Contacts of the helix formed by residues 1323 - 1336 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1316B VAL* 2.6 36.6 - - + +
1317B LYS* 4.6 0.9 - - - +
1319B GLU* 3.2 5.1 - - + +
1320B GLY* 2.9 34.1 + - - +
1321B LYS 3.4 1.0 + - - -
1322B PHE* 1.3 70.9 - - - +
1324B LYS* 1.3 65.1 + - - +
1325B LYS 3.0 4.8 + - - +
1326B CYS* 3.2 4.1 + - - +
1327B GLN* 3.1 21.5 + - - +
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Residues in contact with LYS1324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322B PHE* 2.9 9.7 - - + +
1323B ILE* 1.3 79.0 - - - +
1325B LYS* 1.3 56.4 + - - +
1327B GLN* 3.8 7.2 - - - +
1328B ASP* 2.9 29.5 + - - +
1373B TYR* 5.6 0.7 - - - -
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Residues in contact with LYS1325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322B PHE 3.9 6.4 + - - +
1323B ILE 3.0 1.8 + - - -
1324B LYS* 1.3 77.4 - - - +
1326B CYS* 1.3 59.9 + - - +
1328B ASP* 3.8 5.9 - - - +
1329B MET* 2.9 27.9 + - - +
1373B TYR* 4.1 20.6 - - + +
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Residues in contact with CYS1326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B ALA* 4.0 1.9 - - - +
1271B VAL* 3.3 40.5 - - + +
1319B GLU* 3.1 35.9 - - + +
1323B ILE* 3.2 2.8 + - - +
1325B LYS* 1.3 74.8 - - - +
1327B GLN* 1.3 59.0 - - - +
1329B MET* 3.6 4.5 - - - +
1330B VAL* 2.9 26.4 + - - +
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Residues in contact with GLN1327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B ALA* 4.6 3.0 - - - +
1312B LEU* 6.4 1.8 - - + -
1315B ILE* 6.4 0.4 - - - -
1316B VAL* 4.0 24.2 - - + +
1323B ILE 3.1 15.9 + - - +
1324B LYS* 3.8 8.1 - - - +
1326B CYS* 1.3 77.2 - - - +
1328B ASP* 1.4 50.2 + - - +
1330B VAL* 2.9 12.9 - - - +
1331B MET* 2.8 29.7 + - - +
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Residues in contact with ASP1328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1324B LYS 2.9 19.5 + - - +
1325B LYS* 3.8 5.8 - - - +
1326B CYS 3.2 0.2 - - - -
1327B GLN* 1.4 71.0 - - - +
1329B MET* 1.3 61.5 + - - +
1330B VAL 3.1 1.1 - - - -
1331B MET* 2.9 22.5 + - - +
1332B ALA* 3.0 15.8 + - - +
1373B TYR* 4.1 8.2 - - + +
1374B HIS* 3.2 39.8 - - + +
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Residues in contact with MET1329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271B VAL* 4.9 8.1 - - + +
1274B GLN* 2.8 25.6 - - + +
1275B HIS* 6.4 0.2 - - + -
1325B LYS 2.9 17.2 + - - +
1326B CYS* 3.6 8.7 - - - +
1328B ASP* 1.3 75.2 - - - +
1330B VAL* 1.3 58.0 + - - +
1332B ALA* 3.5 5.0 + - - +
1333B GLU* 3.1 16.8 + - - +
1373B TYR 4.9 3.4 + - - -
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Residues in contact with VAL1330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B ALA* 4.4 9.2 - - + +
1273B MET* 5.1 4.3 - - + -
1274B GLN* 3.1 18.1 - - + +
1312B LEU* 6.1 4.7 - - + -
1326B CYS 2.9 15.9 + - - +
1327B GLN* 2.9 18.6 - - - +
1329B MET* 1.3 77.2 - - - +
1331B MET* 1.3 55.0 + - - +
1333B GLU* 4.2 0.2 - - - +
1334B LEU* 3.0 32.6 + - - +
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Residues in contact with MET1331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308B TYR 6.0 1.3 - - - -
1327B GLN 2.8 11.7 + - - +
1328B ASP* 2.9 14.9 + - + +
1330B VAL* 1.3 75.7 - - - +
1332B ALA* 1.3 59.7 + - - +
1334B LEU* 4.4 2.1 - - - +
1335B VAL* 2.8 33.7 + - - +
1374B HIS* 5.0 7.9 - - + -
1377B LEU* 5.2 2.0 - - + -
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Residues in contact with ALA1332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1328B ASP 3.0 13.1 + - - +
1329B MET* 4.0 5.2 - - - +
1331B MET* 1.3 77.0 - - - +
1333B GLU* 1.3 57.8 + - - +
1335B VAL* 4.4 2.7 - - - -
1336B ASN* 3.0 34.7 + - - +
1374B HIS* 6.2 0.2 - - - -
1377B LEU* 3.4 35.3 - - + +
1380B LEU* 5.6 4.5 - - + -
1381B LEU* 5.2 2.0 - - + -
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Residues in contact with GLU1333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274B GLN* 3.0 46.4 - - - +
1277B PHE* 5.1 8.1 - - + +
1278B MET* 4.7 13.7 - - + +
1329B MET 3.1 10.1 + - - +
1332B ALA* 1.3 74.9 - - - +
1334B LEU* 1.3 66.4 + - - +
1336B ASN 3.2 20.2 - - - +
1337B SER* 4.8 3.3 - - - -
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Residues in contact with LEU1334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274B GLN* 5.3 0.2 - - - +
1277B PHE* 6.2 1.3 - - - -
1308B TYR* 3.5 37.7 - - + +
1330B VAL 3.0 20.9 + - - +
1331B MET* 4.4 2.2 - - - +
1333B GLU* 1.3 77.9 - - - +
1335B VAL* 1.3 61.9 + - - +
1336B ASN 4.8 1.2 - - - -
1337B SER* 5.2 4.2 - - - -
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Residues in contact with VAL1335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331B MET 2.8 22.8 + - - +
1332B ALA* 3.9 4.3 - - - +
1334B LEU* 1.3 79.9 - - - +
1336B ASN* 1.3 60.3 + - + +
1337B SER 3.9 2.3 + - - -
1362B ARG* 6.2 4.3 - - - -
1377B LEU* 6.2 0.7 - - + -
1381B LEU* 5.0 7.4 - - + -
1385B THR* 5.6 0.5 - - - -
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Residues in contact with ASN1336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332B ALA 3.0 11.3 + - - +
1333B GLU* 3.2 14.6 - - - +
1335B VAL* 1.3 74.6 - - - +
1337B SER* 1.4 60.5 - - - +
1381B LEU* 3.3 35.4 - - + +
1384B CYS* 3.3 26.8 - - + +
1385B THR* 4.7 2.5 - - - -
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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