Contacts of the helix formed by residues 220 - 233 (chain J) 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 ASP 220 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206J LYS 5.5 0.5 - - - +
213J LYS* 2.8 65.5 + - + +
214J MET 3.5 3.5 - - - +
217J THR* 2.8 41.1 + - - +
218J LEU 2.9 1.8 - - - -
219J GLU* 1.3 88.3 - - - +
221J GLN* 1.3 49.9 + - - +
222J ILE 3.0 1.1 - - - -
223J ILE* 2.7 7.3 + - - +
224J SER* 2.3 41.5 + - - +
340J ILE* 4.8 0.4 - - + -
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Residues in contact with GLN 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206J LYS* 4.5 4.2 - - - +
216J GLY* 3.6 6.3 + - - +
217J THR* 2.6 39.1 + - - +
218J LEU* 2.4 46.3 - - + +
220J ASP* 1.3 70.0 - - - +
222J ILE* 1.3 64.0 + - - +
224J SER* 4.2 4.7 - - - -
225J ALA* 2.8 24.3 + - - +
340J ILE* 3.6 19.5 - - + +
341J LEU* 3.4 20.9 - - + +
448J GLN* 4.0 22.8 - - - +
449J LEU* 3.6 16.1 - - + +
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Residues in contact with ILE 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J ILE* 4.0 26.3 - - + +
197J ALA* 5.2 6.1 - - + -
218J LEU* 2.9 37.9 - - + -
219J GLU* 3.5 19.7 - - - +
221J GLN* 1.3 78.7 - - - +
223J ILE* 1.3 69.5 + - + +
225J ALA* 3.3 13.5 - - - +
226J ASN* 4.2 5.5 - - - +
250J ILE* 6.0 1.3 - - + -
252J ILE* 5.0 9.9 - - + -
260J LEU* 5.3 10.1 - - + -
262J SER 5.1 1.3 - - - +
263J ALA* 3.2 29.8 - - + -
449J LEU* 4.7 8.5 - - + +
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Residues in contact with ILE 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J ILE* 5.3 3.8 - - + -
194J GLN* 3.2 49.1 - - + +
197J ALA* 4.9 6.3 - - + -
219J GLU 2.8 25.8 - - - +
220J ASP* 2.7 9.2 + - - +
222J ILE* 1.3 85.8 - - + +
224J SER* 1.3 56.3 + - - +
225J ALA 2.6 17.1 + - - -
226J ASN* 2.9 36.7 + - - +
227J PRO* 3.2 5.8 - - + +
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Residues in contact with SER 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J LYS 4.2 3.8 + - - -
220J ASP* 2.3 32.8 + - - +
221J GLN* 3.7 6.1 - - - -
223J ILE* 1.3 67.6 - - - +
225J ALA* 1.3 64.3 - - - +
227J PRO* 3.0 22.0 - - - +
228J LEU 3.9 0.5 + - - -
337J ALA* 3.7 16.7 - - - +
340J ILE* 3.8 24.9 - - - +
341J LEU* 3.4 20.8 - - - +
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Residues in contact with ALA 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J GLN 2.8 10.6 + - - +
222J ILE* 3.3 17.0 - - - +
223J ILE 2.6 5.1 + - - -
224J SER* 1.3 73.8 - - - +
226J ASN* 1.3 68.6 + - - +
228J LEU* 3.0 19.9 + - - +
229J LEU* 3.4 11.1 + - + +
265J ILE* 4.1 25.1 - - + -
341J LEU* 3.7 10.1 - - - -
445J ILE* 4.4 14.9 - - + +
449J LEU* 5.2 1.8 - - + -
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Residues in contact with ASN 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J MLY 4.1 31.7 - - + +
193J ILE* 5.6 8.9 - - - +
194J GLN* 6.0 0.2 + - - -
222J ILE 4.2 6.2 - - - +
223J ILE* 2.9 32.2 + - - +
225J ALA* 1.3 78.1 - - - +
227J PRO* 1.3 57.2 - - + +
228J LEU 2.8 11.3 + - - -
229J LEU* 3.0 8.6 + - - +
230J GLU* 2.8 35.0 + - + +
248J MLY 2.8 37.6 - - - -
250J ILE* 5.4 1.0 - - - +
