Contacts of the helix formed by residues 797 - 812 (chain A) in PDB entry 3NC0
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 GLU 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A ARG* 4.3 20.0 + - - +
752A LYS* 4.1 23.8 - - + +
753A ARG* 3.8 31.7 + - - +
756A LEU* 3.7 23.3 - - + -
788A TYR* 3.3 12.0 - - - -
791A ASN* 4.7 1.2 - - - +
795A ALA 3.5 2.7 + - - +
796A ARG* 1.3 71.7 - - - +
798A PRO* 1.3 81.3 - - - +
799A GLU* 3.1 31.4 - - - +
800A VAL* 3.1 29.4 + - + +
843A GLU* 5.3 0.5 - - - +
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Residues in contact with PRO 798 (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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788A TYR* 5.0 0.9 - - + -
796A ARG 3.4 7.4 - - - +
797A GLU* 1.3 99.0 - - - +
799A GLU* 1.3 55.4 + - - +
801A LEU* 3.0 28.6 + - + +
802A SER 3.6 0.5 + - - -
843A GLU* 3.6 31.9 - - + +
844A HIS* 3.2 36.6 - - + +
847A ASN* 3.1 27.6 + - - +
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Residues in contact with GLU 799 (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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753A ARG* 4.6 14.6 - - + +
756A LEU* 3.9 18.4 - - + -
797A GLU* 3.1 20.3 - - - +
798A PRO* 1.3 73.8 - - - +
800A VAL* 1.3 59.4 + - - +
801A LEU 3.3 0.2 - - - -
802A SER* 3.1 21.7 + - - +
803A THR* 2.8 35.5 + - - +
843A GLU* 3.7 18.5 - - - +
847A ASN* 4.3 8.1 + - - +
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Residues in contact with VAL 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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721A TYR* 3.5 24.5 - - - +
756A LEU* 4.0 8.3 - - + -
784A VAL* 3.8 20.9 - - + -
785A LEU* 4.1 16.2 - - + -
788A TYR* 3.9 32.5 - - + -
797A GLU* 3.1 29.2 + - + +
798A PRO 3.0 0.6 + - - -
799A GLU* 1.3 78.9 - - - +
801A LEU* 1.3 64.5 + - - +
803A THR* 3.7 4.5 - - - -
804A MET* 3.1 24.0 + - + +
826A VAL* 4.8 2.5 - - + -
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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
----------------------------------------------------------
788A TYR* 3.4 26.5 - - + +
798A PRO 3.0 12.7 + - - +
800A VAL* 1.3 77.4 - - - +
802A SER* 1.3 56.8 + - - +
804A MET* 3.2 7.2 + - + +
805A ALA* 2.9 27.4 + - - +
826A VAL* 3.7 35.4 - - + -
830A THR* 3.9 17.7 - - + +
844A HIS* 4.1 11.0 - - - +
847A ASN* 3.9 10.5 - - + -
848A PHE* 3.9 27.1 - - + +
851A LEU* 3.7 25.3 - - + +
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Residues in contact with SER 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A PRO 3.6 1.6 + - - -
799A GLU* 3.1 30.4 + - - +
801A LEU* 1.3 76.2 - - - +
803A THR* 1.3 67.9 + - - +
805A ALA* 3.2 9.6 + - - +
806A ILE* 3.1 30.0 + - - +
847A ASN* 3.6 28.6 - - - +
850A LEU* 5.2 7.4 - - - -
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Residues in contact with THR 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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756A LEU* 3.4 45.4 + - + +
759A ILE* 4.7 10.3 - - + -
760A SER* 3.9 25.3 + - - +
780A LEU* 5.8 2.0 - - + -
799A GLU* 2.8 25.4 + - - +
800A VAL 3.7 4.7 - - - +
802A SER* 1.3 75.0 + - - +
804A MET* 1.3 70.2 + - + +
806A ILE* 3.5 6.0 + - - +
807A ILE* 3.1 25.0 + - + +
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Residues in contact with MET 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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777A VAL* 6.2 0.7 - - - -
780A LEU* 4.6 20.2 - - + -
784A VAL* 5.2 5.8 - - + -
785A LEU* 3.3 35.2 - - + -
800A VAL* 3.1 18.6 + - + +
801A LEU* 3.5 10.1 - - - +
803A THR* 1.3 81.8 - - + +
805A ALA* 1.3 66.7 + - - +
807A ILE* 3.1 49.2 - - + +
808A VAL* 3.1 11.0 + - + +
822A ILE* 4.2 32.8 - - + -
851A LEU* 4.0 13.9 - - + -
