Contacts of the helix formed by residues 224 - 239 (chain A) in PDB entry 3OPY
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 GLY 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A PRO* 1.3 73.6 - - - +
225A MET* 1.4 60.0 + - - +
226A ASN* 3.2 3.9 - - - +
227A ALA* 3.1 9.2 + - - -
228A ALA* 2.8 25.8 + - - +
275A GLY* 4.8 3.6 - - - -
371A ILE* 3.7 16.6 - - - -
500A PRO* 3.7 22.6 - - - +
504A ASP* 5.0 1.1 - - - -
508A ALA* 3.3 9.3 - - - +
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Residues in contact with MET 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A THR* 4.1 20.5 - - + +
218A SER 3.7 16.4 - - - +
219A GLY 5.1 0.2 - - - +
220A GLY 3.7 16.4 - - - +
221A ASP* 4.5 3.4 - - - -
222A ALA* 3.2 31.7 + - + +
224A GLY* 1.4 76.4 - - - +
226A ASN* 1.3 56.8 + - - +
228A ALA* 3.2 10.7 + - - +
229A VAL* 2.9 33.5 + - - +
276A GLY 3.6 11.9 + - - +
277A THR* 4.2 12.8 - - - -
281A THR* 5.5 1.6 - - - -
311A CYS* 3.5 35.9 - - - +
358A GLY* 3.8 23.1 - - - +
371A ILE* 4.4 1.7 - - + +
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLY* 3.2 1.4 - - - +
225A MET* 1.3 72.1 - - - +
227A ALA* 1.3 58.8 + - - +
229A VAL* 3.1 4.9 + - - +
230A ARG* 2.9 26.7 + - - +
271A LEU* 3.3 34.6 - - + +
274A ILE* 3.4 17.0 - - - +
275A GLY* 3.1 26.3 - - - +
276A GLY 3.1 23.4 + - - +
277A THR* 3.4 2.9 + - - +
278A ILE* 2.8 46.9 + - - +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLY* 3.1 17.4 + - - +
226A ASN* 1.3 75.3 - - - +
228A ALA* 1.4 57.6 + - - +
230A ARG* 3.4 6.2 + - - +
231A ALA* 3.0 29.1 + - - +
271A LEU 3.5 7.0 + - - -
272A LEU* 4.2 23.1 - - + +
500A PRO* 4.9 2.0 - - + +
505A ARG* 4.5 11.2 - - - +
508A ALA* 3.8 14.6 - - + -
509A THR* 3.7 16.1 + - - +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 5.3 0.9 - - + -
224A GLY 2.8 12.9 + - - +
225A MET* 3.2 13.4 + - - +
227A ALA* 1.4 75.0 - - - +
229A VAL* 1.3 59.3 + - + +
231A ALA* 3.3 1.9 + - - +
232A VAL* 2.9 36.1 + - - +
311A CYS* 4.4 12.3 - - + -
356A LEU* 4.3 19.3 - - + -
371A ILE* 4.5 4.3 - - + -
508A ALA* 3.7 22.4 - - + +
512A GLY* 4.4 0.6 - - - -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 4.1 15.3 - - + -
217A THR* 3.8 24.2 - - + -
225A MET 2.9 18.8 + - - +
226A ASN* 3.1 11.6 + - - +
228A ALA* 1.3 73.8 - - + +
230A ARG* 1.4 55.8 + - - +
232A VAL* 3.4 1.3 + - - +
233A THR* 2.7 46.4 + - - +
263A LEU* 4.3 5.4 - - + -
268A VAL* 4.1 11.9 - - + -
271A LEU* 4.3 5.8 - - + -
277A THR* 4.6 5.6 - - - +
278A ILE* 4.8 5.2 - - + -
279A ILE* 3.8 31.6 - - + +
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN 2.9 16.1 + - - +
227A ALA 3.7 4.3 - - - +
228A ALA 3.3 0.2 - - - -
229A VAL* 1.4 76.8 - - - +
231A ALA* 1.3 54.6 + - - +
234A ARG* 3.1 49.0 + - - +
268A VAL* 3.3 42.2 + - + +
270A GLY 5.0 1.8 - - - +
271A LEU* 3.8 4.0 - - + +
272A LEU* 3.6 44.4 - - - +
509A THR* 3.6 23.8 + - - +
785A LEU 5.0 2.0 + - - -
788A GLY* 4.0 22.0 - - - -
977A SER 5.5 0.6 + - - -
980A LEU* 3.8 41.4 + - - +
981A SER* 4.7 2.2 - - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ALA 3.0 17.2 + - - +
228A ALA 3.6 4.5 - - - +
230A ARG* 1.3 73.2 - - - +
232A VAL* 1.4 65.7 + - - +
235A ALA* 3.0 29.5 + - - +
