Contacts of the helix formed by residues 1362 - 1366 (chain C) in PDB entry 4GND
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 CYS1362 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1336C CYS* 3.2 14.1 - - + -
1343C LYS* 3.9 5.4 - - - -
1345C TYR* 2.9 44.6 - - + -
1360C TRP* 3.6 10.7 + - + -
1361C GLU* 1.3 77.4 - - - +
1363C PRO* 1.4 70.6 - - + +
1364C TRP* 3.1 18.6 + - - -
1365C HIS* 3.1 16.8 + - - +
1366C GLN* 4.2 2.3 + - - +
1502C ZN 2.3 34.1 - - - -
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Residues in contact with PRO1363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326C GLN* 6.2 0.2 - - - +
1345C TYR* 3.8 15.3 - - + +
1350C LEU* 4.1 15.7 - - + -
1360C TRP* 3.8 14.4 - - + +
1362C CYS* 1.4 90.3 - - + +
1364C TRP* 1.3 54.9 + - - +
1365C HIS 3.0 0.9 - - - -
1366C GLN* 2.9 44.0 + - + +
1368C ASP* 4.9 3.4 - - - +
1382C PRO* 3.8 19.0 - - + +
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Residues in contact with TRP1364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1325C PHE* 3.4 24.3 - + - -
1341C CYS* 3.9 14.4 - - + -
1342C PRO* 4.7 7.9 - - + -
1343C LYS* 3.6 32.5 - - + -
1345C TYR* 4.0 5.6 + - - +
1362C CYS* 3.1 17.0 + - - -
1363C PRO* 1.3 77.6 - - - +
1365C HIS* 1.3 65.6 + + + +
1366C GLN 3.3 0.4 - - - -
1377C PHE* 3.3 39.3 - + + +
1378C CYS 2.6 31.7 + - - +
1379C GLU* 4.5 10.5 - - + -
1382C PRO* 3.4 22.6 + - + +
1383C HIS 3.8 4.0 - - - -
1384C SER* 2.7 27.6 + - - -
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Residues in contact with HIS1365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336C CYS* 3.4 5.9 - - - -
1338C LYS* 3.9 29.2 + - + +
1341C CYS* 3.2 17.9 - - + -
1361C GLU* 4.3 14.6 - - + +
1362C CYS* 3.1 27.6 + - - +
1363C PRO 3.0 1.4 - - - -
1364C TRP* 1.3 88.4 + + - +
1366C GLN* 1.3 58.9 + - - +
1373C ALA* 3.7 7.4 - - - +
1374C ALA* 3.0 25.9 + - - -
1377C PHE* 4.5 11.9 - + + -
1502C ZN 1.9 37.9 - - - -
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Residues in contact with GLN1366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362C CYS 4.2 2.0 + - - +
1363C PRO* 2.9 29.8 + - + +
1364C TRP 3.3 0.6 - - - -
1365C HIS* 1.3 80.6 - - - +
1367C CYS* 1.3 68.1 + - - +
1368C ASP* 3.4 8.0 + - - +
1371C SER* 3.6 38.6 - - - +
1372C SER 3.8 3.6 - - - -
1384C SER* 3.2 8.8 + - - -
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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