Contacts of the helix formed by residues 794 - 813 (chain A) in PDB entry 4N78
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 SER 794 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A PHE* 3.4 14.1 - - - +
790A GLU* 3.0 30.4 - - - +
791A ASP 2.7 19.7 + - - -
792A LEU 3.1 0.2 - - - -
793A THR* 1.3 76.6 + - - +
795A ILE* 1.3 62.8 + - - +
796A VAL 3.2 2.9 - - - -
797A GLU* 3.2 15.3 + - - +
798A LEU* 3.2 19.1 + - - +
906A ARG* 3.7 23.6 - - - +
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Residues in contact with ILE 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A PHE* 3.5 30.9 - - + -
792A LEU* 3.1 18.5 + - + +
793A THR 3.1 1.8 - - - -
794A SER* 1.3 77.6 + - - +
796A VAL* 1.3 71.2 + - + +
797A GLU 3.3 0.2 - - - -
798A LEU* 3.4 6.3 + - + +
799A ASP* 3.0 27.2 + - - +
839A ILE* 4.6 1.8 - - + -
843A VAL* 4.0 13.9 - - + -
913A HIS* 4.4 8.7 - - + +
916A VAL* 3.7 20.3 - - + +
917A ILE* 3.8 32.8 - - + -
920A LEU* 3.9 22.0 - - + -
921A LEU* 5.4 0.2 - - + -
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Residues in contact with VAL 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A THR 4.2 4.3 - - - +
794A SER 3.2 0.4 - - - -
795A ILE* 1.3 79.1 - - + +
797A GLU* 1.3 60.8 + - - +
799A ASP* 3.4 3.6 + - - +
800A GLY* 3.2 18.0 + - - -
902A TYR* 4.0 16.1 - - + -
905A TYR* 4.0 42.2 - - + -
912A PRO* 4.6 1.3 - - + +
913A HIS* 3.7 46.4 - - + +
916A VAL* 4.5 15.7 - - + -
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Residues in contact with GLU 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A ARG* 3.9 23.6 + - - -
790A GLU* 5.0 3.5 - - - +
793A THR 4.9 0.2 + - - -
794A SER* 3.2 17.0 + - - +
796A VAL* 1.3 76.9 - - - +
798A LEU* 1.3 59.6 + - - +
800A GLY* 3.3 1.4 + - - -
801A LEU* 2.9 34.2 + - + +
889A HIS* 4.5 15.9 - - + +
899A SER* 5.2 11.6 + - - +
902A TYR* 3.7 41.9 - - + +
906A ARG* 4.3 18.3 + - - -
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Residues in contact with LEU 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ALA* 3.4 37.0 - - + +
784A ILE* 4.1 6.5 - - + +
787A PHE* 3.6 37.0 - - + -
794A SER 3.2 9.9 + - - +
795A ILE* 3.5 10.3 - - + +
797A GLU* 1.3 79.3 - - - +
799A ASP* 1.3 56.8 + - - +
801A LEU* 3.2 5.1 + - - +
802A LEU* 2.8 54.2 + - + +
839A ILE* 3.8 28.7 - - + -
920A LEU* 4.2 8.7 - - + -
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Residues in contact with ASP 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A ILE 3.0 17.1 + - - +
796A VAL 3.7 5.6 - - - +
797A GLU 3.2 0.2 - - - -
798A LEU* 1.3 77.8 - - - +
800A GLY* 1.3 62.4 + - - +
802A LEU* 3.4 11.6 + - - +
803A GLU* 3.1 26.9 + - - +
916A VAL* 3.8 30.0 - - + +
919A ARG* 5.6 4.3 - - - +
920A LEU* 4.3 14.5 - - + +
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Residues in contact with GLY 800 (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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796A VAL 3.2 9.1 + - - -
797A GLU 3.3 2.7 + - - -
799A ASP* 1.3 81.0 + - - +
801A LEU* 1.3 60.6 + - - +
803A GLU* 3.3 8.1 + - - +
804A ILE* 3.1 28.3 + - - +
902A TYR* 3.2 29.3 + - - -
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Residues in contact with LEU 801 (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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779A SER 5.6 0.2 - - - +
783A ALA* 3.5 35.0 - - + +
786A ARG* 5.1 5.8 - - + +
797A GLU* 2.9 22.2 + - + +
798A LEU* 3.6 6.3 - - - +
800A GLY* 1.3 75.2 - - - +
802A LEU* 1.3 59.6 + - - +
804A ILE* 3.2 7.6 + - + +
805A ASN* 2.6 36.3 + - - +
887A TYR 5.3 0.7 - - - +
888A LEU* 3.5 52.0 - - + +
889A HIS* 3.7 31.3 + - + +
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Residues in contact with LEU 802 (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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780A LEU* 4.1 17.3 - - + -
783A ALA* 4.4 10.1 - - + -
784A ILE* 4.9 4.5 - - + -
798A LEU* 2.8 46.4 + - + +
799A ASP* 3.6 7.6 - - - +
801A LEU* 1.3 76.5 - - - +
803A GLU* 1.3 57.6 + - - +
805A ASN* 3.2 6.9 + - - +
806A ARG* 2.9 32.5 + - - +
821A PHE* 3.7 8.7 - - + -
825A PHE* 3.7 42.4 - - + -
839A ILE* 4.4 1.8 - - + -
920A LEU* 4.3 17.9 - - + -
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Residues in contact with GLU 803 (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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722A LEU* 4.0 14.7 - - + +
799A ASP* 3.1 21.9 + - - +
800A GLY* 3.6 8.5 - - - +
801A LEU 3.2 0.2 - - - -
802A LEU* 1.3 74.6 - - - +
804A ILE* 1.3 60.3 + - - +
806A ARG* 3.3 40.7 + - - +
807A MET* 3.0 26.5 + - - +
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Residues in contact with ILE 804 (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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715A LYS* 3.8 26.5 - - + -