508A ALA 4.1 0.2 - - - +
509A THR* 3.3 34.1 - - - +
512A GLY* 3.9 10.3 - - - -
513A VAL* 4.0 1.7 - - - +
980A LEU* 3.9 20.6 - - + +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 4.9 6.7 - - + -
215A ILE* 3.8 40.6 - - + -
228A ALA 2.9 21.6 + - - +
229A VAL 3.9 3.4 - - - +
231A ALA* 1.4 74.3 - - - +
233A THR* 1.3 62.0 - - - +
236A GLY* 3.0 21.1 + - - -
243A VAL* 4.0 6.7 - - + +
309A VAL* 4.4 16.2 - - + -
356A LEU* 4.1 12.1 - - + -
512A GLY* 3.6 21.8 - - - +
515A ALA* 4.5 1.3 - - + -
516A VAL* 3.2 23.8 - - + +
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 4.7 0.9 - - - +
229A VAL* 2.7 22.5 + - - +
232A VAL* 1.3 77.8 - - - +
234A ARG* 1.3 57.8 + - - +
236A GLY 3.1 0.2 + - - -
237A ILE* 3.0 45.0 + - + +
243A VAL* 3.4 21.5 - - + +
263A LEU* 3.4 45.6 - - + +
264A GLN 4.1 3.4 - - - +
268A VAL* 3.7 23.2 - - + +
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Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ARG* 3.1 31.7 + - - +
233A THR* 1.3 77.2 - - - +
235A ALA* 1.4 55.8 + - - +
237A ILE* 3.5 2.8 + - - +
238A PHE* 3.1 27.7 + - - +
265A TRP* 2.9 83.9 + - + +
268A VAL* 3.5 42.0 + - + -
269A ARG* 3.5 16.8 - - - +
979A LEU* 4.4 1.6 - - - +
980A LEU* 2.9 38.0 + - + +
981A SER* 5.1 1.6 - - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA 3.0 21.8 + - - +
234A ARG* 1.4 72.5 - - - +
236A GLY* 1.3 59.6 + - - +
238A PHE* 3.3 1.9 + - - +
239A TYR* 3.0 38.4 + - + -
513A VAL* 4.2 19.1 - - + +
516A VAL* 3.8 21.3 - - + -
979A LEU* 3.7 21.3 - - + -
980A LEU* 3.9 1.6 - - - +
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Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 4.9 2.0 - - - -
232A VAL 3.0 15.0 + - - -
233A THR 3.1 3.8 + - - -
235A ALA* 1.3 75.7 - - - +
237A ILE* 1.3 54.1 + - - +
239A TYR 3.4 1.9 + - - -
240A GLY 3.3 4.5 + - - -
241A CYS* 2.8 44.0 + - - +
243A VAL* 3.9 11.2 - - - -
516A VAL* 3.6 15.6 - - - +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A THR* 3.0 36.0 + - + +
234A ARG 3.7 4.9 - - - +
235A ALA 3.3 0.2 - - - -
236A GLY* 1.3 75.5 - - - +
238A PHE* 1.4 54.8 - - - +
240A GLY* 2.9 25.3 + - - -
241A CYS 3.6 15.3 + - - +
242A LYS* 5.6 0.2 - - - -
243A VAL* 4.7 6.7 - - + +
262A GLU* 5.6 2.0 - - - +
263A LEU 4.0 7.9 - - - +
264A GLN* 4.0 2.7 - - - -
265A TRP* 3.5 52.9 - - + +
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ARG 3.1 18.1 + - - +
235A ALA 3.5 4.3 - - - +
237A ILE* 1.4 76.9 - - - +
239A TYR* 1.3 84.4 + + - +
240A GLY* 3.3 2.9 + - - -
265A TRP* 5.7 2.2 - - - +
979A LEU* 3.8 40.6 - - + +
984A LEU* 3.6 51.1 - - + -
985A SER* 3.6 23.1 - - - +
988A THR* 4.3 9.4 - - + -
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Residues in contact with TYR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ALA* 3.0 33.3 + - + +
236A GLY 3.4 2.9 + - - +
237A ILE 3.3 0.4 - - - -
238A PHE* 1.3 100.1 - + - +
240A GLY* 1.3 60.1 + - - +
241A CYS* 3.7 5.7 - - - -
513A VAL* 5.3 0.4 - - + -
516A VAL* 4.2 5.2 - - + -
517A ARG* 3.2 47.6 + - + -
520A LEU* 3.7 36.0 - - + +
979A LEU* 3.9 11.6 - - + +
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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