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Residues in contact with PRO 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J MLY 6.2 2.0 - - - -
223J ILE* 3.2 9.6 - - + +
224J SER* 3.0 22.9 - - - +
226J ASN* 1.3 97.6 - - + +
228J LEU* 1.3 58.9 + - - +
230J GLU* 4.1 13.0 - - + +
231J ALA* 3.7 8.8 + - - +
333J ALA* 4.9 16.1 - - + +
334J THR* 3.8 19.3 + - - -
337J ALA* 4.8 9.0 - - + -
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Residues in contact with LEU 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J SER 3.9 5.3 + - - +
225J ALA 3.0 9.1 + - - +
226J ASN 2.8 2.8 + - - -
227J PRO* 1.3 73.5 - - - +
229J LEU* 1.3 71.3 + - + +
230J GLU 3.0 0.7 - - - -
231J ALA* 2.8 14.7 + - - +
232J PHE* 3.2 39.7 - - + -
334J THR* 4.2 9.6 - - + +
337J ALA* 4.6 5.6 - - + -
338J ILE* 3.5 31.2 - - + -
341J LEU* 4.5 9.0 - - + -
343J PHE* 4.1 22.4 - - + -
351J ILE* 5.9 0.2 - - + -
441J MET* 4.3 14.4 - - - -
445J ILE* 3.9 23.3 - - + -
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Residues in contact with LEU 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J ALA* 3.4 13.2 + - + +
226J ASN* 3.4 9.6 - - - +
228J LEU* 1.3 84.8 - - + +
230J GLU* 1.3 51.3 + - + +
232J PHE* 3.1 3.0 + - - +
233J GLY* 2.4 39.0 + - - -
246J PHE* 4.0 19.9 - - + -
248J MLY 5.4 9.6 - - + +
265J ILE* 4.2 29.8 - - + -
267J THR* 5.6 0.7 - - - +
438J PHE* 3.9 23.5 - - + -
441J MET* 5.1 5.6 - - + -
442J VAL* 4.1 22.0 - - + +
445J ILE* 3.9 23.1 - - + -
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Residues in contact with GLU 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J THR* 3.6 12.8 - - + +
190J MLY 2.8 47.1 - - - +
226J ASN* 2.8 30.2 + - + +
227J PRO* 4.1 9.4 - - + +
229J LEU* 1.3 76.2 - - + +
231J ALA* 1.3 63.6 + - - +
232J PHE 3.1 0.2 - - - -
234J ASN* 2.9 45.6 + - + +
242J ASN* 2.6 31.0 + - - +
246J PHE* 6.1 0.9 - - + -
248J MLY 5.5 3.6 - - - -
286J HIS* 3.3 10.5 - - + -
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Residues in contact with ALA 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J PRO 3.7 4.7 + - - +
228J LEU 2.8 12.0 + - - +
230J GLU* 1.3 80.4 - - - +
232J PHE* 1.3 65.6 - - + +
286J HIS* 3.2 16.6 + - - -
287J ILE* 2.7 37.2 + - + +
290J GLN* 3.5 28.9 - - - +
334J THR* 3.8 9.4 - - + +
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Residues in contact with PHE 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J LEU* 3.2 44.6 + - + -
229J LEU* 3.1 4.8 + - - +
231J ALA* 1.3 81.1 - - + +
233J GLY* 1.3 58.9 + - - +
270J LEU* 5.0 0.3 - - - +
285J TYR* 2.8 21.3 - - - -
287J ILE* 3.0 39.5 - - + -
334J THR* 4.9 1.3 - - + -
338J ILE* 5.5 0.9 - - + -
351J ILE* 3.7 22.4 - - + -
355J THR* 3.8 20.2 - - - -
434J TYR* 2.8 39.9 + + + +
437J MET* 4.0 9.0 - - + -
438J PHE* 3.8 19.9 - - + -
441J MET* 3.8 22.9 - - + -
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Residues in contact with GLY 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229J LEU 2.4 19.9 + - - -
232J PHE* 1.3 73.2 - - - +
234J ASN* 1.3 60.6 + - - +
245J ARG* 2.9 27.4 + - - -
246J PHE* 3.0 23.0 - - - -
270J LEU* 4.1 3.1 - - - -
285J TYR* 3.3 13.2 - - - -
438J PHE* 3.8 6.9 - - - -
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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