Contacts of the helix formed by residues 1312 - 1321 (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 LEU1312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273A MET* 5.8 2.8 - - - +
1308A TYR* 3.7 22.0 + - + +
1311A PHE* 1.3 73.0 - - - +
1313A GLN* 1.3 71.5 + - - +
1314A THR 3.3 1.4 + - - +
1315A ILE* 3.4 15.7 + - - +
1316A VAL 3.6 2.8 + - - -
1326A CYS 4.9 0.7 - - - -
1327A GLN* 3.3 28.8 + - + +
1330A VAL* 5.3 4.3 - - + -
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Residues in contact with GLN1313 (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* 1.3 78.1 - - - +
1314A THR* 1.3 55.5 + - - +
1316A VAL 2.6 27.5 + - - -
1323A ILE* 2.9 28.6 - - + -
1324A LYS* 3.3 30.3 - - + +
1327A GLN* 3.1 5.9 - - + +
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Residues in contact with THR1314 (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 PHE* 4.4 19.9 - - - +
1312A LEU 3.3 1.8 - - - +
1313A GLN* 1.3 76.4 - - - +
1315A ILE* 1.3 59.0 + - - +
1317A LYS* 2.8 30.8 + - - +
1318A ALA* 3.4 6.4 + - - +
1323A ILE* 4.7 1.3 - - - -
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Residues in contact with ILE1315 (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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1267A ILE* 5.6 5.8 - - + +
1268A LEU* 3.3 33.7 - - + +
1269A GLU 3.7 13.0 - - - +
1270A ALA* 3.1 15.0 + - - +
1273A MET* 5.9 2.5 - - + -
1311A PHE* 4.6 9.4 + - - +
1312A LEU* 3.4 12.4 + - - +
1313A GLN 2.8 1.2 + - - -
1314A THR* 1.3 76.3 - - - +
1316A VAL* 1.3 66.6 + - - +
1317A LYS 3.0 1.0 + - - -
1318A ALA* 3.3 12.2 + - - +
1319A GLU 4.2 1.6 + - - -
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Residues in contact with VAL1316 (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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1270A ALA* 3.3 21.3 - - - +
1312A LEU 3.6 1.4 + - - -
1313A GLN 2.6 8.0 + - - +
1315A ILE* 1.3 74.9 - - - +
1317A LYS* 1.3 61.2 + - - +
1320A GLY 3.9 6.4 + - - -
1322A PHE* 3.4 14.1 + - + +
1323A ILE* 2.7 42.0 - - - +
1326A CYS* 2.8 28.4 - - + +
1327A GLN 4.1 1.1 - - - +
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Residues in contact with LYS1317 (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 3.1 3.6 + - - -
1314A THR* 2.8 19.0 + - - +
1316A VAL* 1.3 77.5 - - - +
1318A ALA* 1.3 55.8 + - - +
1321A LYS* 2.7 33.7 + - - +
1322A PHE 2.8 23.7 + - - +
1323A ILE* 3.7 9.0 - - + -
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Residues in contact with ALA1318 (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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1314A THR 3.4 4.6 + - - +
1315A ILE* 3.3 10.3 + - - +
1317A LYS* 1.3 80.3 - - - +
1319A GLU* 1.3 60.9 + - - +
1321A LYS 4.7 0.7 + - - -
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Residues in contact with GLU1319 (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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1224A LYS* 3.2 28.0 - - + +
1270A ALA* 4.0 10.3 - - + +
1315A ILE 4.2 1.8 + - - -
1316A VAL 3.9 1.4 + - - -
1317A LYS 3.4 0.6 - - - -
1318A ALA* 1.3 79.4 - - - +
1320A GLY* 1.3 59.4 + - - +
1321A LYS 3.7 0.2 - - - -
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Residues in contact with GLY1320 (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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1224A LYS* 4.1 1.8 - - - +
1225A ALA 3.0 30.0 + - - +
1226A GLU 4.9 1.0 + - - -
1316A VAL 3.9 5.2 + - - -
1317A LYS 3.8 0.6 + - - -
1319A GLU* 1.3 78.6 - - - +
1321A LYS* 1.3 66.0 + - - +
1322A PHE* 3.3 8.7 + - - +
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Residues in contact with LYS1321 (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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1317A LYS* 2.7 24.4 + - - +
1318A ALA 4.5 0.6 + - - -
1319A GLU 3.7 1.0 - - - -
1320A GLY* 1.3 74.3 - - - +
1322A PHE* 1.3 63.8 + - - +
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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