Contacts of the helix formed by residues 229 - 234 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LEU* 4.6 7.9 - - + -
219C LEU* 4.1 2.5 - - + -
224C PHE* 3.5 40.2 - - + +
225C THR 6.0 0.2 - - - +
227C ILE* 3.3 33.1 + - + +
228C LEU* 1.3 73.5 - - - +
230C GLU* 1.3 73.0 + - + +
231C ARG 3.0 2.9 - - - -
232C VAL* 2.9 9.8 + - - +
233C MET* 2.9 26.9 + - + +
239C ILE* 3.8 29.7 - - + +
360C MET* 3.8 23.3 - - + -
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Residues in contact with GLU 230 (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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229C LEU* 1.3 84.3 - - + +
231C ARG* 1.3 61.1 + - + +
233C MET* 3.4 19.3 + - + +
234C HIS* 2.9 49.0 + - + -
360C MET* 6.3 2.9 - - + -
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Residues in contact with ARG 231 (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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202C LEU* 5.1 6.3 - - + +
203C GLU* 6.3 0.7 - - - -
228C LEU* 4.9 25.8 - - + +
229C LEU 4.8 1.6 - - - -
230C GLU* 1.3 80.7 - - + +
232C VAL* 1.3 63.5 + - + +
234C HIS* 4.6 8.0 + - - +
235C GLY* 4.8 2.4 + - - -
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Residues in contact with VAL 232 (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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202C LEU* 3.3 57.7 - - + +
205C VAL* 3.9 22.2 - - + -
212C SER* 5.5 3.6 - - - -
217C TYR* 4.2 8.3 - - + -
229C LEU 2.9 8.2 + - - +
231C ARG* 1.3 79.3 - - + +
233C MET* 1.3 59.7 + - - +
234C HIS 3.4 1.1 - - - -
235C GLY* 3.0 23.0 + - - +
236C GLY 3.5 2.8 + - - -
237C ALA* 3.7 25.8 + - + -
239C ILE* 4.6 6.3 - - + -
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Residues in contact with MET 233 (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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229C LEU 2.9 20.8 + - - +
230C GLU* 3.4 17.2 + - + +
232C VAL* 1.3 75.8 - - - +
234C HIS* 1.3 60.9 + - + +
236C GLY* 3.0 19.0 + - - +
237C ALA 3.4 18.8 - - - +
239C ILE* 3.8 11.2 - - + -
360C MET* 3.6 43.1 - - + +
361C LYS* 3.5 44.4 - - - +
362C VAL* 4.0 6.2 - - - +
365C SER* 6.2 0.4 - - - -
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Residues in contact with HIS 234 (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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230C GLU* 2.9 52.3 + - + +
231C ARG* 4.8 6.0 + - - +
232C VAL 3.4 0.4 - - - -
233C MET* 1.3 72.3 - - + +
235C GLY* 1.3 62.4 + - - +
236C GLY* 2.8 7.6 + - - -
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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