Contacts of the helix formed by residues 1494 - 1499 (chain B) in PDB entry 4ZLP
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 GLY1494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1479B PHE* 3.3 11.3 - - - -
1490B THR 3.0 2.0 + - - -
1491B GLU 3.5 9.6 + - - -
1492B GLU 3.6 0.2 - - - -
1493B CYS* 1.3 79.0 - - - +
1495B TRP* 1.3 73.6 + - - +
1496B ASP 3.1 4.8 + - - -
1497B GLY* 3.1 12.9 + - - -
1536B SER* 3.9 25.5 - - - -
1537B ALA* 4.2 3.0 - - - +
1541B THR 4.8 1.7 - - - +
1542B SER* 4.4 4.5 + - - -
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Residues in contact with TRP1495 (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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1488B CYS 3.9 3.8 - - - -
1489B ASN* 3.4 45.5 - - - +
1490B THR* 2.8 19.3 + - - +
1491B GLU* 3.4 43.5 - - + +
1493B CYS 3.6 0.4 - - - -
1494B GLY* 1.3 79.2 - - - +
1496B ASP* 1.3 62.1 + - - +
1498B LEU* 2.9 26.3 + - + +
1499B ASP 4.0 0.5 + - - -
1500B CYS 4.9 1.0 + - - -
1540B ARG 4.5 1.2 + - - -
1541B THR* 4.4 26.6 - - - +
1542B SER* 4.6 5.4 - - - +
1590B LEU* 3.4 57.0 + - + +
1591B CYS* 5.7 1.8 - - - -
5005B GOL 4.3 9.3 + - - -
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Residues in contact with ASP1496 (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 CYS 4.9 1.0 - - - +
1478B HIS* 2.9 15.1 - - - +
1479B PHE* 3.8 6.6 - - - +
1480B ALA 3.2 4.8 + - - -
1483B ARG 3.0 3.8 - - - +
1484B CYS* 3.6 0.2 - - - -
1485B ASP* 2.7 44.1 + - - +
1488B CYS* 3.4 19.5 + - - +
1489B ASN 4.6 0.4 - - - +
1493B CYS 4.7 1.2 + - - -
1494B GLY* 3.1 2.8 + - - -
1495B TRP* 1.3 76.9 - - - +
1497B GLY* 1.3 60.8 + - - +
1499B ASP* 2.9 27.0 + - + +
1500B CYS* 4.0 7.6 - - - -
5003B CA 2.4 31.0 - - - -
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Residues in contact with GLY1497 (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 PHE* 3.3 31.4 - - - -
1480B ALA* 3.8 20.7 - - - +
1494B GLY 3.1 7.1 + - - -
1495B TRP 3.0 1.8 - - - -
1496B ASP* 1.3 78.5 - - - +
1498B LEU* 1.3 71.8 + - - +
1499B ASP* 3.3 2.1 + - - +
1542B SER* 4.3 4.3 - - - -
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Residues in contact with LEU1498 (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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1495B TRP* 2.9 12.4 + - + -
1497B GLY* 1.3 78.1 - - - +
1499B ASP* 1.3 63.2 + - - +
1500B CYS 3.1 4.6 + - - +
1501B ALA* 3.2 19.8 + - + +
1502B SER* 3.9 4.3 + - - -
1542B SER* 3.3 30.2 + - - +
1544B ARG* 6.4 1.6 - - - -
1587B ASP* 3.6 17.9 - - + +
1589B ARG* 3.6 45.0 + - + +
1590B LEU* 3.5 35.0 - - + -
5005B GOL 5.5 0.4 - - - -
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Residues in contact with ASP1499 (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 ALA* 3.1 9.2 + - - -
1481B ASP* 2.8 13.4 + - - +
1482B GLY* 2.7 35.4 + - - +
1483B ARG 3.3 13.2 - - - +
1484B CYS* 4.1 8.9 + - - +
1495B TRP 4.0 0.2 + - - -
1496B ASP* 2.9 36.6 + - - +
1497B GLY 4.3 1.4 - - - +
1498B LEU* 1.3 77.2 - - - +
1500B CYS* 1.3 56.1 + - - +
1501B ALA 3.4 0.6 + - - -
1502B SER* 4.6 9.5 + - - -
5003B CA 2.4 26.2 - - - -
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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