Contacts of the helix formed by residues 223 - 233 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218W TYR 4.1 0.2 - - - -
219W VAL* 3.5 22.2 - - + -
220W ALA* 3.2 39.3 - - + -
221W LEU 3.5 0.4 - - - -
222W ASP* 1.3 75.2 - - - +
224W GLU* 1.4 60.4 - - - +
226W GLU* 3.6 5.3 - - - +
227W MET* 3.4 27.9 + - - +
255W PHE* 3.0 54.1 - + + -
259W GLU* 3.1 49.2 - - + +
262W PHE* 3.9 2.9 - + - -
312W ARG* 2.9 39.1 - - - +
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Residues in contact with GLU 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222W ASP* 3.0 18.0 - - - +
223W PHE* 1.4 75.2 - - - +
225W ASN* 1.3 84.4 + - - +
226W GLU 3.1 7.7 + - - -
227W MET* 3.5 6.9 + - - +
228W ALA* 3.5 14.6 + - - +
259W GLU* 4.5 1.1 + - - -
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Residues in contact with ASN 225 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222W ASP* 3.2 23.3 + - - +
224W GLU* 1.3 109.8 + - - +
226W GLU* 1.3 57.3 + - - +
227W MET 3.8 0.2 - - - -
228W ALA* 3.8 18.4 - - + +
229W THR* 2.6 22.7 + - - -
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Residues in contact with GLU 226 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220W ALA* 3.7 22.0 - - + +
221W LEU 5.1 2.1 - - - +
222W ASP 3.2 17.2 - - - +
223W PHE* 3.6 11.9 - - - +
224W GLU 3.1 0.2 - - - -
225W ASN* 1.3 78.2 - - - +
227W MET* 1.3 61.9 + - - +
228W ALA 3.4 0.4 - - - -
229W THR* 3.1 23.6 + - - +
230W ALA* 2.9 20.8 + - - +
236W LEU* 4.6 7.7 - - - +
255W PHE* 3.4 37.6 - - + -
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Residues in contact with MET 227 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223W PHE 3.4 15.9 - - - +
224W GLU* 3.6 8.1 - - - +
226W GLU* 1.3 77.2 - - - +
228W ALA* 1.4 57.0 + - - +
230W ALA* 2.9 29.5 + - - +
231W ALA* 3.2 7.6 + - - +
252W ASN* 5.7 1.8 - - - -
255W PHE* 3.3 22.0 - - + -
256W ARG* 3.7 31.0 - - + +
259W GLU* 3.9 16.2 - - - +
266W PHE* 5.6 5.2 - - + -
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Residues in contact with ALA 228 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224W GLU 3.5 4.6 + - - +
225W ASN* 3.8 31.0 - - + +
227W MET* 1.4 77.1 - - - +
229W THR* 1.3 61.0 + - - +
231W ALA* 3.4 20.0 + - - +
232W SER* 3.5 11.0 + - - -
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Residues in contact with THR 229 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225W ASN 2.6 25.6 + - - -
226W GLU* 3.1 21.3 + - - +
227W MET 3.2 0.2 - - - -
228W ALA* 1.3 77.0 - - - +
230W ALA* 1.4 63.0 + - - +
231W ALA 3.3 0.5 + - - -
232W SER* 3.4 10.8 + - - -
233W SER* 3.3 16.3 + - - -
234W SER* 4.1 22.4 + - - +
236W LEU* 5.4 3.1 - - + -
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Residues in contact with ALA 230 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226W GLU 2.9 14.5 + - - +
227W MET* 2.9 19.4 + - - +
229W THR* 1.4 74.2 - - - +
231W ALA* 1.4 51.5 + - - +
233W SER* 2.9 33.1 + - - -
236W LEU* 3.8 16.8 - - + +
252W ASN* 3.3 36.9 + - + +
255W PHE* 4.8 2.0 - - + -
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Residues in contact with ALA 231 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227W MET 3.2 5.9 + - - +
228W ALA* 3.4 13.7 - - - +
229W THR 3.2 0.2 - - - -
230W ALA* 1.4 75.1 - - - +
232W SER* 1.3 60.4 + - - +
233W SER* 3.0 11.4 + - - -
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Residues in contact with SER 232 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228W ALA 3.5 9.3 + - - -
229W THR* 3.4 12.3 + - - -
231W ALA* 1.3 75.1 - - - +
233W SER* 1.4 68.7 + - - +
234W SER* 5.1 1.8 - - - -
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Residues in contact with SER 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229W THR 3.3 1.6 + - - -
230W ALA 2.9 22.2 + - - -
231W ALA 3.0 7.3 + - - -
232W SER* 1.4 85.4 - - - +
234W SER* 1.3 68.5 - - - +
236W LEU* 4.1 3.4 - - - +
237W GLU* 5.7 4.4 + - - +
252W ASN* 5.0 2.6 + - - -
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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