Contacts of the helix formed by residues 229 - 234 (chain B) in PDB entry 3P3W
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU* 4.5 5.4 - - + -
219B LEU* 3.8 17.3 - - + -
224B PHE* 3.3 44.0 - - + +
227B ILE* 3.2 33.4 + - + +
228B LEU* 1.3 72.1 - - - +
230B GLU* 1.3 64.2 + - - +
231B ARG 3.6 1.8 - - - -
232B VAL* 3.3 11.2 + - + +
233B MET* 3.0 33.9 + - + +
239B ILE* 4.3 18.6 - - + +
360B MET* 3.5 20.2 - - + -
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Residues in contact with GLU 230 (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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228B LEU* 3.6 7.9 - - + -
229B LEU* 1.3 80.0 - - - +
231B ARG* 1.3 67.1 + - + +
233B MET* 3.5 6.5 + - - +
234B HIS* 2.9 41.1 + - + -
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Residues in contact with ARG 231 (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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206B VAL* 3.8 35.6 - - + +
212B SER* 5.8 0.7 - - - -
228B LEU 5.5 0.2 + - - -
229B LEU 3.6 0.2 - - - -
230B GLU* 1.3 81.2 - - + +
232B VAL* 1.3 64.0 + - + +
234B HIS* 3.9 11.3 + - - +
235B GLY* 4.3 4.9 + - - -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 4.2 43.5 - - + +
205B VAL* 5.0 11.4 - - + -
206B VAL* 5.0 5.8 - - + -
212B SER* 2.9 30.4 + - - +
217B TYR* 4.7 15.7 - - + -
228B LEU 4.8 2.7 - - - +
229B LEU* 3.3 12.8 + - + +
230B GLU 3.3 0.2 - - - -
231B ARG* 1.3 77.2 - - + +
233B MET* 1.3 63.1 + - - +
234B HIS 3.4 0.5 + - - -
235B GLY 3.4 1.0 + - - -
237B ALA* 3.7 23.2 - - + +
239B ILE* 4.0 14.6 - - + -
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 3.0 22.9 + - + +
230B GLU* 3.6 8.7 - - - +
231B ARG 3.4 0.2 - - - -
232B VAL* 1.3 77.9 - - - +
234B HIS* 1.3 68.1 + - + +
235B GLY 3.2 3.9 + - - -
236B GLY* 3.7 9.5 + - - -
237B ALA 4.4 5.6 + - - +
239B ILE* 4.3 11.7 - - + -
360B MET* 3.7 52.3 - - + +
361B LYS* 4.1 21.3 - - - +
362B VAL* 4.8 12.0 - - - +
365B SER* 4.4 13.5 - - - -
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Residues in contact with HIS 234 (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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230B GLU* 2.9 40.1 + - + +
231B ARG* 3.9 7.5 + - - +
232B VAL 3.3 1.2 - - - -
233B MET* 1.3 84.9 - - + +
235B GLY* 1.3 57.8 + - - +
236B GLY 3.7 0.2 - - - -
362B VAL* 6.3 1.1 - - - -
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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