Contacts of the helix formed by residues 1471 - 1489 (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 ASP1471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1468A LYS* 4.8 9.6 - - + +
1469A HIS 3.7 3.4 + - - +
1470A ALA* 1.3 73.1 - - - +
1472A SER* 1.3 61.6 + - - +
1473A ILE 3.1 3.1 + - - -
1474A LEU* 3.4 8.8 + - + +
1475A GLU* 2.9 36.4 + - + +
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Residues in contact with SER1472 (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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1470A ALA* 3.7 2.0 - - - +
1471A ASP* 1.3 78.3 - - - +
1473A ILE* 1.3 50.4 + - - +
1475A GLU* 4.8 2.5 - - - -
1476A LYS* 2.3 45.3 + - - +
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Residues in contact with ILE1473 (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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1470A ALA* 5.1 6.0 - - + +
1471A ASP 3.1 1.4 - - - +
1472A SER* 1.3 77.4 - - - +
1474A LEU* 1.3 60.6 + - - +
1476A LYS* 3.8 2.0 - - - +
1477A TYR* 2.8 33.7 + - - +
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Residues in contact with LEU1474 (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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1470A ALA 5.3 2.0 + - - +
1471A ASP* 3.4 12.2 + - + +
1473A ILE* 1.3 79.0 - - - +
1475A GLU* 1.3 58.2 + - - +
1477A TYR* 3.8 3.9 - - - +
1478A VAL* 2.9 30.0 + - - +
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Residues in contact with GLU1475 (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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1471A ASP* 2.9 22.9 + - + +
1472A SER* 4.7 2.5 - - - +
1474A LEU* 1.3 75.9 - - - +
1476A LYS* 1.3 59.4 + - - +
1478A VAL* 3.7 6.9 - - - +
1479A THR* 2.9 30.0 + - - -
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Residues in contact with LYS1476 (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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1472A SER* 2.3 32.6 + - - +
1473A ILE* 3.8 3.4 - - - +
1475A GLU* 1.3 77.2 - - - +
1477A TYR* 1.3 57.7 + - - +
1479A THR* 3.5 4.7 + - - -
1480A GLU* 3.0 28.6 + - - +
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Residues in contact with TYR1477 (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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1473A ILE 2.8 21.7 + - - +
1474A LEU* 4.0 4.5 - - - +
1476A LYS* 1.3 73.4 - - - +
1478A VAL* 1.3 57.0 + - - +
1480A GLU* 3.9 5.2 - - - +
1481A ILE* 3.0 27.2 + - - +
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Residues in contact with VAL1478 (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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1474A LEU 2.9 21.0 + - - +
1475A GLU* 3.9 7.2 - - - +
1476A LYS 3.3 0.2 - - - -
1477A TYR* 1.3 76.0 - - - +
1479A THR* 1.3 57.4 + - - +
1481A ILE* 3.7 7.4 - - - +
1482A VAL* 3.0 22.7 + - - +
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Residues in contact with THR1479 (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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1475A GLU 2.9 18.4 + - - -
1476A LYS* 3.5 5.6 + - - -
1477A TYR 3.4 0.2 - - - -
1478A VAL* 1.3 74.8 - - - +
1480A GLU* 1.4 59.2 + - - +
1481A ILE 3.2 1.1 - - - -
1482A VAL* 3.5 9.4 - - - +
1483A MET* 3.0 25.8 + - - +
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Residues in contact with GLU1480 (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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1476A LYS 3.0 17.7 + - - +
1477A TYR* 4.2 5.4 - - - +
1479A THR* 1.4 74.5 - - - +
1481A ILE* 1.4 57.2 + - - +
1483A MET* 3.8 8.3 - - - +
1484A SER* 2.9 27.4 + - - -
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Residues in contact with ILE1481 (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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1429A CYS* 5.4 6.6 - - + +
1477A TYR 3.0 18.8 + - - +
1478A VAL* 3.7 8.9 + - - +
1480A GLU* 1.4 75.5 - - - +
1482A VAL* 1.3 50.9 + - - +
1483A MET 3.4 0.4 - - - -
1484A SER* 4.3 6.3 - - - +
1485A ILE* 2.5 37.7 + - - +
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Residues in contact with VAL1482 (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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1478A VAL 3.0 17.7 + - - +
1479A THR* 3.2 10.7 + - - +
1481A ILE* 1.3 75.1 - - - +
1483A MET* 1.3 51.5 + - - +
1485A ILE* 3.9 5.2 - - - -
1486A VAL* 2.6 36.2 + - - +
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Residues in contact with MET1483 (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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1479A THR 3.0 14.9 + - - +
1480A GLU* 3.8 8.1 - - - +
1482A VAL* 1.3 74.8 - - - +
1484A SER* 1.3 61.3 + - - +
1485A ILE 3.2 0.9 - - - -
1486A VAL* 3.5 5.2 - - - +
1487A THR* 2.8 31.0 + - - -
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Residues in contact with SER1484 (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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1480A GLU 2.9 19.8 + - - -
1481A ILE* 4.4 4.5 - - - -
1483A MET* 1.3 76.7 - - - +
1485A ILE* 1.3 61.0 + - - +
1487A THR* 3.7 14.3 + - - -
1488A THR* 4.2 7.4 + - - -
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Residues in contact with ILE1485 (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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1429A CYS* 4.4 25.1 - - + +
1432A ASP* 6.3 0.9 - - + -
1433A THR* 5.8 3.7 - - - +
1481A ILE 2.5 26.4 + - - +
1482A VAL* 3.9 5.2 - - - -
1484A SER* 1.3 75.7 - - - +
1486A VAL* 1.3 65.1 + - - +
1487A THR 3.1 0.7 + - - -
1488A THR* 3.8 6.9 + - - -
1489A PHE* 3.9 12.1 + - - +
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Residues in contact with VAL1486 (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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1482A VAL 2.6 25.7 + - - +
1483A MET* 3.2 6.9 + - - +
1485A ILE* 1.3 76.5 - - - +
1487A THR* 1.3 62.6 + - - +
1488A THR 3.4 1.0 + - - -
1489A PHE* 3.9 11.6 + - - +
1490A PHE 5.4 0.2 + - - -
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Residues in contact with THR1487 (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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1483A MET 2.8 17.7 + - - -
1484A SER* 3.8 10.1 - - - -
1485A ILE 3.1 1.0 - - - -
1486A VAL* 1.3 78.2 - - - +
1488A THR* 1.3 59.3 + - - +
1490A PHE 5.4 0.5 + - - -
1491A SER 5.6 0.5 + - - -
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Residues in contact with THR1488 (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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1433A THR* 4.3 9.2 - - - -
1484A SER 4.2 7.3 + - - -
1485A ILE 3.8 3.5 + - - -
1486A VAL 3.4 0.2 - - - -
1487A THR* 1.3 78.2 - - - +
1489A PHE* 1.3 60.4 + - - +
1490A PHE 3.3 2.5 - - - -
1491A SER* 3.1 3.5 + - - +
1492A SER* 2.4 68.7 + - - +
1493A PRO* 4.1 10.3 - - - -
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Residues in contact with PHE1489 (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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1432A ASP 5.2 3.8 - - - +
1433A THR* 4.0 11.2 - - - +
1434A GLU 3.8 0.9 - - - +
1435A VAL* 3.1 30.2 - - + +
1485A ILE 3.9 12.8 + - - +
1486A VAL* 3.9 9.4 + - - +
1487A THR 3.7 1.4 - - - -
1488A THR* 1.3 78.8 - - - +
1490A PHE* 1.3 63.8 + - - +
1492A SER 3.8 3.1 + - - -
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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