Contacts of the helix formed by residues 1489 - 1498 (chain B) in PDB entry 5ZCS
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 GLU1489 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483B CYS 5.8 0.2 - - - +
1484B LEU* 2.8 52.3 + - + +
1487B LEU* 3.7 10.7 - - + +
1488B GLY* 1.3 81.9 - - - +
1490B TRP* 1.3 59.5 + - - +
1491B GLY* 3.3 7.9 + - - +
1492B GLN* 4.3 3.9 + - + +
1493B LEU* 4.2 3.5 + - - +
1667B ALA* 4.6 11.4 - - - +
1668B LEU* 4.9 6.6 + - - +
1671B LYS* 2.9 41.3 + - - +
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Residues in contact with TRP1490 (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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1485B GLU* 3.6 37.2 - - + -
1488B GLY* 3.6 18.2 + - - -
1489B GLU* 1.3 72.3 - - - +
1491B GLY* 1.3 61.7 + - - +
1492B GLN 3.7 0.4 - - - -
1493B LEU* 3.6 32.9 - - + +
1494B HIS* 3.8 18.0 + - - +
1514B ARG* 5.7 1.1 - - - -
1515B MET 4.8 0.7 - - - -
1518B ALA* 3.5 46.0 - - + -
1519B ALA* 3.8 12.9 - - + +
1522B GLY* 5.3 8.3 - - - -
1523B LEU* 4.3 16.6 - - + +
1634B GLN* 3.1 21.8 - - - +
1638B MET* 3.6 34.1 - - + +
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Residues in contact with GLY1491 (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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1489B GLU* 3.3 4.2 + - - +
1490B TRP* 1.3 78.2 - - - +
1492B GLN* 1.3 64.9 + - - +
1494B HIS* 3.8 9.0 + - - +
1495B GLN* 3.9 16.6 + - - +
1523B LEU* 5.1 11.0 - - - +
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Residues in contact with GLN1492 (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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1484B LEU* 3.8 29.3 - - + +
1489B GLU* 4.3 4.6 + - + +
1491B GLY* 1.3 73.7 - - - +
1493B LEU* 1.3 60.7 + - - +
1494B HIS 3.3 0.2 - - - -
1495B GLN* 3.2 17.1 + - - +
1496B GLN* 2.9 36.9 + - + +
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Residues in contact with LEU1493 (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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1481B MET* 3.7 45.1 - - + +
1484B LEU* 3.6 19.0 - - + +
1485B GLU* 3.8 27.8 - - + +
1489B GLU 4.2 5.1 + - - +
1490B TRP* 3.6 37.9 + - + +
1491B GLY 3.3 1.0 - - - -
1492B GLN* 1.3 76.8 - - - +
1494B HIS* 1.3 60.2 + - - +
1496B GLN* 3.2 10.7 + - - +
1497B CYS* 2.9 41.5 + - - -
1515B MET* 5.0 6.5 - - + +
1519B ALA* 4.2 4.3 - - + -
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Residues in contact with HIS1494 (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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1490B TRP 3.8 7.6 + - - +
1491B GLY 4.1 3.6 - - - +
1492B GLN 3.3 0.4 - - - -
1493B LEU* 1.3 79.0 - - - +
1495B GLN* 1.3 64.5 + - + +
1497B CYS* 3.8 4.5 + - + +
1498B CYS* 3.6 33.1 + - - -
1516B ALA 5.4 0.9 - - - -
1519B ALA* 3.5 31.1 - - + +
1520B ALA* 3.6 18.9 - - + +
1523B LEU* 3.8 25.9 - - + +
1525B GLN* 2.8 36.4 + - - -
1528B SER* 5.8 1.2 - - - -
1532B TYR* 6.2 2.0 - + - -
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Residues in contact with GLN1495 (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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1491B GLY 4.0 14.0 + - - +
1492B GLN* 3.2 18.7 + - - +
1493B LEU 3.2 0.2 - - - -
1494B HIS* 1.3 81.7 - - + +
1496B GLN* 1.3 60.7 + - + +
1497B CYS 3.6 0.2 + - - -
1498B CYS* 3.7 8.1 + - - +
1499B GLU* 3.4 26.0 - - - +
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Residues in contact with GLN1496 (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 ARG* 3.4 34.8 + - - +
1481B MET* 4.3 20.3 - - + +
1484B LEU* 3.4 31.1 - - - +
1492B GLN* 2.9 24.0 + - + +
1493B LEU* 3.2 14.5 + - + +
1495B GLN* 1.3 76.0 - - + +
1497B CYS* 1.3 61.6 + - - +
1498B CYS 3.3 0.6 + - - -
1499B GLU* 3.9 24.4 + - - +
1500B LYS* 4.7 3.8 + - - +
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Residues in contact with CYS1497 (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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1481B MET* 3.7 24.7 - - - -
1493B LEU* 2.9 27.8 + - - +
1494B HIS* 4.2 6.7 - - + +
1495B GLN 3.4 0.6 - - - -
1496B GLN* 1.3 77.8 - - - +
1498B CYS* 1.3 61.3 + - - +
1499B GLU 3.3 2.8 + - - -
1500B LYS 4.3 4.2 + - - +
1501B TRP* 2.8 26.3 + - - -
1512B MET* 5.2 5.9 - - - +
1515B MET* 3.9 9.9 - - - -
1516B ALA* 3.8 37.5 - - + +
1519B ALA* 4.0 7.6 - - + -
1532B TYR* 6.0 0.4 - - + -
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Residues in contact with CYS1498 (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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1494B HIS* 3.6 33.6 + - - +
1495B GLN* 3.7 5.9 + - - +
1496B GLN 3.3 1.4 - - - -
1497B CYS* 1.3 79.8 - - - +
1499B GLU* 1.3 61.7 + - - +
1501B TRP* 3.5 13.8 - - - +
1532B TYR* 4.0 22.9 - - - -
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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