Contacts of the helix formed by residues 1323 - 1335 (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 ILE1323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1313A GLN* 2.9 35.6 - - + +
1314A THR* 4.7 0.9 - - - -
1316A VAL* 2.7 22.0 - - - +
1317A LYS* 3.7 8.5 - - + -
1322A PHE* 1.3 87.5 - - - +
1324A LYS* 1.3 67.4 + - + +
1325A LYS* 2.9 3.9 + - - +
1327A GLN 3.0 10.0 + - - -
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Residues in contact with LYS1324 (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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1313A GLN* 3.3 15.8 - - + +
1323A ILE* 1.3 79.5 - - + +
1325A LYS* 1.3 56.1 + - - +
1327A GLN* 3.9 3.4 - - - -
1328A ASP* 2.9 32.9 + - - +
1373A TYR* 4.3 0.3 - - - +
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Residues in contact with LYS1325 (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 PHE* 4.2 18.2 - - + -
1323A ILE 2.9 1.6 + - - +
1324A LYS* 1.3 78.8 - - - +
1326A CYS* 1.3 57.4 + - - +
1329A MET* 2.9 30.1 + - - +
1373A TYR* 3.3 17.9 - - + +
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Residues in contact with CYS1326 (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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1225A ALA* 6.5 1.1 - - + -
1270A ALA* 4.7 1.8 - - - -
1271A VAL* 4.0 23.6 - - + +
1273A MET* 3.9 10.0 - - + +
1274A GLN* 4.1 3.2 + - + +
1312A LEU 4.9 1.1 - - - -
1316A VAL* 2.8 30.8 - - + +
1322A PHE* 4.8 2.4 - - + +
1323A ILE 3.0 2.8 + - - -
1325A LYS* 1.3 76.1 - - - +
1327A GLN* 1.3 53.3 + - - +
1329A MET* 4.1 6.3 - - - -
1330A VAL* 2.6 33.9 + - - +
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Residues in contact with GLN1327 (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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1312A LEU* 3.3 17.5 + - + +
1313A GLN* 3.1 41.5 - - + +
1316A VAL* 4.1 0.8 - - - +
1323A ILE 3.0 7.2 + - - +
1324A LYS* 4.1 3.1 - - - +
1326A CYS* 1.3 74.9 - - - +
1328A ASP* 1.3 59.5 + - - +
1330A VAL* 2.9 23.4 - - - +
1331A MET* 2.9 14.0 + - - +
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Residues in contact with ASP1328 (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* 2.9 21.6 + - + +
1327A GLN* 1.3 73.4 - - - +
1329A MET* 1.3 64.0 + - - +
1331A MET* 2.9 13.7 + - - -
1332A ALA 3.1 8.5 + - - -
1371A LEU* 4.6 3.6 - - + -
1373A TYR* 2.8 17.0 - - + +
1374A HIS* 2.7 41.1 - - + +
1377A LEU* 3.1 4.3 - - - +
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Residues in contact with MET1329 (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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1274A GLN* 3.4 25.9 - - + +
1325A LYS 2.9 21.3 + - - +
1326A CYS* 4.1 4.7 - - - -
1328A ASP* 1.3 74.3 - - - +
1330A VAL* 1.3 63.0 + - - +
1331A MET 2.9 1.6 + - - -
1332A ALA* 3.0 16.8 + - - +
1333A GLU 3.1 10.6 + - - -
1373A TYR* 3.2 12.4 + - + +
1376A HIS* 5.7 0.9 - - - -
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Residues in contact with VAL1330 (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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1273A MET* 3.7 20.4 - - + +
1274A GLN* 3.4 13.0 - - - +
1277A PHE* 3.7 4.5 - - - +
1312A LEU* 5.3 4.9 - - + -
1326A CYS 2.6 24.8 + - - +
1327A GLN* 2.9 15.3 - - - +
1329A MET* 1.3 74.4 - - - +
1331A MET* 1.3 48.2 + - - +
1334A LEU* 2.6 37.6 + - - +
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Residues in contact with MET1331 (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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1327A GLN 2.9 9.4 + - - +
1328A ASP* 2.9 7.0 + - - +
1330A VAL* 1.3 77.2 - - - +
1332A ALA* 1.3 52.4 + - - +
1334A LEU* 3.5 8.9 - - + +
1335A VAL* 2.6 38.3 + - - +
1377A LEU* 2.8 24.6 - - + +
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Residues in contact with ALA1332 (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 1.7 + - - +
1329A MET* 3.0 11.2 + - - +
1331A MET* 1.3 76.1 - - - +
1333A GLU* 1.3 58.3 + - - +
1335A VAL* 2.8 27.4 + - - +
1336A ASN* 5.1 0.7 - - - +
1376A HIS* 2.9 52.6 - - + +
1377A LEU* 3.0 7.6 - - - +
1384A CYS* 5.3 2.3 - - - +
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Residues in contact with GLU1333 (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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1274A GLN* 2.6 39.9 - - + +
1277A PHE* 3.6 5.1 - - + +
1278A MET* 3.1 34.5 + - + +
1281A PHE* 5.3 4.0 - - - +
1329A MET 3.1 3.4 + - - +
1332A ALA* 1.3 76.3 - - - +
1334A LEU* 1.3 69.0 + - - +
1335A VAL 3.1 8.5 + - - +
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Residues in contact with LEU1334 (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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1277A PHE* 3.2 17.5 - - + +
1281A PHE* 6.0 1.2 - - - +
1330A VAL 2.6 23.7 + - - +
1331A MET* 3.5 11.2 - - + +
1333A GLU* 1.3 77.8 - - - +
1335A VAL* 1.3 61.2 + - - +
1337A SER* 4.3 13.5 + - - -
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Residues in contact with VAL1335 (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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1281A PHE* 6.1 0.5 - - - +
1331A MET 2.6 21.6 + - - +
1332A ALA* 2.8 13.4 + - - +
1333A GLU 3.1 12.0 - - - +
1334A LEU* 1.3 77.1 - - - +
1336A ASN* 1.3 70.0 + - - +
1376A HIS 4.6 1.6 - - - +
1377A LEU* 4.7 0.7 - - - -
1384A CYS 4.4 1.8 - - - +
1385A THR* 2.8 36.1 - - - +
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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