Contacts of the helix formed by residues 764 - 779 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727B LYS* 3.4 24.1 + - - +
728B TYR* 3.9 1.7 - - + +
762B ILE* 4.7 3.1 - - + -
763B GLU* 1.3 75.4 - - - +
765B SER* 1.4 56.8 + - - +
766B GLU* 3.3 14.2 + - - +
767B LEU* 3.2 31.5 + - + +
768B LEU* 2.9 25.7 + - - +
798B CYS 2.8 29.5 + - - +
799B SER* 3.2 23.0 + - - +
886B TYR* 3.1 17.3 + - + -
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Residues in contact with SER 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B LYS 4.7 3.5 + - - -
763B GLU* 4.2 5.8 - - - +
764B ASN* 1.4 68.1 + - - +
766B GLU* 1.3 57.6 + - - +
768B LEU* 3.3 9.3 + - - +
769B ASP* 2.8 48.3 + - - +
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Residues in contact with GLU 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B LYS* 3.8 35.2 + - + +
764B ASN* 3.3 9.8 + - - +
765B SER* 1.3 79.2 + - - +
767B LEU* 1.3 66.6 + - + +
769B ASP* 3.5 6.3 + - - +
770B LYS* 3.2 48.5 + - + +
799B SER 4.8 3.1 - - - +
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Residues in contact with LEU 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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764B ASN* 3.2 37.0 + - + +
766B GLU* 1.3 85.9 - - + +
768B LEU* 1.3 56.9 + - - +
770B LYS* 3.5 15.6 + - + +
771B PHE* 3.1 27.7 + - - +
798B CYS 3.8 8.5 - - - +
799B SER 4.2 4.3 - - - +
800B ASN* 4.2 5.4 - - - +
801B ASN* 3.7 47.2 + - + +
882B LYS* 6.0 0.7 - - + -
883B ASP* 6.0 0.2 - - - -
885B VAL 4.7 2.8 - - - +
886B TYR* 3.8 12.5 - - + -
887B PRO* 3.9 22.2 - - + -
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Residues in contact with LEU 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B GLU* 6.5 1.3 - - + -
764B ASN 2.9 17.2 + - - +
765B SER* 3.3 9.6 + - - +
767B LEU* 1.3 74.1 - - - +
769B ASP* 1.3 63.6 + - - +
771B PHE* 3.3 11.3 + - + +
772B THR* 2.8 45.8 + - - +
886B TYR* 3.6 35.3 - - + +
888B GLN* 5.8 0.4 - - - +
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Residues in contact with ASP 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B SER* 2.8 34.8 + - - +
766B GLU* 3.9 6.5 + - - +
767B LEU 3.4 0.2 - - - -
768B LEU* 1.3 77.6 - - - +
770B LYS* 1.4 58.4 + - + +
772B THR* 4.0 5.4 - - - -
773B TRP* 3.0 30.0 + - - +
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Residues in contact with LYS 770 (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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766B GLU* 3.2 39.6 + - + +
767B LEU* 3.8 15.7 - - + +
768B LEU 3.3 0.2 - - - -
769B ASP* 1.4 75.9 - - + +
771B PHE* 1.4 56.3 + - - +
773B TRP* 3.5 7.2 + - - +
774B LYS* 3.0 28.1 + - - +
883B ASP* 4.0 23.6 - - + +
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Residues in contact with PHE 771 (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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767B LEU 3.1 17.4 + - - +
768B LEU* 3.3 11.9 + - + +
770B LYS* 1.4 73.6 - - - +
772B THR* 1.4 61.2 + - - +
774B LYS* 3.1 4.5 + - - +
775B LYS* 2.8 53.5 + - + +
782B GLY* 4.6 6.7 - - - -
844B GLN* 3.3 44.9 - - + -
845B VAL 4.5 0.4 - - - -
846B LEU* 3.6 23.6 - - + +
883B ASP* 3.4 12.0 + - - +
884B GLN 3.4 14.6 - - - -
885B VAL 3.5 26.9 - - - +
886B TYR* 3.7 15.3 - - + -
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Residues in contact with THR 772 (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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768B LEU* 2.8 39.0 + - - +
769B ASP* 4.0 6.5 - - - -
771B PHE* 1.4 73.2 - - - +
773B TRP* 1.3 61.6 + - - +
775B LYS* 3.5 12.2 + - + +
776B SER* 3.1 23.9 + - - -
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Residues in contact with TRP 773 (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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769B ASP 3.0 18.9 + - - +
770B LYS* 3.7 7.0 - - - +
772B THR* 1.3 75.8 - - - +
774B LYS* 1.4 59.4 + - + +
776B SER* 3.2 17.6 + - - -
777B GLN* 3.0 67.8 + - + +
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Residues in contact with LYS 774 (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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770B LYS 3.0 10.7 + - - +
771B PHE 3.6 2.2 - - - +
773B TRP* 1.4 78.7 - - + +
775B LYS* 1.3 56.0 + - - +
777B GLN* 3.3 18.3 + - + +
778B MET* 2.9 56.8 + - + +
846B LEU* 3.8 11.4 - - + -
881B GLN* 3.2 29.8 + - - +
883B ASP* 3.3 45.3 + - + +
884B GLN* 3.8 15.5 - - + -
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Residues in contact with LYS 775 (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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771B PHE* 2.8 37.9 + - + +
772B THR* 3.6 12.1 - - + +
774B LYS* 1.3 70.5 - - - +
776B SER* 1.4 53.1 + - - +
778B MET* 4.6 0.9 - - - -
779B LYS* 2.8 31.5 + - - -
780B GLU 3.4 17.6 + - - +
781B GLU* 3.8 34.5 + - - +
782B GLY 4.7 3.4 - - - +
846B LEU* 3.5 21.9 - - + +
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Residues in contact with SER 776 (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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772B THR* 3.1 14.4 + - - -
773B TRP* 3.2 24.5 + - - -
775B LYS* 1.4 75.3 - - - +
777B GLN* 1.4 64.1 + - - +
778B MET 3.5 0.2 + - - -
779B LYS* 3.6 34.7 + - - +
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Residues in contact with GLN 777 (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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773B TRP* 3.0 62.5 + - + +
774B LYS* 3.3 19.6 + - + +
776B SER* 1.4 75.6 - - - +
778B MET* 1.3 63.3 + - + +
779B LYS* 4.9 3.5 - - - +
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Residues in contact with MET 778 (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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774B LYS* 2.9 47.7 + - - +
775B LYS* 4.0 3.8 - - - +
777B GLN* 1.3 79.0 - - + +
779B LYS* 1.3 67.6 + - - +
780B GLU* 3.3 31.7 - - + +
846B LEU* 3.7 40.6 - - + +
848B GLY* 3.9 6.5 - - - +
865B ASP* 3.7 35.7 - - + +
884B GLN* 4.0 4.9 - - - -
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Residues in contact with LYS 779 (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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775B LYS 2.8 12.3 + - - -
776B SER* 3.6 29.8 + - - +
777B GLN 3.5 2.6 - - - +
778B MET* 1.3 78.8 - - - +
780B GLU* 1.3 62.8 + - - +
781B GLU* 5.9 0.2 - - - -
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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