Contacts of the helix formed by residues 223 - 233 (chain V) in PDB entry 1O1F
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 PHE 223 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219V VAL* 3.5 22.0 - - + -
220V ALA* 3.2 40.6 - - + -
221V LEU 3.5 0.4 - - - -
222V ASP* 1.3 74.6 - - - +
224V GLU* 1.4 60.3 + - - +
226V GLU* 3.6 5.9 - - - +
227V MET* 3.4 27.7 + - - +
255V PHE* 3.0 54.1 - + + -
258V PRO 4.1 0.2 - - - -
259V GLU* 3.1 49.5 - - + +
262V PHE* 3.9 2.7 - + - -
312V ARG* 2.9 38.9 - - - +
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Residues in contact with GLU 224 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222V ASP* 3.0 17.3 - - - +
223V PHE* 1.4 75.1 - - - +
225V ASN* 1.3 83.9 + - - +
226V GLU 3.1 8.3 + - - -
227V MET* 3.5 7.1 + - - +
228V ALA* 3.5 14.6 + - - +
259V GLU* 4.5 1.1 + - - -
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Residues in contact with ASN 225 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222V ASP* 3.2 24.8 + - - +
224V GLU* 1.3 111.8 + - - +
226V GLU* 1.3 57.1 + - - +
228V ALA* 3.8 18.1 - - + +
229V THR* 2.6 22.8 + - - -
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Residues in contact with GLU 226 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220V ALA* 3.7 23.0 - - + +
221V LEU 5.1 2.5 - - - +
222V ASP 3.2 17.8 - - - +
223V PHE* 3.6 11.9 - - - +
224V GLU 3.1 0.4 - - - -
225V ASN* 1.3 79.9 - - - +
227V MET* 1.3 61.9 + - - +
228V ALA 3.4 0.7 - - - -
229V THR* 3.1 24.1 + - - +
230V ALA* 2.9 21.0 + - - +
236V LEU* 4.6 6.7 - - - +
255V PHE* 3.4 37.5 - - + -
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Residues in contact with MET 227 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223V PHE 3.4 15.9 - - - +
224V GLU* 3.6 8.1 - - - +
226V GLU* 1.3 76.5 - - - +
228V ALA* 1.4 57.9 + - - +
230V ALA* 2.9 30.4 + - - +
231V ALA* 3.2 7.8 + - - +
252V ASN* 5.7 1.6 - - - -
255V PHE* 3.3 22.7 - - + -
256V ARG* 3.7 30.1 - - + +
259V GLU* 3.9 16.2 - - - +
266V PHE* 5.6 5.2 - - + -
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Residues in contact with ALA 228 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224V GLU 3.5 4.0 + - - +
225V ASN* 3.8 31.0 - - + +
227V MET* 1.4 78.1 - - - +
229V THR* 1.3 61.6 + - - +
231V ALA* 3.4 20.2 + - - +
232V SER* 3.5 11.5 + - - -
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Residues in contact with THR 229 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225V ASN 2.6 25.5 + - - -
226V GLU* 3.1 22.0 + - - +
227V MET 3.2 0.2 - - - -
228V ALA* 1.3 75.7 - - - +
230V ALA* 1.4 63.2 + - - +
231V ALA 3.3 0.7 + - - -
232V SER* 3.4 10.6 + - - -
233V SER* 3.3 16.1 + - - -
234V SER* 4.1 22.5 + - - +
236V LEU* 4.9 3.6 - - + -
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Residues in contact with ALA 230 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226V GLU 2.9 14.1 + - - +
227V MET* 2.9 20.0 + - - +
229V THR* 1.4 74.2 - - - +
231V ALA* 1.4 51.1 + - - +
233V SER* 2.9 33.1 + - - -
236V LEU* 3.8 17.8 - - + +
252V ASN* 3.3 35.9 + - + +
255V PHE* 4.8 2.2 - - + -
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Residues in contact with ALA 231 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227V MET 3.2 5.3 + - - +
228V ALA* 3.4 13.9 - - - +
230V ALA* 1.4 75.7 - - - +
232V SER* 1.3 60.2 + - - +
233V SER* 3.0 11.0 + - - -
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Residues in contact with SER 232 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228V ALA 3.5 9.4 + - - -
229V THR* 3.4 12.5 + - - -
231V ALA* 1.3 75.5 - - - +
233V SER* 1.4 67.5 + - - +
234V SER* 5.1 1.6 - - - -
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Residues in contact with SER 233 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229V THR 3.3 1.6 + - - -
230V ALA 2.9 21.8 + - - -
231V ALA 3.0 7.1 + - - -
232V SER* 1.4 86.2 - - - +
234V SER* 1.3 68.5 - - - +
236V LEU* 4.1 3.5 - - - +
237V GLU* 5.7 4.5 + - - +
252V ASN* 5.0 2.4 + - - -
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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