Contacts of the helix formed by residues 856 - 866 (chain A) in PDB entry 1WXR
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 856 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854A ASP 3.5 5.0 + - - +
855A LEU* 1.3 75.4 - - - +
857A LEU* 1.3 64.9 + - - +
858A GLN* 3.2 29.0 - - - +
859A ASN* 3.0 35.3 + - - +
860A GLN* 2.9 21.4 + - - +
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Residues in contact with LEU 857 (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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856A THR* 1.3 73.9 - - - +
858A GLN* 1.3 65.4 + - - +
860A GLN* 3.2 25.0 + - + +
861A MET* 2.9 46.5 + - + +
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Residues in contact with GLN 858 (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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856A THR* 3.2 32.7 - - - +
857A LEU* 1.3 84.2 + - - +
859A ASN* 1.3 59.7 + - - +
861A MET* 3.4 15.2 + - - +
862A LEU* 3.1 26.5 + - - +
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Residues in contact with ASN 859 (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 LEU* 3.7 31.0 - - - +
806A PRO* 3.7 28.1 - - + +
855A LEU* 3.8 17.0 - - + +
856A THR* 3.0 37.7 + - - +
858A GLN* 1.3 79.4 - - - +
860A GLN* 1.3 56.5 + - - +
862A LEU* 3.6 4.5 + - - +
863A TYR* 2.9 27.0 + - - +
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Residues in contact with GLN 860 (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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855A LEU* 3.0 38.0 + - + +
856A THR 2.9 15.5 + - - +
857A LEU* 3.4 26.0 - - + +
859A ASN* 1.3 73.7 - - - +
861A MET* 1.3 60.0 + - + +
863A TYR* 3.2 12.3 + - + +
864A SER* 2.9 30.8 + - - -
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Residues in contact with MET 861 (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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857A LEU* 2.9 39.7 + - + +
858A GLN* 3.4 15.5 + - - +
859A ASN 3.4 0.2 - - - -
860A GLN* 1.3 75.1 - - + +
862A LEU* 1.3 63.2 + - - +
864A SER* 3.3 10.6 + - - -
865A LEU* 3.2 29.4 + - + +
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Residues in contact with LEU 862 (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 PRO* 3.7 39.0 - - + +
807A VAL 4.5 2.7 - - - +
808A TYR* 3.6 52.5 - - + +
830A MET* 4.2 16.8 - - + -
858A GLN 3.1 16.6 + - - +
859A ASN* 3.6 7.4 + - - +
861A MET* 1.3 74.6 - - - +
863A TYR* 1.3 66.9 + - - +
865A LEU* 3.3 27.0 + - + +
866A PHE* 3.3 11.3 + - + -
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Residues in contact with TYR 863 (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 PRO* 4.5 4.2 - - + +
828A TYR* 3.9 30.0 + + - -
851A LEU* 3.5 31.0 - - + -
855A LEU* 5.1 5.2 - - + -
859A ASN 2.9 16.7 + - - +
860A GLN* 3.2 14.3 + - + +
862A LEU* 1.3 76.3 - - - +
864A SER* 1.3 67.6 + - - +
866A PHE* 3.0 29.2 + - + +
867A ASN 4.2 1.0 + - - -
868A GLY* 5.3 8.5 + - - -
869A TYR 5.7 1.1 - - - -
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Residues in contact with SER 864 (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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860A GLN 2.9 14.4 + - - -
861A MET* 3.3 12.7 + - - -
863A TYR* 1.3 82.1 - - - +
865A LEU* 1.3 61.8 + - - +
867A ASN* 2.9 24.6 + - - +
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Residues in contact with LEU 865 (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 TYR* 5.5 2.9 - - + +
830A MET* 4.7 15.0 - - + +
861A MET* 3.2 18.3 + - + +
862A LEU* 3.3 25.1 + - + +
863A TYR 3.3 0.8 - - - -
864A SER* 1.3 77.3 - - - +
866A PHE* 1.3 61.9 + - - +
867A ASN* 3.1 5.2 + - - +
872A ILE* 4.8 4.2 - - - +
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Residues in contact with PHE 866 (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 PRO* 3.9 23.3 - - + -
807A VAL 4.4 0.7 - - - -
828A TYR* 3.3 31.9 - + + -
829A SER 3.5 15.0 - - - -
830A MET* 3.5 33.0 - - + -
862A LEU* 3.3 22.4 - - + -
863A TYR* 3.0 21.6 + - + +
865A LEU* 1.3 78.4 - - - +
867A ASN* 1.3 67.6 + - - +
868A GLY 4.5 1.8 - - - +
869A TYR* 3.0 45.5 + - - +
870A ARG 3.4 20.9 - - - -
871A ASN* 4.2 1.6 - - - -
872A ILE* 3.6 21.0 - - + +
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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