Contacts of the helix formed by residues 1410 - 1415 (chain A) 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 CYS1410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1387A CYS* 2.1 52.7 - - - -
1388A PRO* 4.5 6.1 - - - -
1389A ARG* 5.2 3.4 - - - -
1392A CYS* 4.4 8.7 - - + -
1396A ARG* 3.5 14.5 + - - +
1404A GLU 5.3 1.3 - - - -
1405A CYS* 3.1 26.9 - - + +
1407A SER* 3.1 15.8 + - - +
1409A GLY* 1.3 77.8 - - - +
1411A GLY* 1.3 63.0 - - - +
1412A TRP 3.2 1.1 - - - -
1413A ASP* 3.1 9.9 + - - -
1414A GLY 3.2 8.8 + - - -
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Residues in contact with GLY1411 (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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1396A ARG* 4.7 7.2 - - - -
1408A PRO 3.0 15.2 + - - -
1409A GLY 3.3 1.2 - - - -
1410A CYS* 1.3 75.2 - - - +
1412A TRP* 1.3 80.5 + - - +
1414A GLY* 3.3 3.0 + - - -
1415A GLY* 2.9 19.2 + - - -
1422A GLY* 4.2 9.8 - - - +
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Residues in contact with TRP1412 (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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1405A CYS 3.9 0.2 - - - -
1406A ASN* 3.5 33.7 - - - +
1407A SER* 2.8 21.7 + - - +
1408A PRO* 3.7 32.7 + - + +
1411A GLY* 1.3 77.4 - - - +
1413A ASP* 1.3 62.3 + - - +
1415A GLY 3.0 13.5 + - - -
1417A CYS 3.2 12.6 + - - -
1418A SER* 3.7 23.3 - - - +
1422A GLY 3.2 25.6 + - - -
1423A ASP* 4.1 8.6 + - - +
1424A PRO* 3.5 19.9 - - + +
1425A TRP* 3.5 27.6 - + - -
1434A TRP* 3.4 40.6 - + - -
1616A ALA* 3.7 20.6 - - + -
1617A VAL* 5.5 1.1 - - + -
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Residues in contact with ASP1413 (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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1392A CYS 5.0 0.3 - - - +
1395A LYS* 3.0 11.8 - - - +
1396A ARG* 3.6 8.3 + - - +
1400A ARG 3.0 2.3 - - - +
1401A CYS* 3.3 1.0 - - - -
1402A ASP* 2.4 36.1 + - - +
1405A CYS* 3.0 32.2 + - + +
1410A CYS 3.1 3.6 + - - -
1412A TRP* 1.3 76.8 - - - +
1414A GLY* 1.3 63.3 + - - +
1416A ASP* 3.0 18.3 + - + +
1417A CYS* 3.8 13.9 - - - -
5001A CA 2.4 30.6 - - - -
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Residues in contact with GLY1414 (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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1396A ARG* 3.6 41.6 + - - +
1397A GLY* 4.3 9.4 + - - -
1410A CYS 3.2 10.5 + - - -
1411A GLY 3.3 4.9 + - - -
1413A ASP* 1.3 74.8 - - - +
1415A GLY* 1.3 57.0 + - - +
1416A ASP* 3.3 2.0 + - - +
1420A SER* 5.4 0.5 - - - -
1422A GLY* 6.4 0.7 - - - -
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Residues in contact with GLY1415 (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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1411A GLY 2.9 11.6 + - - -
1412A TRP 3.0 5.3 + - - -
1414A GLY* 1.3 75.6 - - - +
1416A ASP* 1.3 64.6 + - - +
1417A CYS 3.1 3.8 + - - -
1418A SER* 3.3 18.1 + - - -
1419A LEU* 3.5 0.5 + - - -
1420A SER* 2.8 39.7 + - - -
1421A VAL 4.6 2.2 - - - -
1422A GLY* 5.6 2.2 - - - -
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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