Contacts of the helix formed by residues 892 - 901 (chain A) in PDB entry 3AVR
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 SER 892 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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890A TYR 3.9 0.2 + - - -
891A PRO* 1.3 76.7 - - - +
893A SER* 1.3 64.6 + - - +
894A ALA* 3.6 8.7 + - - +
895A GLU* 3.0 36.9 + - - +
896A VAL* 3.0 21.1 + - - +
1387A TYR* 3.8 1.3 - - - -
1388A ASP* 3.7 13.7 - - - -
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Residues in contact with SER 893 (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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892A SER* 1.3 72.4 - - - +
894A ALA* 1.3 60.8 + - - +
896A VAL* 3.2 7.8 + - - +
897A LEU* 2.9 29.6 + - - +
1300A LEU* 4.3 4.0 - - - -
1304A GLN* 4.1 1.7 + - - -
1384A MET* 3.5 46.5 - - - +
1387A TYR* 3.7 12.9 - - - -
1388A ASP* 2.6 35.9 + - - -
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Residues in contact with ALA 894 (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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892A SER* 3.1 8.6 + - - +
893A SER* 1.3 84.1 + - - +
895A GLU* 1.3 57.4 + - + +
897A LEU* 3.4 3.8 + - - +
898A LYS* 3.0 32.7 + - + +
901A ARG* 5.3 0.9 + - - -
1384A MET* 4.2 10.8 - - + -
1388A ASP* 4.7 0.4 + - - +
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Residues in contact with GLU 895 (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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4A EDO 4.5 2.9 + - - -
891A PRO* 3.3 19.7 - - + +
892A SER* 3.0 37.1 + - - +
894A ALA* 1.3 75.0 - - + +
896A VAL* 1.3 64.1 + - - +
898A LYS* 3.2 35.6 + - - +
899A ALA* 3.0 23.6 + - - +
913A ILE* 4.8 5.0 - - + +
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Residues in contact with VAL 896 (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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891A PRO* 3.8 12.3 - - + -
892A SER 3.0 17.6 + - - +
893A SER* 3.5 10.3 - - - +
895A GLU* 1.3 76.2 - - - +
897A LEU* 1.3 63.8 + - - +
899A ALA* 3.2 5.0 + - - +
900A CYS* 3.1 21.5 + - - -
913A ILE* 4.2 12.6 - - + -
1297A LEU* 3.6 25.1 - - + -
1300A LEU* 4.3 10.3 - - + -
1301A LYS* 4.0 31.4 - - + +
1304A GLN* 3.2 16.4 - - - +
1387A TYR* 4.4 3.4 - - - +
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Residues in contact with LEU 897 (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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893A SER 2.9 12.9 + - - +
894A ALA* 3.7 4.9 - - - +
896A VAL* 1.3 77.7 - - - +
898A LYS* 1.3 62.2 - - - +
900A CYS* 3.0 15.4 + - + +
901A ARG* 3.2 56.4 + - + +
1304A GLN* 3.2 40.3 + - + +
1308A GLU* 4.7 10.8 - - + +
1380A MET* 5.3 4.3 - - + -
1384A MET* 3.8 25.6 - - + -
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Residues in contact with LYS 898 (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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894A ALA* 3.0 24.2 + - + +
895A GLU* 3.2 42.1 + - - +
897A LEU* 1.3 76.3 - - - +
899A ALA* 1.3 60.8 + - - +
901A ARG* 3.3 28.2 + - - +
902A ASN* 3.4 13.3 - - - +
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Residues in contact with ALA 899 (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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895A GLU 3.0 15.2 + - - +
896A VAL 3.3 10.1 - - - +
898A LYS* 1.3 78.4 - - - +
900A CYS* 1.3 62.6 + - - +
901A ARG 3.3 0.2 + - - -
902A ASN* 3.3 26.9 + - - +
913A ILE* 3.8 32.8 - - + +
1301A LYS* 5.6 4.3 - - - -
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Residues in contact with CYS 900 (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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896A VAL 3.1 17.4 + - - -
897A LEU* 3.0 9.2 + - + +
899A ALA* 1.3 77.2 - - - +
901A ARG* 1.3 62.7 + - - +
902A ASN 3.2 8.5 + - - -
1301A LYS* 3.7 28.9 - - - +
1304A GLN* 3.9 25.8 - - + +
1305A THR* 3.3 32.7 - - - +
1308A GLU* 4.3 15.0 - - + +
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Residues in contact with ARG 901 (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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894A ALA 5.3 0.8 + - - -
897A LEU* 3.2 53.7 + - + +
898A LYS* 3.6 22.9 - - - +
899A ALA 3.2 1.8 - - - -
900A CYS* 1.3 78.2 - - - +
902A ASN* 1.3 59.4 + - - +
1308A GLU* 4.1 31.1 + - - +
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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