718A ALA* 3.7 0.4 - - + +
719A GLY* 4.2 21.1 - - - +
722A LEU* 4.3 18.6 - - + -
800A GLY 3.1 15.2 + - - +
801A LEU* 3.5 8.5 - - + +
803A GLU* 1.3 75.6 - - - +
805A ASN* 1.3 58.4 + - - +
807A MET* 3.3 3.2 + - - +
808A THR* 2.8 31.0 + - - -
888A LEU 4.3 5.8 - - - +
889A HIS* 3.3 35.2 - - + +
898A TYR* 3.8 29.2 - - + +
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Residues in contact with ASN 805 (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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715A LYS* 3.7 10.3 + - - +
776A MET* 3.6 11.0 - - + +
779A SER* 3.0 33.1 + - - -
780A LEU* 3.8 26.4 + - + +
783A ALA* 4.5 8.5 - - - +
801A LEU* 2.6 48.5 + - - +
802A LEU* 3.4 9.3 - - - +
804A ILE* 1.3 76.0 - - - +
806A ARG* 1.3 58.6 + - - +
808A THR* 3.3 8.3 + - - -
809A HIS* 2.9 28.4 + - - +
821A PHE* 3.7 3.1 - - + -
887A TYR 5.6 0.4 + - - -
888A LEU 5.0 0.2 + - - -
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Residues in contact with ARG 806 (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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802A LEU* 2.9 17.8 + - - +
803A GLU* 3.3 41.4 + - - +
805A ASN* 1.3 75.7 - - - +
807A MET* 1.3 61.9 + - - +
809A HIS* 3.3 3.6 + - - +
810A LYS* 3.0 29.4 + - - +
821A PHE* 3.5 50.0 - - + -
822A ASP* 6.4 0.2 - - - +
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Residues in contact with MET 807 (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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718A ALA* 3.6 23.1 - - + +
721A LEU* 3.4 31.6 - - + -
722A LEU* 4.0 23.8 - - + -
803A GLU 3.0 14.9 + - - +
804A ILE 3.6 7.6 - - - +
806A ARG* 1.3 74.6 - - - +
808A THR* 1.3 64.7 + - - +
810A LYS* 3.2 27.4 + - + +
811A LEU* 2.9 48.3 + - + +
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Residues in contact with THR 808 (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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711A PHE* 4.0 7.4 - - + -
714A TYR 4.1 6.5 - - - +
715A LYS* 3.1 42.8 - - - +
718A ALA* 3.4 15.7 - - - +
776A MET* 4.0 11.0 - - - -
804A ILE 2.8 20.9 + - - -
805A ASN* 3.5 5.6 - - - -
806A ARG 3.3 0.2 - - - -
807A MET* 1.3 75.5 - - - +
809A HIS* 1.3 62.6 + - - +
811A LEU* 3.4 3.1 + - - +
812A LEU* 3.0 42.5 + - + +
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Residues in contact with HIS 809 (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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776A MET* 4.0 10.7 - - + -
805A ASN 2.9 13.4 + - - +
806A ARG 3.4 9.4 - - - +
808A THR* 1.3 76.5 - - - +
810A LYS* 1.3 59.4 + - - +
812A LEU* 3.2 5.5 + - - +
813A SER* 2.8 50.9 + - - -
818A LEU* 3.8 19.2 - - + +
819A ASP 2.7 29.2 + - - -
820A GLY* 4.3 2.5 - - - -
821A PHE* 3.6 37.4 + + + +
824A MET* 3.9 20.6 - - - -
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Residues in contact with LYS 810 (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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806A ARG* 3.0 21.6 + - - +
807A MET* 3.2 34.5 + - + +
809A HIS* 1.3 78.8 + - - +
811A LEU* 1.3 65.5 + - + +
813A SER* 3.3 15.4 + - - -
814A ARG* 3.7 16.5 + - + +
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Residues in contact with LEU 811 (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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714A TYR* 3.7 33.5 - - + +
717A MET* 3.8 27.4 - - + -
718A ALA* 3.9 14.1 - - + +
721A LEU* 4.2 3.6 - - + -
807A MET* 2.9 46.1 + - + +
808A THR 3.8 3.6 - - - +
810A LYS* 1.3 78.9 - - + +
812A LEU* 1.3 60.9 + - - +
814A ARG* 3.0 55.3 + - - +
815A TYR* 3.8 6.6 - - - -
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Residues in contact with LEU 812 (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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710A ILE* 4.5 11.0 - - + +
711A PHE* 4.0 12.3 - - + -
714A TYR* 3.8 33.7 - - + -
750A LEU* 6.1 1.3 - - + -
772A VAL* 3.5 32.5 - - + -
776A MET* 4.2 9.0 - - + -
808A THR* 3.0 38.9 + - + +
809A HIS 3.7 3.4 - - - +
811A LEU* 1.3 72.5 - - - +
813A SER* 1.3 58.5 + - - +
814A ARG 3.1 6.6 + - - -
815A TYR* 3.2 7.0 + - + +
816A LEU* 3.0 39.7 + - + +
818A LEU* 3.9 12.3 - - + -
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Residues in contact with SER 813 (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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809A HIS* 2.8 46.9 + - - -
810A LYS* 3.3 9.1 + - - -
812A LEU* 1.3 74.3 - - - +
814A ARG* 1.3 63.0 + - - +
815A TYR 3.2 0.7 - - - -
816A LEU 3.2 20.6 + - - +
818A LEU* 4.2 9.5 + - - +
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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
------------------------------------------------------------
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