Contacts of the helix formed by residues 1474 - 1486 (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 LEU1474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1471B ASP* 3.9 14.1 + - + +
1473B ILE* 1.3 77.8 - - - +
1475B GLU* 1.4 49.3 - - - +
1478B VAL* 2.2 41.1 + - - +
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Residues in contact with GLU1475 (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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1471B ASP* 3.0 22.5 + - + +
1472B SER* 4.4 2.2 - - - -
1474B LEU* 1.4 75.6 - - - +
1476B LYS* 1.3 52.6 + - - +
1478B VAL* 4.0 2.9 - - - -
1479B THR* 2.8 34.0 + - - -
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Residues in contact with LYS1476 (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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1472B SER* 2.0 41.2 + - - +
1473B ILE* 4.3 0.2 - - - -
1475B GLU* 1.3 75.8 - - - +
1477B TYR* 1.3 57.5 + - - +
1478B VAL 3.3 0.7 - - - -
1479B THR* 3.9 5.2 - - - -
1480B GLU* 2.9 28.6 + - - +
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Residues in contact with TYR1477 (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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1473B ILE* 2.1 43.4 + - + +
1476B LYS* 1.3 73.8 - - - +
1478B VAL* 1.3 57.3 + - - +
1480B GLU* 3.5 5.5 + - - +
1481B ILE* 3.0 28.1 + - - +
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Residues in contact with VAL1478 (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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1474B LEU* 2.2 34.1 + - - +
1475B GLU* 4.0 4.9 - - - +
1477B TYR* 1.3 77.8 - - - +
1479B THR* 1.3 56.1 + - - +
1481B ILE* 3.3 7.7 + - - +
1482B VAL* 2.9 27.9 + - - +
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Residues in contact with THR1479 (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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1475B GLU 2.8 25.5 + - - -
1476B LYS* 3.9 5.8 - - - -
1477B TYR 3.3 0.4 - - - -
1478B VAL* 1.3 75.7 - - - +
1480B GLU* 1.3 61.2 + - - +
1482B VAL* 3.2 9.3 + - - +
1483B MET* 3.1 21.0 + - - +
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Residues in contact with GLU1480 (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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1476B LYS 2.9 18.4 + - - +
1477B TYR* 3.8 6.3 - - - +
1479B THR* 1.3 76.0 - - - +
1481B ILE* 1.3 62.7 + - - +
1483B MET* 3.1 8.8 + - - +
1484B SER* 3.1 21.0 + - - -
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Residues in contact with ILE1481 (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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1477B TYR 3.0 18.6 + - - +
1478B VAL* 3.3 7.8 + - - +
1480B GLU* 1.3 75.4 - - - +
1482B VAL* 1.4 56.1 + - - +
1484B SER* 3.9 8.3 - - - +
1485B ILE* 2.9 28.1 + - - +
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Residues in contact with VAL1482 (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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1478B VAL 2.9 16.4 + - - +
1479B THR* 3.5 9.6 - - - +
1480B GLU 3.1 0.8 - - - -
1481B ILE* 1.4 75.7 - - - +
1483B MET* 1.3 59.6 + - - +
1484B SER 3.4 0.7 - - - -
1485B ILE* 4.2 6.2 - - - +
1486B VAL* 2.9 29.7 + - - +
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Residues in contact with MET1483 (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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1479B THR 3.1 11.3 + - - +
1480B GLU* 3.1 9.8 + - - +
1482B VAL* 1.3 77.1 - - - +
1484B SER* 1.4 58.8 + - - +
1486B VAL* 3.9 5.1 - - - +
1487B THR* 3.0 24.7 + - - -
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Residues in contact with SER1484 (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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1480B GLU 3.1 15.5 + - - -
1481B ILE* 4.0 7.4 - - - -
1483B MET* 1.4 75.4 - - - +
1485B ILE* 1.3 59.0 + - - +
1487B THR* 3.0 20.7 + - - -
1488B THR* 3.1 16.3 + - - -
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Residues in contact with ILE1485 (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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1432B ASP* 5.5 10.7 - - + +
1481B ILE 2.9 19.9 + - - +
1482B VAL* 3.9 6.7 - - - +
1484B SER* 1.3 76.0 - - - +
1486B VAL* 1.3 60.0 + - - +
1488B THR* 3.9 14.6 + - - +
1489B PHE* 4.6 5.7 + - - +
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Residues in contact with VAL1486 (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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1482B VAL 2.9 23.2 + - - +
1483B MET* 4.1 6.5 - - - +
1485B ILE* 1.3 73.1 - - - +
1487B THR* 1.3 62.3 + - - +
1488B THR 3.5 3.7 - - - +
1489B PHE* 5.6 1.1 - - - +
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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