Contacts of the helix formed by residues 1379 - 1389 (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 LYS1379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1319A TRP* 3.6 52.7 - - + +
1376A GLU* 5.1 6.0 + - - +
1378A TYR* 1.3 73.4 - - - +
1380A MET* 1.3 64.4 + - - +
1381A GLU* 3.9 17.0 - - + +
1382A ASP* 2.8 35.0 + - + +
1383A LEU* 3.2 7.1 + - - +
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Residues in contact with MET1380 (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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897A LEU* 5.3 5.2 - - + -
1300A LEU* 3.7 14.6 - - - -
1303A CYS* 4.0 23.3 - - + -
1304A GLN* 3.5 43.5 - - + +
1307A ARG* 4.3 24.2 - - - +
1340A ASP* 4.4 10.8 - - - +
1376A GLU* 4.5 8.9 + - - +
1378A TYR 3.4 4.4 + - - -
1379A LYS* 1.3 72.0 - - - +
1381A GLU* 1.3 66.3 + - - +
1383A LEU* 3.3 8.9 + - + +
1384A MET* 2.9 47.6 + - - +
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Residues in contact with GLU1381 (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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1379A LYS* 3.9 17.6 - - + +
1380A MET* 1.3 91.7 + - - +
1382A ASP* 1.3 56.3 + - - +
1384A MET* 3.5 13.9 + - - +
1385A GLN* 3.1 35.8 + - + +
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Residues in contact with ASP1382 (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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1279A ARG* 2.8 42.2 + - - -
1378A TYR* 4.1 11.5 - - - +
1379A LYS* 2.8 27.4 + - + +
1381A GLU* 1.3 76.4 - - - +
1383A LEU* 1.3 62.9 + - + +
1385A GLN* 3.1 9.2 + - - +
1386A VAL* 3.0 23.2 + - - +
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Residues in contact with LEU1383 (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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1275A TRP* 3.2 40.5 - - + -
1279A ARG* 4.5 7.4 - - - +
1300A LEU* 4.0 13.2 - - + -
1303A CYS* 4.8 4.0 - - - -
1339A PHE* 4.1 20.2 - - + -
1340A ASP* 3.8 24.9 - - - +
1378A TYR* 4.0 31.2 - - + -
1379A LYS 3.2 9.3 + - - +
1380A MET* 3.7 21.8 - - + +
1382A ASP* 1.3 76.0 - - - +
1384A MET* 1.3 63.9 + - - +
1386A VAL* 3.3 2.0 + - - +
1387A TYR* 2.9 21.7 + - - +
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Residues in contact with MET1384 (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* 3.5 45.8 - - - +
894A ALA* 4.1 7.2 - - + +
897A LEU* 3.8 24.5 - - + -
1300A LEU* 4.5 3.1 - - + -
1304A GLN* 3.9 15.5 - - - +
1380A MET* 2.9 41.0 + - + +
1381A GLU* 3.7 13.0 - - - +
1383A LEU* 1.3 75.7 - - - +
1385A GLN* 1.3 58.9 + - + +
1387A TYR* 3.6 3.6 - - - +
1388A ASP* 3.0 34.6 + - - -
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Residues in contact with GLN1385 (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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1381A GLU* 3.1 20.8 + - + +
1382A ASP* 3.5 10.8 - - - +
1384A MET* 1.3 75.7 - - + +
1386A VAL* 1.3 61.1 + - + +
1388A ASP* 3.3 8.5 + - - +
1389A GLN* 2.9 51.5 + - + +
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Residues in contact with VAL1386 (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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1275A TRP* 3.9 17.5 - - + +
1278A ALA* 3.7 29.4 - - + +
1279A ARG* 3.4 53.4 - - + +
1382A ASP* 3.0 20.5 + - - +
1383A LEU* 3.7 6.7 - - - +
1385A GLN* 1.3 74.8 - - + +
1387A TYR* 1.3 63.9 + - - +
1389A GLN* 3.3 4.9 + - - -
1390A PHE* 3.0 22.7 + - - +
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Residues in contact with TYR1387 (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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890A TYR* 3.5 16.1 - - - +
891A PRO* 2.6 30.5 + - - +
892A SER* 3.8 1.6 - - - -
893A SER* 3.7 20.9 - - - -
896A VAL* 4.6 1.3 - - + -
1275A TRP* 4.1 8.7 - - + -
1293A LYS* 3.0 48.9 + - + -
1296A LEU* 3.8 22.4 - - + -
1297A LEU* 3.8 41.6 - - + +
1300A LEU* 3.9 17.7 - - + -
1383A LEU 2.9 18.3 + - - +
1384A MET 3.6 2.9 - - - +
1386A VAL* 1.3 77.6 - - - +
1388A ASP* 1.3 74.2 + - - +
1390A PHE* 3.2 10.8 + - - +
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Residues in contact with ASP1388 (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* 3.7 11.7 - - - -
893A SER* 2.6 46.1 + - - -
894A ALA* 4.7 0.7 + - - +
1293A LYS* 4.5 4.4 + - - +
1384A MET 3.0 13.7 + - - +
1385A GLN* 4.0 10.6 - - - +
1387A TYR* 1.3 81.8 - - - +
1389A GLN* 1.3 71.7 + - - +
1390A PHE 3.2 1.1 + - - +
1391A THR* 3.6 16.3 - - - +
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Residues in contact with GLN1389 (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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1278A ALA 5.3 2.7 - - - +
1282A LYS* 5.6 3.8 + - - -
1385A GLN* 2.9 37.1 + - + +
1386A VAL* 3.7 5.6 - - - +
1387A TYR 3.3 0.2 - - - -
1388A ASP* 1.3 85.2 + - - +
1390A PHE* 1.3 57.3 + - - +
1391A THR* 3.4 11.5 + - - -
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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