Contacts of the helix formed by residues 235 - 242 (chain B) in PDB entry 3GZN
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 PRO 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASN 4.1 2.9 - - - +
234B PHE* 1.4 87.0 - - + +
236B MET* 1.3 57.4 + - - +
237B CYS* 3.0 5.4 - - + +
238B THR* 2.8 49.0 + - + +
239B ILE* 3.2 9.2 + - - +
244B ARG* 5.4 2.5 - - - +
248B HIS* 5.7 0.9 - - - +
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Residues in contact with MET 236 (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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234B PHE 3.3 5.6 + - - -
235B PRO* 1.3 69.4 - - - +
237B CYS* 1.3 59.1 + - - +
239B ILE* 3.8 8.0 - - + +
240B ALA* 2.8 42.6 + - + +
255B MET* 5.0 15.5 - - + -
256B LEU* 4.3 25.1 - - - -
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Residues in contact with CYS 237 (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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235B PRO* 2.9 6.4 + - + +
236B MET* 1.3 83.2 - - - +
238B THR* 1.3 59.1 + - - +
240B ALA* 3.5 7.7 - - - +
241B SER* 3.1 23.9 + - - -
242B MET* 3.7 21.0 + - + +
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Residues in contact with THR 238 (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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235B PRO* 2.8 35.8 + - + +
237B CYS* 1.3 71.3 - - - +
239B ILE* 1.3 65.1 + - - +
242B MET* 2.8 46.6 + - - +
243B PRO* 3.2 13.2 - - - +
244B ARG* 3.1 42.1 + - - +
248B HIS* 4.0 19.7 - - + +
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Residues in contact with ILE 239 (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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234B PHE* 3.7 27.6 - - + +
235B PRO 3.2 11.6 + - - +
236B MET* 3.8 11.2 - - - +
238B THR* 1.3 78.7 - - - +
240B ALA* 1.3 63.3 + - - +
241B SER* 3.3 1.9 + - - -
243B PRO* 5.0 0.7 - - - +
248B HIS* 3.7 34.7 - - + +
251B GLU* 3.7 26.7 - - + +
252B TYR* 3.1 49.7 - - - +
255B MET* 4.7 10.8 - - + -
256B LEU* 3.9 14.8 - - + -
288B ARG* 4.2 2.6 + - - -
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Residues in contact with ALA 240 (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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236B MET* 2.8 36.8 + - + +
237B CYS* 3.5 11.0 - - - +
238B THR 3.3 0.8 - - - -
239B ILE* 1.3 74.1 - - - +
241B SER* 1.3 68.5 + - - +
252B TYR* 3.7 17.0 - - - -
256B LEU* 3.7 13.5 - - + +
288B ARG* 4.4 0.9 + - - -
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Residues in contact with SER 241 (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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343A SER* 4.9 0.9 + - - -
237B CYS 3.1 7.2 + - - -
239B ILE 3.3 0.6 + - - -
240B ALA* 1.3 86.1 + - - +
242B MET* 1.3 69.7 + - - +
243B PRO* 3.6 9.4 - - - -
288B ARG* 4.5 6.7 - - - +
292B TYR* 4.4 15.5 + - - -
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Residues in contact with MET 242 (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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218A HIS* 3.5 42.6 - - + +
341A ALA 3.8 14.7 - - - +
342A ASP* 3.8 22.7 - - + -
343A SER* 3.8 7.0 - - - +
237B CYS* 3.7 21.2 + - + +
238B THR* 2.8 39.5 + - + +
241B SER* 1.3 78.6 - - - +
243B PRO* 1.4 68.2 - - - +
244B ARG* 3.5 13.6 + - - +
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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