Contacts of the helix formed by residues 860 - 869 (chain A) in PDB entry 4C48
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 860 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 3.5 16.3 - - - -
79A SER* 5.8 1.6 - - - -
681A ASP* 3.1 43.9 + - - +
683A GLU* 3.8 13.0 - - + +
819A TYR* 3.3 30.6 + - + -
826A GLU* 4.5 1.6 - - - +
858A ASP 4.2 0.2 + - - -
859A TRP* 1.3 72.3 - - - +
861A GLY* 1.3 76.4 + - - +
862A MET 3.2 0.3 + - - -
863A SER* 2.9 10.4 + - - -
864A TYR* 2.8 17.7 + - - -
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Residues in contact with GLY 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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77A TYR* 3.3 22.1 + - - -
681A ASP* 5.5 2.2 - - - -
860A THR* 1.3 79.9 + - - +
862A MET* 1.3 63.7 + - - -
864A TYR* 3.4 3.3 - - - +
865A GLN* 3.0 29.1 + - - +
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Residues in contact with MET 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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462A SER* 5.6 6.3 - - - +
563A PHE* 4.6 23.8 - - + -
671A ILE* 4.9 20.9 - - + -
679A GLY 5.2 9.0 - - - +
680A PHE* 5.4 4.9 - - - -
681A ASP* 5.1 5.4 - - + +
860A THR 3.2 0.6 + - - -
861A GLY* 1.3 72.2 - - - -
863A SER* 1.3 65.4 + - - +
865A GLN* 3.1 12.2 + - + +
866A GLU* 3.0 23.8 + - - +
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Residues in contact with SER 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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680A PHE* 3.1 14.8 - - - +
681A ASP 2.6 37.6 + - - +
841A MET* 4.2 13.0 - - - +
859A TRP* 3.4 33.0 - - - +
860A THR 2.9 7.8 + - - -
862A MET* 1.3 79.3 - - - +
864A TYR* 1.3 65.9 + - - +
866A GLU* 3.4 12.4 + - - +
867A ARG* 3.6 9.0 + - - +
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Residues in contact with TYR 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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76A MET* 3.3 43.4 + - + +
77A TYR* 3.3 22.7 - + - -
95A GLU* 3.8 15.6 + - - -
859A TRP* 3.8 16.8 - - + +
860A THR* 2.8 34.2 + - - -
861A GLY 3.4 2.2 - - - +
863A SER* 1.3 73.9 - - - +
865A GLN* 1.3 68.6 + - - +
867A ARG* 3.1 27.1 - - + +
868A LEU* 3.9 22.3 + - + +
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Residues in contact with GLN 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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40A PRO* 4.4 19.4 - - - +
76A MET* 3.9 28.3 - - - +
77A TYR* 5.3 2.0 + - - -
96A SER* 5.8 2.8 - - - -
461A GLY* 4.3 17.4 - - - -
462A SER* 5.3 10.4 - - - +
861A GLY 3.0 21.0 + - - +
862A MET* 3.1 15.5 + - + +
864A TYR* 1.3 73.7 - - + +
866A GLU* 1.3 55.6 + - - +
867A ARG 2.8 15.7 + - - -
868A LEU* 2.9 42.7 + - - +
869A SER 3.8 5.4 + - - +
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Residues in contact with GLU 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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837A THR* 5.0 12.1 - - + -
841A MET* 4.9 16.2 - - + +
862A MET 3.0 15.6 + - - +
863A SER* 3.9 7.9 - - - +
864A TYR 3.4 0.8 - - - -
865A GLN* 1.3 75.1 - - - +
867A ARG* 1.3 61.0 + - - +
869A SER 3.9 18.0 - - - -
870A GLY* 4.0 8.2 + - - -
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Residues in contact with ARG 867 (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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841A MET* 5.6 6.7 - - + -
859A TRP* 6.1 4.5 - - + -
863A SER 3.6 6.6 + - - +
864A TYR* 3.1 24.6 + - + +
865A GLN 2.8 1.6 + - - -
866A GLU* 1.3 79.4 - - - +
868A LEU* 1.3 64.8 + - + +
869A SER* 4.0 1.6 - - - -
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Residues in contact with LEU 868 (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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76A MET* 5.4 5.4 - - + -
95A GLU* 5.5 5.6 - - - +
461A GLY* 5.7 6.5 - - - +
864A TYR* 4.4 27.1 - - + +
865A GLN* 2.9 44.6 + - - +
867A ARG* 1.3 77.7 - - + +
869A SER* 1.3 73.1 + - - +
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Residues in contact with SER 869 (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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460A GLY* 5.7 4.8 - - - +
461A GLY* 6.2 0.3 - - - -
463A THR* 5.3 5.2 + - - +
865A GLN 3.8 8.2 + - - +
866A GLU* 3.9 7.3 - - - +
867A ARG 4.0 3.1 - - - -
868A LEU* 1.3 94.3 + - - +
870A GLY* 1.3 58.2 + - - +
872A GLN* 3.2 41.2 + - - +
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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