Contacts of the helix formed by residues 1490 - 1499 (chain A) in PDB entry 5CZV
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 THR1490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1486A GLN 5.1 2.5 - - - +
1487A GLY 4.6 6.2 + - - +
1488A CYS 3.0 1.8 + - - +
1489A ASN* 1.3 81.9 - - - +
1491A GLU* 1.4 61.7 + - - +
1492A GLU* 3.5 27.6 - - - +
1493A CYS* 3.2 27.9 + - - +
1495A TRP* 3.0 30.6 + - - -
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Residues in contact with GLU1491 (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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1459A HIS* 3.2 24.6 + - - -
1464A GLU* 5.0 5.6 - - - +
1490A THR* 1.4 71.8 - - - +
1492A GLU* 1.3 67.0 + - - +
1493A CYS 3.5 0.7 + - - -
1494A GLY* 3.5 9.0 + - - -
1495A TRP* 3.5 43.5 - - + +
1536A SER 3.9 5.5 - - - +
1537A ALA* 4.1 0.2 - - - -
1540A ARG* 2.8 69.4 + - - +
1541A THR 4.5 0.3 + - - -
1591A CYS* 5.6 7.5 - - - +
1594A SER 5.1 2.4 - - - +
1595A PRO* 5.0 10.7 - - - +
1596A GLU 5.6 0.7 - - - +
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Residues in contact with GLU1492 (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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1464A GLU* 3.3 46.8 - - - +
1466A THR* 3.6 25.0 - - - +
1467A CYS* 3.4 15.6 + - - +
1490A THR* 3.5 28.7 + - - +
1491A GLU* 1.3 79.2 + - - +
1493A CYS* 1.4 59.1 + - - +
1494A GLY 3.5 0.2 - - - -
1537A ALA* 3.1 25.0 - - - +
1540A ARG* 3.6 21.2 + - - +
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Residues in contact with CYS1493 (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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1467A CYS* 2.1 51.4 - - - -
1468A ASN 4.4 1.8 - - - -
1471A TYR* 5.5 4.0 - - - -
1475A CYS* 4.2 8.0 - - - +
1487A GLY 4.3 11.4 - - - -
1488A CYS* 3.7 21.6 - - - +
1490A THR* 3.2 22.1 + - - +
1492A GLU* 1.4 78.6 - - - +
1494A GLY* 1.3 56.4 + - - +
1495A TRP 3.7 0.7 - - - -
1496A ASP 4.9 0.7 + - - -
1533A GLN* 2.7 30.8 + - - +
1537A ALA* 4.2 2.0 - - - -
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Residues in contact with GLY1494 (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 PHE* 3.4 13.2 - - - -
1490A THR 3.4 1.2 + - - -
1491A GLU 3.5 5.6 + - - -
1492A GLU 3.5 3.2 - - - -
1493A CYS* 1.3 77.1 - - - +
1495A TRP* 1.4 70.3 + - - +
1496A ASP 3.1 5.1 + - - -
1497A GLY* 3.2 11.4 + - - -
1533A GLN* 4.1 3.4 - - - -
1536A SER* 3.7 26.9 - - - -
1537A ALA* 4.1 6.1 - - - +
1541A THR 5.1 0.4 - - - +
1542A SER* 4.8 2.1 + - - -
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Residues in contact with TRP1495 (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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1488A CYS 3.4 4.4 + - - -
1489A ASN* 3.5 36.7 - - - +
1490A THR* 3.0 24.0 + - - -
1491A GLU* 3.5 45.9 - - + +
1494A GLY* 1.4 72.7 - - - +
1496A ASP* 1.4 60.8 + - - +
1497A GLY 3.1 4.7 - - - +
1498A LEU* 3.0 27.0 + - + +
1499A ASP 4.3 0.2 + - - -
1500A CYS 5.0 0.3 + - - -
1540A ARG 4.4 4.9 + - - -
1541A THR* 4.2 24.3 - - - +
1542A SER* 4.3 7.2 - - - -
1590A LEU* 3.6 62.5 - - + +
1591A CYS* 4.5 3.5 - - - +
1593A GLN* 6.3 0.4 - - + -
1594A SER 5.6 3.4 - - - -
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Residues in contact with ASP1496 (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 CYS 5.9 0.2 - - - -
1478A HIS 2.9 14.9 - - - +
1479A PHE* 3.9 6.0 - - - +
1480A ALA 3.2 4.9 + - - -
1483A ARG 3.1 3.1 - - - +
1484A CYS* 3.6 0.9 - - - -
1485A ASP* 2.8 43.1 + - - +
1488A CYS* 3.1 22.3 + - + +
1489A ASN 4.3 1.1 - - - +
1493A CYS 4.9 0.6 + - - -
1494A GLY 3.1 2.2 + - - -
1495A TRP* 1.4 76.9 - - - +
1497A GLY* 1.3 60.6 + - - +
1498A LEU 3.1 0.2 - - - -
1499A ASP* 3.0 26.7 + - + +
1500A CYS* 3.9 8.5 - - - -
5003A CA 2.4 31.5 - - - -
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Residues in contact with GLY1497 (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 PHE* 3.3 34.0 - - - -
1480A ALA* 3.8 18.2 - - - +
1494A GLY 3.2 7.6 + - - -
1495A TRP 3.1 2.2 - - - -
1496A ASP* 1.3 78.1 - - - +
1498A LEU* 1.4 67.5 + - - +
1499A ASP* 3.5 1.4 + - - +
1542A SER* 4.5 4.3 - - - -
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Residues in contact with LEU1498 (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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1495A TRP* 3.0 14.8 + - + -
1497A GLY* 1.4 74.6 - - - +
1499A ASP* 1.3 61.0 + - - +
1500A CYS 3.1 2.7 - - - -
1501A ALA* 3.1 15.2 + - + +
1502A SER* 3.5 11.6 + - - -
1542A SER* 3.4 29.8 + - - +
1544A ARG* 6.3 1.8 - - - -
1587A ASP* 3.5 18.4 - - + +
1589A ARG* 3.4 51.1 + - + +
1590A LEU* 3.7 28.9 - - + -
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Residues in contact with ASP1499 (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 ALA* 3.2 12.0 + - - -
1481A ASP* 2.9 13.8 + - - +
1482A GLY* 3.0 29.4 + - - +
1483A ARG 3.4 13.1 + - - +
1484A CYS* 3.8 9.8 + - - +
1496A ASP* 3.0 31.5 + - - +
1497A GLY 3.4 1.6 - - - +
1498A LEU* 1.3 75.5 - - - +
1500A CYS* 1.3 58.6 + - - +
1501A ALA 3.4 0.4 + - - -
1502A SER* 4.5 10.0 + - - -
5003A CA 2.3 27.5 - - - -
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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