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Residues in contact with ALA 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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801A LEU 2.9 13.0 + - - +
802A SER* 3.2 14.3 + - - +
804A MET* 1.3 76.7 - - - +
806A ILE* 1.3 63.4 + - + +
808A VAL* 3.3 4.7 + - - +
809A ASN* 3.1 31.1 + - - +
850A LEU* 4.0 12.1 - - + +
851A LEU* 3.7 35.1 - - - +
854A ALA* 3.8 4.1 - - + +
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Residues in contact with ILE 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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760A SER* 4.1 29.6 - - - +
763A VAL* 5.8 0.7 - - + -
764A SER* 3.2 29.8 - - - +
802A SER* 3.1 15.4 + - - +
803A THR* 3.7 7.6 - - - +
804A MET 3.3 0.2 - - - -
805A ALA* 1.3 80.2 - - + +
807A ILE* 1.3 61.9 + - + +
809A ASN* 3.3 14.6 + - - +
810A LYS* 3.1 20.8 + - + +
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Residues in contact with ILE 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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759A ILE* 5.5 1.1 - - + -
760A SER* 5.0 4.9 - - - -
763A VAL* 4.3 32.8 - - + -
777A VAL* 4.6 12.6 - - + -
780A LEU* 4.7 11.0 - - + -
803A THR* 3.1 25.1 - - + +
804A MET* 3.1 37.4 + - - +
806A ILE* 1.3 75.7 - - + +
808A VAL* 1.3 64.6 + - + +
811A LEU* 2.8 41.6 + - + +
815A ILE* 3.5 27.6 - - + -
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Residues in contact with VAL 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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804A MET* 3.1 17.2 + - + +
805A ALA 3.6 7.0 - - - +
807A ILE* 1.3 87.5 - - + +
809A ASN* 1.3 57.6 + - - +
812A GLY* 2.8 29.5 + - - -
815A ILE* 4.2 21.3 - - + -
819A ILE* 4.6 4.7 - - + -
822A ILE* 5.5 1.6 - - + -
851A LEU* 4.6 6.3 - - + -
854A ALA* 3.7 33.4 - - + +
855A VAL* 3.8 22.2 - - + +
858A HIS* 4.0 4.0 - - + -
859A CYS* 4.2 16.4 - - - -
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Residues in contact with ASN 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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805A ALA* 3.1 23.4 + - - +
806A ILE* 3.4 14.1 - - - +
808A VAL* 1.3 77.6 - - - +
810A LYS* 1.3 58.8 + - - +
812A GLY* 4.5 0.7 + - - -
854A ALA* 3.4 22.4 - - - +
857A SER* 5.5 0.3 - - - -
858A HIS* 3.3 34.5 + - + +
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Residues in contact with LYS 810 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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763A VAL* 3.1 36.8 - - + +
764A SER* 3.0 30.1 + - - +
766A SER* 2.9 27.9 + - - +
767A ASN* 4.6 6.7 - - - +
769A PRO* 5.4 10.6 - - + +
806A ILE 3.1 14.8 + - - +
807A ILE 3.8 2.0 - - - +
808A VAL 3.2 0.2 - - - -
809A ASN* 1.3 79.2 - - - +
811A LEU* 1.3 74.6 + - + +
812A GLY* 3.5 0.5 + - - -
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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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763A VAL* 4.4 2.7 - - + -
769A PRO* 3.6 28.4 - - + +
772A VAL* 3.6 27.8 - - + -
773A ALA* 4.2 10.1 - - + -
777A VAL* 3.6 31.4 - - + -
807A ILE* 2.8 28.8 + - + +
810A LYS* 1.3 88.9 - - + +
812A GLY* 1.3 64.4 + - - +
813A GLY 3.2 0.9 + - - -
814A HIS* 3.2 25.7 + - + +
815A ILE* 4.2 24.2 - - + -
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Residues in contact with GLY 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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808A VAL* 2.8 25.7 + - - +
809A ASN 4.9 0.9 - - - -
810A LYS 3.3 2.3 - - - -
811A LEU* 1.3 70.9 - - - +
813A GLY* 1.3 58.5 + - - -
815A ILE* 2.8 31.2 + - - +
858A HIS* 3.9 17.9 - - - -
859A CYS* 3.2 12.0 - - - -
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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