Contacts of the helix formed by residues 814 - 822 (chain A) in PDB entry 2XR9
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 TRP 814 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A ARG* 3.7 28.9 - - + +
711A VAL* 3.7 21.3 - - + -
801A ASN* 3.6 38.8 - - - -
804A SER* 3.6 27.6 + - - -
806A ASN* 3.5 31.0 - - + -
807A SER* 3.3 14.0 + - - +
809A GLU* 3.0 18.8 + - + -
810A ASP 3.2 23.3 + - - -
811A GLU* 3.2 10.2 + - + +
812A SER 3.5 1.2 + - - -
813A LYS* 1.3 81.0 - - - +
815A VAL* 1.3 83.5 + - + +
816A GLU 3.5 2.2 - - - +
817A GLU* 3.5 15.2 + - - +
818A LEU* 3.1 21.4 + - + +
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Residues in contact with VAL 815 (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 VAL* 3.9 31.6 - - + +
714A TYR* 3.8 22.4 - - + -
719A LEU* 4.5 0.7 - - + -
811A GLU* 3.0 46.4 + - + +
814A TRP* 1.3 98.1 - - + +
816A GLU* 1.3 65.3 + - - +
818A LEU* 3.1 7.5 + - - +
819A MET* 3.0 35.8 + - - +
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Residues in contact with GLU 816 (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* 5.0 3.9 + - + -
719A LEU* 3.6 28.9 - - + +
722A LYS* 3.4 34.1 + - - -
723A TYR* 3.5 22.8 + - - +
811A GLU 4.6 1.0 + - - -
812A SER 6.0 2.6 - - - +
814A TRP 3.5 0.8 - - - +
815A VAL* 1.3 80.8 - - - +
817A GLU* 1.3 56.7 + - - +
819A MET* 3.2 6.1 + - + +
820A LYS* 3.0 56.8 + - + +
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Residues in contact with GLU 817 (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 ASN* 5.7 2.6 - - - +
813A LYS 4.3 12.7 - - - +
814A TRP* 3.5 14.2 + - - +
815A VAL 3.2 0.6 - - - -
816A GLU* 1.3 74.2 - - - +
818A LEU* 1.3 66.2 + - - +
820A LYS* 3.3 13.1 + - - +
821A MET* 3.2 21.1 + - - +
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Residues in contact with LEU 818 (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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708A PHE* 6.2 1.3 - - + -
711A VAL* 3.7 39.0 - - + -
795A LEU* 4.8 6.5 - - + -
796A PRO* 5.3 6.7 - - + +
801A ASN* 4.5 4.5 - - - +
803A GLU* 3.6 36.1 - - + +
804A SER* 3.9 22.2 - - - +
814A TRP* 3.1 16.9 + - + +
815A VAL* 3.1 9.7 + - - +
817A GLU* 1.3 77.9 - - - +
819A MET* 1.3 63.9 + - - +
821A MET* 3.2 13.1 + - + +
822A HIS* 3.3 30.8 - - + -
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Residues in contact with MET 819 (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 VAL* 4.8 3.1 - - + -
715A PHE* 3.9 17.9 - - + -
719A LEU* 3.5 25.1 - - - -
723A TYR* 4.0 16.4 - - + +
793A PHE* 3.2 46.2 - - + +
795A LEU* 3.7 29.2 - - + -
815A VAL* 3.0 24.9 + - + +
816A GLU* 3.2 6.9 + - + +
818A LEU* 1.3 74.9 - - - +
820A LYS* 1.3 62.6 + - + +
822A HIS 3.1 12.0 + - - -
823A THR* 3.1 12.3 + - - -
858A TYR* 5.2 0.8 - - - -
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Residues in contact with LYS 820 (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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479A LYS* 3.7 12.4 + - - +
816A GLU* 3.0 45.5 + - + +
817A GLU* 3.7 10.4 - - - +
818A LEU 3.2 0.4 - - - -
819A MET* 1.3 73.2 - - + +
821A MET* 1.3 65.8 + - - +
823A THR* 3.3 22.3 - - - +
858A TYR* 3.6 59.0 - - + +
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Residues in contact with MET 821 (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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423A TYR* 4.2 13.2 - - - +
429A PRO* 3.6 18.2 - - + +
431A ARG* 3.0 45.5 + - - +
446A LEU* 3.1 35.7 - - + -
477A ASP* 3.7 15.7 - - - +
479A LYS* 4.4 7.2 - - - +
803A GLU* 4.4 2.7 - - - +
817A GLU* 3.2 11.9 + - + +
818A LEU* 3.4 12.8 - - + +
820A LYS* 1.3 76.2 - - - +
822A HIS* 1.3 65.6 + - + +
823A THR 3.4 0.9 - - - -
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Residues in contact with HIS 822 (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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427A HIS 4.0 7.4 - - - -
428A LEU 4.8 0.2 - - - -
429A PRO* 3.6 39.9 - - + +
430A LYS* 4.7 2.3 + - - +
766A HIS* 6.1 0.4 - - - -
793A PHE* 3.4 1.6 - - - -
794A ILE* 3.0 38.6 + - - +
795A LEU* 4.2 9.4 - - + -
796A PRO* 3.7 28.3 - - + +
803A GLU* 2.8 31.1 + - - -
818A LEU* 3.3 36.1 + - + +
819A MET 3.1 9.9 + - - +
821A MET* 1.3 80.6 - - + +
823A THR* 1.3 69.2 + - - +
824A ALA* 4.1 0.9 - - - +
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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