Contacts of the helix formed by residues 1410 - 1416 (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 CYS1410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1392B CYS* 3.1 37.0 - - - -
1405B CYS 3.7 19.5 - - - +
1407B SER* 3.1 12.3 + - - +
1409B GLY* 1.3 78.9 - - - +
1411B GLY* 1.3 64.3 + - - +
1412B TRP 3.2 2.7 + - - -
1413B ASP* 3.4 8.9 + - - +
1414B GLY* 3.4 8.3 + - - -
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Residues in contact with GLY1411 (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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1407B SER 3.3 2.0 + - - -
1408B PRO 3.3 12.0 + - - -
1409B GLY 3.5 1.2 + - - -
1410B CYS* 1.3 77.8 - - - +
1412B TRP* 1.3 73.0 + - - +
1414B GLY* 3.4 4.3 + - - -
1415B GLY* 3.0 22.9 + - - -
1422B GLY* 4.0 8.9 - - - +
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Residues in contact with TRP1412 (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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1406B ASN* 3.2 43.3 - - - +
1407B SER* 3.1 18.9 + - - +
1408B PRO* 3.6 43.4 - - + +
1411B GLY* 1.3 81.8 - - - +
1413B ASP* 1.3 62.0 + - - +
1415B GLY 2.9 16.5 + - - -
1416B ASP 3.0 9.7 + - - -
1417B CYS 3.5 3.6 + - - -
1418B SER* 4.0 23.3 - - - +
1422B GLY 3.8 15.7 + - - -
1423B ASP* 4.6 3.8 + - - -
1424B PRO* 3.8 21.7 - - + +
1425B TRP* 3.4 32.1 - + - -
1434B TRP* 4.7 9.9 - - + -
1616B ALA* 3.7 25.1 - - + -
1617B VAL* 5.0 7.4 - - + -
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Residues in contact with ASP1413 (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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1392B CYS* 5.7 2.8 - - - +
1397B GLY 3.8 1.8 + - - -
1398B ASP* 2.6 7.6 - - - +
1400B ARG 3.0 0.2 - - - +
1402B ASP* 2.8 27.5 + - - +
1405B CYS* 3.2 40.8 + - + +
1410B CYS* 3.4 4.4 + - - -
1412B TRP* 1.3 76.0 - - - +
1414B GLY* 1.3 55.8 - - - +
1416B ASP* 2.5 41.2 - - + +
1417B CYS* 4.2 7.4 - - - -
5001B CA 2.3 31.7 - - - -
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Residues in contact with GLY1414 (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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1397B GLY* 4.0 20.8 + - - -
1410B CYS 3.4 8.5 + - - -
1411B GLY* 3.4 8.6 + - - -
1412B TRP 3.2 0.8 - - - -
1413B ASP* 1.3 77.6 - - - +
1415B GLY* 1.3 57.3 + - - +
1416B ASP* 3.4 2.3 + - - +
1420B SER* 5.5 0.5 - - - -
1422B GLY* 5.8 2.1 - - - -
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Residues in contact with GLY1415 (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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1411B GLY 3.0 8.5 + - - -
1412B TRP 2.9 8.3 + - - -
1414B GLY* 1.3 75.8 - - - +
1416B ASP* 1.3 61.8 + - - +
1417B CYS 3.2 3.5 + - - -
1418B SER* 3.4 18.9 + - - -
1420B SER* 2.6 39.0 + - - -
1421B VAL 4.0 8.3 - - - -
1422B GLY* 5.0 2.2 - - - -
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Residues in contact with ASP1416 (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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1397B GLY* 4.3 1.7 + - - -
1398B ASP* 1.8 51.0 + - - +
1399B GLN* 3.6 12.4 + - - +
1400B ARG 3.4 9.8 + - - +
1401B CYS* 3.4 16.9 + - - +
1412B TRP 3.0 1.6 + - - -
1413B ASP* 2.5 28.5 - - + +
1414B GLY 4.2 3.8 - - - +
1415B GLY* 1.3 80.1 - - - +
1417B CYS* 1.3 60.7 + - - +
1419B LEU* 4.4 5.2 + - - +
1420B SER 5.0 0.2 - - - -
1627B ARG 5.5 1.7 - - - +
5001B CA 2.4 5.5 - - - -
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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