Contacts of the helix formed by residues 1355 - 1366 (chain A) in PDB entry 2XBA
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 PRO1355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1223A MET* 3.9 21.8 - - + -
1323A PHE* 4.7 0.9 - - + -
1353A ASN 3.3 7.4 - - - +
1354A CYS* 1.3 90.5 - - - +
1356A GLY* 1.3 66.7 + - - +
1357A PRO* 3.3 10.3 - - + -
1358A VAL* 3.1 12.4 + - + +
1359A TYR* 3.0 18.5 + - - +
1391A ASP 5.1 0.7 - - - +
1392A VAL* 3.8 37.7 - - + +
1395A THR* 3.8 20.4 - - + +
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Residues in contact with GLY1356 (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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1354A CYS 3.4 3.7 + - - -
1355A PRO* 1.3 70.7 - - - +
1357A PRO* 1.3 63.5 - - - +
1359A TYR* 3.2 9.2 + - - +
1360A ARG* 2.9 50.5 + - - +
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Residues in contact with PRO1357 (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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1355A PRO* 3.4 10.3 - - + -
1356A GLY* 1.3 90.5 - - - +
1358A VAL* 1.3 59.5 + - - +
1360A ARG* 3.5 27.3 + - + +
1361A ILE* 3.4 23.9 + - - +
1385A TYR* 6.4 2.0 - - + -
1386A CYS* 3.8 21.1 - - - -
1389A ASP* 4.4 8.3 - - - +
1392A VAL* 3.9 17.5 - - + -
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Residues in contact with VAL1358 (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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1227A LEU* 4.3 6.3 - - + -
1319A LEU* 4.4 8.0 - - + +
1323A PHE* 3.7 47.3 - - + -
1354A CYS* 3.8 13.2 - - - -
1355A PRO* 3.1 14.2 + - + +
1357A PRO* 1.3 75.5 - - - +
1359A TYR* 1.3 65.8 + - - +
1361A ILE* 3.0 18.8 + - + +
1362A MET* 3.3 16.3 + - + +
1386A CYS* 4.1 17.5 - - - -
1392A VAL* 4.1 21.3 - - + -
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Residues in contact with TYR1359 (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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1347A ARG* 5.0 3.1 - - - +
1348A MET 2.6 26.4 + - - -
1349A ASP* 3.6 6.4 + - - -
1350A PRO* 3.4 50.7 - - + +
1351A PRO* 4.7 0.2 - - + -
1354A CYS* 3.8 10.9 - - + +
1355A PRO 3.0 12.0 + - - +
1356A GLY* 3.2 11.4 + - - +
1358A VAL* 1.3 76.0 - - - +
1360A ARG* 1.3 61.9 + - + +
1362A MET* 3.1 20.5 + - - +
1363A THR* 3.0 51.3 + - + +
1366A TRP* 4.4 7.0 - + - -
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Residues in contact with ARG1360 (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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1356A GLY* 2.9 28.3 + - - +
1357A PRO* 3.5 36.1 - - + +
1358A VAL 3.1 0.2 - - - -
1359A TYR* 1.3 79.3 - - + +
1361A ILE* 1.3 65.7 + - - +
1363A THR* 3.2 10.9 + - - +
1364A GLN* 3.1 27.8 + - + +
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Residues in contact with ILE1361 (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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1227A LEU* 6.1 1.3 - - + -
1319A LEU* 3.5 21.8 - - + -
1357A PRO 3.4 9.6 + - - +
1358A VAL* 3.0 13.5 + - + +
1360A ARG* 1.3 75.8 - - - +
1362A MET* 1.3 64.4 + - - +
1364A GLN* 3.3 7.0 + - + +
1365A CYS* 3.0 31.6 + - - -
1374A PRO* 6.1 1.1 - - + -
1379A ILE* 4.4 19.3 - - + -
1382A ARG* 3.8 49.4 - - + +
1383A ILE* 3.8 13.9 - - + +
1386A CYS* 3.8 18.6 - - - -
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Residues in contact with MET1362 (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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1316A GLY* 3.8 14.4 - - - +
1319A LEU* 3.9 21.1 - - + +
1320A TRP* 3.8 41.1 - - - -
1323A PHE* 4.2 1.8 - - + -
1351A PRO* 3.7 13.0 - - + -
1354A CYS* 3.7 29.8 - - - -
1358A VAL* 3.3 17.2 + - + +
1359A TYR* 3.1 20.3 + - - +
1361A ILE* 1.3 77.9 - - - +
1363A THR* 1.3 62.5 + - - +
1365A CYS* 3.1 9.0 + - - +
1366A TRP* 3.0 45.9 + - + -
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Residues in contact with THR1363 (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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1347A ARG* 5.6 5.6 - - + -
1359A TYR* 3.0 52.8 + - + +
1360A ARG* 3.2 19.8 + - - +
1362A MET* 1.3 78.9 - - - +
1364A GLN* 1.3 61.0 + - - +
1366A TRP* 3.3 23.7 + - + +
1367A GLN* 3.2 22.3 + - - -
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Residues in contact with GLN1364 (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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1360A ARG* 3.1 19.9 + - + +
1361A ILE* 3.6 4.7 - - - +
1363A THR* 1.3 74.9 + - - +
1365A CYS* 1.3 63.0 + - - +
1366A TRP 3.1 1.0 + - - -
1367A GLN* 3.4 40.4 + - - +
1372A ASP 4.4 9.5 + - - +
1373A ARG* 3.8 1.0 - - - -
1374A PRO* 3.2 21.8 - - + +
1382A ARG* 3.3 38.5 + - - +
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Residues in contact with CYS1365 (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 THR* 3.4 30.1 - - - +
1313A TRP* 3.5 12.1 - - - -
1315A PHE* 4.4 3.6 - - - -
1316A GLY* 3.5 23.1 - - - -
1361A ILE* 3.0 28.1 + - - -
1362A MET 3.1 8.3 + - - +
1364A GLN* 1.3 76.1 - - - +
1366A TRP* 1.3 58.4 + - + +
1367A GLN 3.3 0.4 - - - -
1373A ARG* 3.4 22.5 - - - -
1374A PRO* 4.1 2.5 - - - -
1379A ILE* 3.7 28.9 - - - -
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Residues in contact with TRP1366 (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 TRP* 3.5 38.2 + + + -
1316A GLY* 3.3 23.5 - - - -
1317A VAL* 3.3 24.9 - - + +
1320A TRP* 4.1 2.5 - + + -
1330A TYR* 5.2 3.6 - - - -
1347A ARG* 2.8 57.9 + - + +
1348A MET* 3.7 57.7 - - + -
1359A TYR* 4.4 7.0 - + - -
1362A MET* 3.0 41.5 + - + +
1363A THR* 3.3 14.3 + - + +
1364A GLN 3.1 1.0 - - - -
1365A CYS* 1.3 80.1 - - - +
1367A GLN* 1.3 59.9 + - - +
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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