - - + +
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Residues in contact with SER 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772D THR* 3.1 14.9 + - - -
773D TRP* 3.4 24.6 - - - -
774D LYS 3.2 0.2 - - - -
775D LYS* 1.4 73.2 - - - +
777D GLN* 1.3 63.4 + - - +
779D LYS* 3.4 22.9 - - - +
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Residues in contact with GLN 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773D TRP* 3.0 61.5 + - + +
774D LYS* 3.5 30.0 + - + +
776D SER* 1.3 77.1 - - - +
778D MET* 1.3 62.2 + - + +
779D LYS* 4.3 7.8 - - - +
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Residues in contact with MET 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D LYS* 2.9 48.0 + - + +
775D LYS* 4.0 3.8 - - - +
777D GLN* 1.3 77.1 - - + +
779D LYS* 1.3 69.9 + - - +
780D GLU* 3.3 36.2 + - + +
846D LEU* 3.7 39.0 - - + +
848D GLY* 4.0 3.8 - - - -
865D ASP* 3.6 35.4 - - + +
884D GLN* 4.0 5.2 - - - +
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Residues in contact with LYS 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775D LYS 2.8 11.9 + - - -
776D SER* 3.4 16.6 - - - +
777D GLN* 4.3 6.3 - - - +
778D MET* 1.3 79.2 - - - +
780D GLU* 1.3 62.4 + - - +
781D GLU* 5.7 0.7 - - - -
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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