Contacts of the helix formed by residues 229 - 237 (chain G) in PDB entry 6MZL
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 LEU 229 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227G CYS 5.5 1.8 - - - +
228G SER* 1.3 85.0 - - - +
230G ASP* 1.3 65.5 + - - +
231G CYS* 3.7 2.7 - - - +
232G HIS* 3.4 34.0 - - + +
233G ARG* 3.0 26.7 + - - +
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Residues in contact with ASP 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G LEU* 1.3 78.5 - - - +
231G CYS* 1.3 60.5 + - - +
233G ARG* 3.9 1.3 - - - +
234G ALA* 2.9 30.6 + - - +
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Residues in contact with CYS 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G LEU* 5.3 1.1 - - - -
230G ASP* 1.3 77.9 - - - +
232G HIS* 1.3 84.8 + - - +
234G ALA* 3.6 8.0 - - - +
235G GLU* 2.9 35.1 + - + +
312G ASP* 5.3 3.6 - - - -
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Residues in contact with HIS 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G SER* 4.0 9.4 - - - -
229G LEU* 3.4 49.9 - - + +
230G ASP 3.2 0.4 - - - -
231G CYS* 1.3 89.7 - - - +
233G ARG* 1.3 57.1 + - - +
235G GLU* 3.4 1.1 + - - +
236G LEU* 2.9 39.9 + - + +
310G SER* 5.3 0.2 + - - -
312G ASP* 3.2 39.9 + - + -
313G SER* 4.6 7.8 + - - -
316G LEU* 3.4 30.1 - - + +
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Residues in contact with ARG 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ILE* 4.3 22.7 - - - +
226G GLU* 4.4 33.2 + - - +
228G SER* 4.5 5.1 - - - +
229G LEU 3.0 20.5 + - - +
230G ASP 4.2 1.3 - - - +
232G HIS* 1.3 76.3 - - - +
234G ALA* 1.3 53.3 + - - +
236G LEU* 4.3 3.6 - - - +
237G SER* 2.5 50.1 + - - +
240G PHE* 5.2 10.6 - - + -
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Residues in contact with ALA 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ASP 2.9 21.1 + - - +
231G CYS* 3.6 9.9 - - - +
232G HIS 3.2 0.4 - - - -
233G ARG* 1.3 78.4 - - - +
235G GLU* 1.3 61.6 + - + +
237G SER* 4.4 8.2 + - - -
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Residues in contact with GLU 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G CYS* 2.9 18.6 + - + +
232G HIS 4.5 0.7 - - - +
234G ALA* 1.3 79.3 - - + +
236G LEU* 1.3 66.9 + - + +
237G SER 3.6 1.1 - - - -
238G GLN* 2.4 35.9 + - - +
308G ARG 3.8 11.4 - - - +
309G ILE* 5.2 0.9 - - - -
310G SER* 3.7 14.0 + - - -
313G SER* 5.2 2.7 - - - +
342G PHE* 3.3 48.5 - - + +
343G ASP* 4.3 8.1 - - - +
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Residues in contact with LEU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ILE* 4.2 17.8 - - + +
228G SER* 5.8 1.6 - - - +
232G HIS* 2.9 23.0 + - + +
233G ARG 3.6 1.6 - - - -
235G GLU* 1.3 87.9 - - - +
237G SER* 1.3 64.3 + - - +
238G GLN 3.1 1.6 - - - +
239G LEU* 3.1 49.5 + - + +
240G PHE* 3.5 11.7 - - - -
309G ILE* 3.9 15.5 - - + -
313G SER* 3.6 46.0 - - - +
316G LEU* 5.0 10.8 - - + -
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Residues in contact with SER 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G ARG* 2.5 35.3 + - - +
234G ALA* 4.4 8.5 - - - -
235G GLU 3.6 0.6 - - - -
236G LEU* 1.3 77.6 - - - +
238G GLN* 1.3 60.5 + - - +
240G PHE* 3.2 31.8 + - - +
241G TYR 4.6 0.2 + - - -
271G GLN* 4.5 4.3 - - - +
272G GLU* 5.1 16.2 - - - +
275G TYR* 5.8 0.3 + - - -
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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