Contacts of the helix formed by residues 823 - 831 (chain A) in PDB entry 2X5Y
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 ASP 823 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750A SER* 3.9 19.8 - - - +
786A PHE* 3.8 2.7 - - - -
821A ALA* 3.4 14.9 - - - +
822A LYS* 1.3 114.8 + - - +
824A ALA* 1.3 66.2 + - - +
825A ILE* 4.2 10.0 - - + +
826A TYR* 3.0 16.5 + - + +
875A SER* 4.6 9.8 + - - -
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Residues in contact with ALA 824 (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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746A HIS 5.6 0.2 + - - -
747A PHE* 3.8 14.8 - - + +
750A SER* 3.2 6.0 + - - +
751A MET* 3.6 24.2 - - + -
786A PHE* 3.3 44.8 - - + -
823A ASP* 1.3 71.6 - - - +
825A ILE* 1.3 63.3 + - - +
827A SER* 3.1 3.6 + - - -
828A HIS* 3.0 19.4 + - - +
840A MET* 3.5 11.5 - - + +
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Residues in contact with ILE 825 (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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750A SER* 3.0 40.7 + - - +
751A MET* 3.5 22.4 - - - -
754A PHE* 4.4 10.3 - - + -
823A ASP* 4.2 9.0 - - + +
824A ALA* 1.3 76.6 - - - +
826A TYR* 1.3 61.5 + - + +
828A HIS* 3.8 17.0 - - + -
829A LYS* 2.9 51.6 + - + +
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Residues in contact with TYR 826 (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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810A HIS* 2.6 39.9 + + - -
813A LYS* 5.5 1.4 + - - +
814A TYR* 4.8 5.4 + - - -
819A TYR* 6.1 0.4 - - + -
820A PHE 6.3 0.2 - - - -
821A ALA* 3.9 17.0 - - + -
823A ASP* 3.0 18.6 + - + +
825A ILE* 1.3 82.5 - - + +
827A SER* 1.3 66.4 + - - +
829A LYS* 3.5 10.6 + - + +
830A ASN* 3.0 49.9 + - + +
875A SER* 5.1 6.1 - - - +
876A VAL* 3.4 32.6 - - + +
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Residues in contact with SER 827 (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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786A PHE* 4.0 5.5 + - - -
787A TYR* 3.5 6.1 - - - -
788A ALA* 2.8 34.1 + - - +
819A TYR 5.1 3.5 + - - -
821A ALA* 4.1 15.4 - - - +
823A ASP 3.7 1.6 + - - -
824A ALA 3.1 7.9 + - - -
826A TYR* 1.3 83.1 - - - +
828A HIS* 1.3 62.5 + - - +
830A ASN* 3.4 3.9 + - - +
831A CYS* 3.2 24.6 + - - +
840A MET* 4.1 7.2 - - - -
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Residues in contact with HIS 828 (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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751A MET* 3.7 12.1 - - + -
754A PHE* 3.5 32.3 - + - -
788A ALA* 4.4 3.4 - - - -
824A ALA 3.0 16.2 + - - +
825A ILE* 3.6 23.1 - - + +
827A SER* 1.3 79.1 - - - +
829A LYS* 1.3 70.7 + - + +
830A ASN 3.3 0.7 + - - -
831A CYS* 3.4 15.4 + - - +
835A ALA* 6.0 6.3 - - + -
838A VAL* 5.3 1.8 - - - +
840A MET* 3.9 6.4 - - + +
893A TYR* 2.7 32.5 + + - +
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Residues in contact with LYS 829 (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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825A ILE* 2.9 46.5 + - + +
826A TYR* 3.7 12.8 - - + +
827A SER 3.4 0.2 - - - -
828A HIS* 1.3 86.8 - - + +
830A ASN* 1.3 72.4 + - - +
831A CYS 3.4 2.7 + - - +
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Residues in contact with ASN 830 (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 THR* 4.8 5.9 + - - +
810A HIS* 4.8 18.4 + - + -
826A TYR* 3.0 49.0 + - + +
827A SER* 3.8 3.6 - - - +
828A HIS 3.2 0.6 - - - -
829A LYS* 1.3 91.2 + - - +
831A CYS* 1.3 61.1 + - - +
832A PRO* 3.6 5.7 - - - +
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Residues in contact with CYS 831 (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 ALA* 3.9 29.2 - - + +
789A THR 4.4 0.7 - - - -
809A THR* 4.9 2.7 - - - -
827A SER 3.2 16.3 + - - +
828A HIS* 3.4 12.8 + - - +
829A LYS 4.6 2.6 - - - +
830A ASN* 1.3 77.2 - - - +
832A PRO* 1.4 69.1 - - - +
833A TYR* 3.5 32.6 + - - +
838A VAL* 3.8 21.5 - - + -
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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
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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