Contacts of the helix formed by residues 1372 - 1384 (chain A) in PDB entry 5XA0
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 MET1372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1370A PRO 3.8 4.6 + - - -
1371A LEU* 1.3 66.3 - - - +
1373A TYR* 1.3 57.7 + - - +
1375A ILE* 2.4 41.0 + - + +
1376A HIS* 2.9 8.1 + - - +
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Residues in contact with TYR1373 (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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1324A LYS 4.3 0.2 - - - +
1325A LYS* 3.3 38.6 - - + +
1328A ASP* 2.8 27.9 - - + +
1329A MET* 3.2 9.6 + - + +
1371A LEU* 3.4 1.5 - - + -
1372A MET* 1.3 78.1 - - - +
1374A HIS* 1.3 60.6 + - - +
1376A HIS* 3.5 10.1 + - - +
1377A LEU 3.6 0.9 + - - -
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Residues in contact with HIS1374 (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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1328A ASP* 2.7 22.4 - - + +
1368A ASN* 4.5 10.8 - - + -
1371A LEU* 2.5 30.9 + - + +
1373A TYR* 1.3 72.7 - - - +
1375A ILE* 1.3 53.8 + - - +
1376A HIS 3.3 0.2 - - - -
1377A LEU* 3.5 4.0 - - + -
1378A VAL* 2.0 59.4 + - + +
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Residues in contact with ILE1375 (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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1371A LEU 2.0 20.2 + - - +
1372A MET* 2.4 37.3 + - + +
1374A HIS 1.3 68.8 - - - -
1376A HIS* 1.3 50.8 + - - +
1379A GLU* 2.8 26.6 - - + +
1380A LEU* 2.0 35.9 + - - +
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Residues in contact with HIS1376 (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* 5.7 0.7 - - - -
1332A ALA* 2.9 36.8 - - + +
1335A VAL* 4.6 0.9 - - - +
1372A MET 2.9 8.2 + - - +
1373A TYR* 3.5 5.4 + - - +
1374A HIS 3.3 0.2 - - - -
1375A ILE* 1.3 73.6 - - - +
1377A LEU* 1.3 55.3 + - - +
1380A LEU* 2.7 26.4 - - + +
1384A CYS* 3.7 8.0 - - - +
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Residues in contact with LEU1377 (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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1328A ASP* 3.1 9.0 - - - +
1331A MET* 2.8 43.1 - - + -
1332A ALA* 3.0 11.0 - - - +
1335A VAL* 4.7 0.2 - - - -
1373A TYR 3.6 0.6 + - - -
1374A HIS* 3.2 9.4 + - + +
1376A HIS* 1.3 76.0 - - - +
1378A VAL* 1.3 54.7 + - - +
1381A LEU* 2.4 40.5 + - - +
1385A THR* 3.8 4.9 - - - -
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Residues in contact with VAL1378 (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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1368A ASN* 4.6 14.1 - - + -
1369A SER* 6.0 0.9 - - - +
1370A PRO 6.3 0.2 - - - -
1371A LEU* 4.8 2.7 - - + +
1374A HIS* 2.0 42.2 + - + +
1377A LEU* 1.3 69.5 - - + +
1379A GLU* 1.3 61.5 + - - +
1381A LEU* 3.1 20.6 - - - +
1382A ALA* 3.6 5.4 + - - +
1412A GLU* 6.6 0.4 - - + -
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Residues in contact with GLU1379 (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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1371A LEU 4.6 1.3 + - - +
1374A HIS 2.8 7.9 + - - -
1375A ILE* 2.8 30.3 - - + +
1378A VAL* 1.3 75.0 - - - +
1380A LEU* 1.3 56.8 + - - +
1382A ALA* 3.9 14.5 - - - +
1383A VAL* 4.2 3.3 + - - +
1412A GLU* 6.5 1.8 - - + -
1413A ASP 5.1 10.1 - - - +
1414A CYS* 6.4 0.9 - - + -
1423A ILE* 5.2 3.6 - - - +
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Residues in contact with LEU1380 (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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1375A ILE 2.0 23.5 + - - +
1376A HIS* 2.7 32.8 - - - +
1377A LEU 3.4 0.4 - - - -
1379A GLU* 1.3 68.3 - - - +
1381A LEU* 1.3 61.8 + - - +
1382A ALA 3.1 1.6 - - - -
1383A VAL* 2.7 3.9 - - - +
1384A CYS* 1.9 56.6 + - + +
1385A THR 3.5 2.2 - - - -
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Residues in contact with LEU1381 (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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1377A LEU 2.4 32.8 + - - +
1378A VAL* 3.1 14.4 - - - +
1380A LEU* 1.3 72.4 - - - +
1382A ALA* 1.3 66.9 + - - +
1383A VAL 2.9 0.7 + - - -
1385A THR* 2.2 44.6 + - - +
1386A GLU* 4.3 0.9 - - - +
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Residues in contact with ALA1382 (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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1378A VAL 3.6 4.9 + - - +
1379A GLU* 3.9 10.1 - - - +
1380A LEU 3.1 0.4 - - - -
1381A LEU* 1.3 78.7 - - - +
1383A VAL* 1.3 60.6 + - - +
1386A GLU* 4.9 4.9 - - - +
1409A VAL* 6.5 0.7 - - + -
1422A TYR 4.9 2.5 - - - +
1423A ILE* 2.9 53.3 - - + +
1427A ASN* 4.5 13.3 - - - +
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Residues in contact with VAL1383 (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 GLU 4.9 2.0 - - - +
1380A LEU* 2.7 10.0 + - + +
1381A LEU 3.8 1.4 - - - +
1382A ALA* 1.3 81.4 - - + +
1384A CYS* 1.3 64.7 + - + +
1385A THR 3.4 0.8 + - - -
1386A GLU* 4.2 10.2 - - - +
1422A TYR 5.9 2.2 - - - +
1423A ILE* 6.0 1.3 - - - -
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Residues in contact with CYS1384 (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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1332A ALA 5.5 2.0 - - - +
1335A VAL* 4.1 2.1 - - + -
1336A ASN* 2.9 29.9 + - - +
1376A HIS* 3.7 7.0 - - + +
1380A LEU* 1.9 46.5 + - + -
1383A VAL* 1.3 72.8 - - + +
1385A THR* 1.3 55.1 + - - +
1386A GLU* 4.1 1.0 + - - -
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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