Contacts of the helix formed by residues 764 - 779 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727C LYS* 3.4 22.1 + - - +
728C TYR* 3.9 1.7 - - + +
762C ILE* 4.7 3.1 - - + -
763C GLU* 1.3 75.6 - - - +
765C SER* 1.4 57.8 + - - +
766C GLU* 3.3 14.4 + - - +
767C LEU* 3.2 30.4 + - + +
768C LEU* 2.9 29.7 + - - +
798C CYS 2.8 30.1 + - - +
799C SER* 3.2 23.6 + - - +
886C TYR* 3.2 13.1 + - + +
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Residues in contact with SER 765 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727C LYS 4.7 3.1 + - - -
763C GLU* 4.1 5.2 - - - +
764C ASN* 1.4 71.7 + - - +
766C GLU* 1.4 55.5 + - - +
768C LEU* 3.3 10.2 + - - +
769C ASP* 2.8 49.4 + - - +
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Residues in contact with GLU 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C LYS* 3.9 33.3 + - + +
764C ASN* 3.3 10.0 + - - +
765C SER* 1.4 80.5 + - - +
767C LEU* 1.3 68.2 + - + +
769C ASP* 3.5 5.9 + - - +
770C LYS* 3.2 48.8 + - + +
799C SER 4.7 3.8 - - - +
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Residues in contact with LEU 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764C ASN* 3.2 35.0 + - + +
766C GLU* 1.3 85.5 - - - +
768C LEU* 1.3 62.3 + - - +
770C LYS* 3.5 15.9 + - + +
771C PHE* 3.1 23.6 + - - +
798C CYS 3.8 8.7 - - - +
799C SER 4.2 4.9 - - - +
800C ASN 4.2 4.7 - - - +
801C ASN* 3.6 46.4 + - + +
882C LYS* 6.0 0.9 - - + -
885C VAL 4.7 2.8 - - - +
886C TYR* 3.7 14.6 - - + -
887C PRO* 3.9 22.7 - - + -
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Residues in contact with LEU 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763C GLU* 6.4 2.7 - - + -
764C ASN 2.9 17.2 + - - +
765C SER* 3.7 8.7 - - - +
767C LEU* 1.3 76.3 - - - +
769C ASP* 1.4 57.4 + - - +
771C PHE* 3.2 12.0 + - + +
772C THR* 2.8 50.8 + - - +
886C TYR* 3.5 35.6 - - + +
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Residues in contact with ASP 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C SER* 2.8 34.1 + - - +
766C GLU* 3.9 6.5 + - - +
767C LEU 3.4 0.2 - - - -
768C LEU* 1.4 74.8 - - - +
770C LYS* 1.3 66.5 + - + +
772C THR* 4.0 5.7 - - - -
773C TRP* 3.0 25.5 + - - +
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Residues in contact with LYS 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766C GLU* 3.2 37.5 + - + +
767C LEU* 3.8 15.1 - - + +
769C ASP* 1.3 77.1 - - + +
771C PHE* 1.4 57.6 + - - +
773C TRP* 3.7 7.3 - - - +
774C LYS* 3.0 28.2 + - - +
883C ASP* 3.9 24.4 - - + +
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Residues in contact with PHE 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767C LEU 3.1 17.3 + - - +
768C LEU* 3.5 10.5 - - + +
770C LYS* 1.4 73.2 - - - +
772C THR* 1.4 60.6 + - - +
774C LYS* 3.1 3.8 + - - +
775C LYS* 2.8 54.8 + - + +
782C GLY* 4.6 5.8 - - - -
844C GLN* 3.2 45.3 - - + -
845C VAL 4.5 0.7 - - - -
846C LEU* 3.6 23.7 - - + +
883C ASP* 3.4 12.5 + - - +
884C GLN 3.5 14.4 - - - -
885C VAL 3.5 26.0 - - - +
886C TYR* 3.6 16.2 - + + -
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Residues in contact with THR 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768C LEU* 2.8 39.0 + - - +
769C ASP* 4.0 6.3 - - - -
771C PHE* 1.4 73.5 - - - +
773C TRP* 1.3 60.6 + - - +
775C LYS* 3.5 11.7 + - + +
776C SER* 3.1 24.2 + - - -
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Residues in contact with TRP 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769C ASP 3.0 18.3 + - - +
770C LYS* 3.7 7.2 - - - +
771C PHE 3.2 0.2 - - - -
772C THR* 1.3 76.2 - - - +
774C LYS* 1.3 58.8 + - + +
776C SER* 3.3 15.5 + - - -
777C GLN* 3.0 67.2 + - + +
883C ASP* 6.1 1.6 - - - -
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Residues in contact with LYS 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770C LYS 3.0 11.1 + - - +
771C PHE 3.1 1.3 + - - +
773C TRP* 1.3 78.3 - - + +
775C LYS* 1.3 55.1 + - - +
777C GLN* 3.3 18.2 + - + +
778C MET* 2.9 56.6 + - - +
846C LEU* 3.8 12.1 - - + -
865C ASP* 6.1 0.2 - - - -
881C GLN* 3.2 29.3 + - - +
883C ASP* 3.3 46.2 + - + +
884C GLN* 3.8 15.0 - - + -
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Residues in contact with LYS 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771C PHE* 2.8 38.3 + - + +
772C THR* 3.6 11.7 - - + +
774C LYS* 1.3 71.8 - - - +
776C SER* 1.4 51.5 + - - +
778C MET* 4.6 0.4 - - - -
779C LYS* 2.9 32.2 + - - -
780C GLU 3.4 18.0 + - - +
781C GLU* 3.8 35.7 + - - +
782C GLY 4.7 3.6 - - - +
846C LEU* 3.5 21.0 - - + +
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Residues in contact with SER 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772C THR* 3.1 13.6 + - - -
773C TRP* 3.3 24.3 - - - -
775C LYS* 1.4 74.1 - - - +
777C GLN* 1.3 63.5 + - - +
779C LYS* 3.4 26.0 + - - +
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Residues in contact with GLN 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C TRP* 3.0 62.2 + - + +
774C LYS* 3.3 20.2 + - + +
776C SER* 1.3 77.0 - - - +
778C MET* 1.3 62.9 + - + +
779C LYS* 4.1 13.5 + - - +
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Residues in contact with MET 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774C LYS* 2.9 48.2 + - - +
775C LYS* 4.0 4.0 - - - +
777C GLN* 1.3 76.5 - - + +
779C LYS* 1.3 69.7 - - - +
780C GLU* 3.5 37.6 + - + +
846C LEU* 3.7 38.6 - - + +
848C GLY* 3.9 4.3 - - - +
865C ASP* 3.6 35.9 - - + +
884C GLN* 4.0 5.2 - - - +
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Residues in contact with LYS 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775C LYS 2.9 12.3 + - - -
776C SER* 3.4 20.0 + - - +
777C GLN* 4.1 10.9 + - - +
778C MET* 1.3 79.8 - - - +
780C GLU* 1.3 62.9 + - - +
781C GLU* 5.8 0.4 - - - -
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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