Contacts of the helix formed by residues 1380 - 1387 (chain A) in PDB entry 5A31
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 ASN1380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1311A SER* 3.9 16.6 + - - -
1375A TYR* 3.5 12.4 - - + -
1378A THR* 3.6 25.4 + - + +
1379A ASN* 1.3 74.0 - - - +
1381A ARG* 1.3 65.4 + - - +
1382A SER* 4.5 5.3 - - - +
1383A ILE* 3.1 39.7 - - + +
1384A ALA* 3.1 22.4 + - - +
1414A ILE* 4.2 3.1 - - + +
13W LEU* 6.3 0.6 - - - +
17W GLU* 5.2 6.6 + - - +
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Residues in contact with ARG1381 (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 ASN* 3.2 20.2 + - - +
1380A ASN* 1.3 72.3 - - - +
1382A SER* 1.3 54.4 + - - +
1384A ALA* 4.5 0.9 - - - -
1385A ASP* 2.8 55.9 + - - +
1411A ARG* 5.4 2.0 - - - +
1415A LEU* 4.2 29.1 - - - +
1418A ASP* 5.6 7.4 - - - +
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Residues in contact with SER1382 (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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1380A ASN* 4.9 5.6 - - - -
1381A ARG* 1.3 76.6 - - - +
1383A ILE* 1.3 70.4 + - - +
1385A ASP* 4.0 1.7 - - - +
1386A TRP* 3.1 42.7 + - - +
517K THR* 4.8 6.2 + - - -
521K HIS* 5.8 8.1 - - - -
13W LEU* 4.1 16.5 - - - +
16W ILE* 4.5 16.7 - - - +
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Residues in contact with ILE1383 (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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1311A SER* 5.3 0.4 - - - -
1322A PRO* 4.6 3.6 - - + -
1371A LEU* 4.0 27.8 - - + -
1375A TYR* 3.1 58.1 - - + +
1380A ASN* 3.1 24.7 + - + +
1381A ARG 3.4 0.2 - - - -
1382A SER* 1.3 80.9 - - - +
1384A ALA* 1.3 66.8 + - - +
1386A TRP* 3.2 24.6 + - + +
1387A LEU* 3.0 21.8 + - + +
1414A ILE* 4.2 13.5 - - + -
13W LEU* 4.6 6.7 - - + -
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Residues in contact with ALA1384 (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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1380A ASN 3.1 18.9 + - - +
1381A ARG* 4.5 0.2 - - - -
1383A ILE* 1.3 78.5 - - - +
1385A ASP* 1.3 67.5 + - - +
1387A LEU* 3.3 21.1 + - - +
1388A ARG 3.3 5.9 + - - -
1411A ARG* 3.4 15.4 - - + -
1414A ILE* 3.7 15.8 - - + +
1415A LEU* 3.6 33.4 - - + -
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Residues in contact with ASP1385 (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 ARG* 2.8 44.4 + - - +
1382A SER* 4.2 2.0 - - - +
1384A ALA* 1.3 81.4 - - - +
1386A TRP* 1.3 56.9 + - - +
1388A ARG* 3.0 40.8 + - + +
1411A ARG* 4.8 8.3 + - - +
1415A LEU* 5.1 0.3 - - - +
521K HIS* 6.4 0.4 - - - +
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Residues in contact with TRP1386 (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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1322A PRO* 3.5 30.3 - - + -
1326A TYR* 3.1 50.8 - + + +
1329A MET* 4.6 8.7 - - - +
1371A LEU* 3.8 22.6 - - + +
1382A SER* 3.1 30.1 + - - +
1383A ILE* 3.2 13.3 + - + -
1385A ASP* 1.3 75.6 - - - +
1387A LEU* 1.3 65.9 + - - +
1388A ARG 3.1 6.0 + - - +
1407A ARG* 5.3 3.5 + - - -
513K THR* 4.7 12.3 - - - -
517K THR* 4.5 23.3 - - - -
13W LEU* 3.7 34.1 - - + -
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Residues in contact with LEU1387 (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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1329A MET* 3.3 35.9 - - + -
1368A THR* 4.7 3.8 - - + -
1371A LEU* 4.0 22.0 - - + -
1383A ILE 3.0 11.9 + - - +
1384A ALA* 3.3 13.9 - - - +
1385A ASP 3.3 0.2 - - - -
1386A TRP* 1.3 74.7 - - - +
1388A ARG* 1.3 59.5 + - - +
1407A ARG* 3.1 42.3 - - + +
1408A THR* 5.6 0.3 - - - -
1410A ALA* 4.1 24.0 - - + -
1411A ARG* 4.2 12.5 - - + +
1414A ILE* 3.7 30.1 - - + -
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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