Contacts of the helix formed by residues 796 - 809 (chain A) in PDB entry 1R4X
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 THR 796 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794A ILE* 3.4 9.2 - - - +
795A LYS* 1.3 88.1 - - + +
797A LEU* 1.3 62.4 + - - +
798A GLU* 3.5 17.4 + - - +
799A GLU* 2.8 41.3 + - - +
800A ALA 3.3 13.9 + - - -
848A LEU* 4.2 5.2 - - + -
852A VAL* 3.8 7.5 - - - +
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Residues in contact with LEU 797 (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 THR* 1.3 70.3 - - - +
798A GLU* 1.3 63.2 + - - +
800A ALA* 3.3 4.6 + - - +
801A VAL* 2.9 36.6 + - + +
819A VAL* 4.0 25.4 - - + -
823A LYS 3.6 24.2 - - - +
824A ASN* 3.8 16.2 - - - -
825A THR 3.8 13.5 - - - +
826A HIS* 4.1 4.0 - - + -
846A LEU* 3.9 31.4 - - + -
848A LEU* 3.9 33.0 - - + +
852A VAL* 4.4 8.1 - - + -
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Residues in contact with GLU 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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796A THR* 3.5 19.7 - - - +
797A LEU* 1.3 81.5 + - - +
799A GLU* 1.3 58.6 + - + +
801A VAL* 3.6 1.5 + - - +
802A GLY* 3.0 26.3 + - - -
819A VAL* 4.0 38.6 - - + +
820A PRO 5.2 1.2 - - - +
821A ASP* 5.7 1.0 - - - +
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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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794A ILE* 3.9 20.1 - - + +
795A LYS* 4.1 8.0 + - - +
796A THR* 2.8 45.1 + - - +
798A GLU* 1.3 76.5 - - + +
800A ALA* 1.3 66.1 + - - +
802A GLY* 5.1 0.4 - - - -
803A ASN* 2.9 37.0 + - - +
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Residues in contact with ALA 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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791A LEU* 3.8 23.8 - - + -
794A ILE* 3.8 7.1 - - + +
796A THR 3.3 10.2 + - - +
797A LEU 3.3 8.2 + - - +
799A GLU* 1.3 79.6 - - - +
801A VAL* 1.3 63.0 + - - +
803A ASN* 3.7 5.0 - - - +
804A ILE* 3.0 31.5 + - - +
846A LEU* 3.8 22.0 - - + -
852A VAL* 4.1 8.3 - - + -
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Residues in contact with VAL 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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797A LEU* 2.9 21.9 + - + +
798A GLU* 4.1 2.7 - - - +
800A ALA* 1.3 76.3 - - - +
802A GLY* 1.3 64.5 + - - +
804A ILE* 3.3 2.6 + - - +
805A VAL* 3.0 31.8 + - + +
816A SER 4.0 1.1 - - - +
817A ASP* 3.8 37.0 - - + +
819A VAL* 4.1 8.3 - - + -
826A HIS* 3.7 26.7 - - + +
828A LEU* 4.0 21.5 - - + -
846A LEU* 4.2 18.4 - - + -
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Residues in contact with GLY 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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798A GLU 3.0 17.4 + - - -
799A GLU 3.9 0.4 - - - -
801A VAL* 1.3 79.5 - - - +
803A ASN* 1.3 58.0 + - - +
805A VAL* 3.9 4.9 - - - +
806A LYS* 3.1 30.5 + - - +
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Residues in contact with ASN 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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794A ILE* 4.1 21.4 - - - +
799A GLU* 2.9 30.3 + - - +
800A ALA* 3.7 5.1 - - - +
802A GLY* 1.3 74.3 - - - +
804A ILE* 1.3 61.9 + - + +
806A LYS* 3.5 5.3 + - - +
807A PHE* 2.9 31.6 + - - +
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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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791A LEU* 5.1 3.1 - - + -
800A ALA* 3.0 25.5 + - + +
801A VAL 3.8 2.9 - - - +
803A ASN* 1.3 77.0 - - + +
805A VAL* 1.3 63.0 + - - +
807A PHE* 3.3 5.4 + - - +
808A LEU* 3.0 46.9 + - + +
828A LEU* 3.8 24.7 - - + -
830A LEU* 4.0 4.9 - - + -
842A VAL* 6.2 0.4 - - + -
844A SER* 4.5 6.1 - - - +
846A LEU* 4.5 7.0 - - + -
854A MET* 3.4 40.6 - - + -
873A VAL* 5.3 7.0 - - + -
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Residues in contact with VAL 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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766A LYS* 5.9 0.4 - - - +
801A VAL* 3.0 27.1 + - + +
802A GLY* 3.9 5.4 - - - +
804A ILE* 1.3 76.3 - - - +
806A LYS* 1.3 63.3 + - - +
808A LEU* 5.4 0.2 - - - -
809A GLY* 3.2 21.7 + - - -
810A MET 4.1 11.9 + - - +
812A PRO* 4.1 24.7 - - + -
817A ASP* 4.4 5.4 - - + -
828A LEU* 4.0 28.0 - - + -
830A LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 806 (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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761A ALA* 5.0 2.4 - - - +
802A GLY 3.1 18.4 + - - +
803A ASN* 3.9 4.9 - - - +
805A VAL* 1.3 80.7 - - - +
807A PHE* 1.3 63.1 + - - +
809A GLY* 3.7 7.6 + - - -
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Residues in contact with PHE 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 THR* 4.5 16.7 + - + -
760A VAL* 3.6 29.8 - - + +
761A ALA* 3.7 9.2 - - - +
803A ASN 2.9 18.9 + - - +
804A ILE* 3.9 4.5 - - - +
806A LYS* 1.3 80.0 - - - +
808A LEU* 1.3 74.7 + - + +
809A GLY 3.5 0.2 + - - -
872A SER* 3.3 44.4 - - - -
873A VAL* 4.2 6.3 - - + -
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Residues in contact with LEU 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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760A VAL* 4.0 11.0 - - + -
761A ALA* 3.6 14.9 + - - -
764A ILE* 4.1 8.8 - - - +
804A ILE* 3.0 27.2 + - + +
805A VAL 4.7 0.4 - - - +
807A PHE* 1.3 100.6 - - + +
809A GLY* 1.3 63.9 + - - +
810A MET* 3.4 27.4 + - + +
830A LEU* 3.8 26.0 - - + -
842A VAL* 4.7 5.6 - - + -
869A ILE* 3.8 27.6 - - + -
872A SER* 4.8 2.5 - - - -
873A VAL* 4.1 19.1 - - + -
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Residues in contact with GLY 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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631A LYS* 5.6 0.5 + - - -
761A ALA* 4.0 13.9 - - - +
764A ILE* 4.4 9.9 - - - +
766A LYS* 3.5 29.1 + - - +
805A VAL 3.2 12.8 + - - -
806A LYS 3.7 4.5 + - - -
807A PHE 3.3 3.2 - - - -
808A LEU* 1.3 78.4 - - - +
810A MET* 1.3 61.1 + - - +
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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