Contacts of the helix formed by residues 225 - 243 (chain B) in PDB entry 1CCW
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 PRO 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU 3.4 8.0 - - - +
224B VAL* 1.3 85.9 - - + +
226B PRO* 1.3 75.0 - - + +
227B SER 4.5 0.4 - - - +
228B MET* 3.0 14.0 + - + -
229B SER* 3.1 10.7 + - - -
407B PRO* 4.1 2.7 - - + -
418B MET* 3.8 25.4 - - + -
420B PRO* 4.2 7.9 - - + -
428B VAL* 3.8 18.8 - - + +
429B ARG 4.5 1.8 - - - +
430B TYR* 3.5 45.8 - - + +
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Residues in contact with PRO 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL 3.4 4.7 - - - +
225B PRO* 1.3 83.6 - - + +
227B SER* 1.3 58.5 + - - +
229B SER* 3.4 2.2 + - - -
230B ASN* 2.8 36.8 + - - +
252B TYR* 3.6 31.0 - - + +
255B CYS* 4.4 4.7 - - - -
260B GLN* 3.7 36.3 - - + +
264B ALA* 3.7 20.2 - - + -
372B ILE* 3.9 16.6 - - + -
428B VAL 4.3 3.1 - - - +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B PRO* 3.2 0.6 - - - +
226B PRO* 1.3 78.9 - - - +
228B MET* 1.3 56.1 + - - +
231B ALA* 3.0 27.9 + - - +
372B ILE* 4.0 7.7 - - - +
375B GLU* 2.6 50.2 + - - +
376B THR* 3.4 23.3 + - - +
379B ILE* 4.0 4.1 - - - +
430B TYR* 2.8 24.2 + - - -
438B PHE* 4.0 0.3 - - - -
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Residues in contact with MET 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 5.2 0.2 - - - -
224B VAL* 4.7 3.8 - - + -
225B PRO* 3.0 10.5 + - + +
227B SER* 1.3 80.1 + - - +
229B SER* 1.3 64.9 + - - +
231B ALA* 3.3 4.0 + - - +
232B VAL* 3.2 23.5 + - - +
379B ILE* 3.8 22.4 - - + -
403B VAL 4.0 3.8 - - - +
404B MET* 3.9 19.3 - - - -
405B ASP 3.5 41.7 - - - +
406B ILE* 3.9 13.2 - - + -
418B MET* 4.2 12.1 - - + -
430B TYR* 3.5 13.6 + - - +
436B VAL* 3.7 28.9 - - + -
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLY* 2.9 30.7 + - - +
218B PRO* 5.0 0.5 - - - +
219B LEU* 4.2 8.1 - - - -
224B VAL* 3.8 20.0 - - - +
225B PRO 3.1 11.4 + - - -
226B PRO* 3.7 11.0 - - - -
228B MET* 1.3 76.4 - - - +
230B ASN* 1.3 64.5 + - - +
232B VAL* 3.2 7.1 + - - +
233B GLY* 3.1 17.7 + - - -
251B GLY 4.6 5.0 + - - +
252B TYR* 4.5 13.4 - - - -
253B GLY 5.0 0.5 + - - -
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Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PRO* 2.8 25.2 + - - +
227B SER 4.1 2.0 - - - +
229B SER* 1.3 70.5 + - - +
231B ALA* 1.3 67.1 + - - +
233B GLY* 3.8 0.2 - - - -
234B ILE* 2.9 36.3 + - + +
251B GLY 4.8 0.6 - - - +
252B TYR* 4.2 13.9 - - - +
264B ALA* 3.1 27.1 + - - +
267B CYS* 4.1 1.6 - - - +
268B LEU* 3.5 39.8 - - + +
271B GLN* 5.5 1.0 + - - +
372B ILE* 3.9 18.2 - - - +
376B THR* 4.2 11.6 + - + +
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B SER 3.0 19.3 + - - +
228B MET* 3.3 6.0 + - - +
230B ASN* 1.3 76.8 - - - +
232B VAL* 1.3 60.4 + - - +
234B ILE* 4.7 0.2 - - - -
235B THR* 2.9 29.3 + - - -
376B THR* 3.9 13.6 - - + +
379B ILE* 3.8 24.2 - - + -
380B LEU* 3.9 11.1 - - + +
404B MET* 3.8 16.6 - - + -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ILE* 3.8 28.5 - - + -
176B SER* 4.4 0.9 - - - -
216B PHE 5.4 1.1 - - - +
217B GLY* 6.5 0.7 - - - -
219B LEU* 4.1 21.3 - - + -
228B MET 3.2 14.3 + - - +
229B SER 3.2 7.6 + - - +
231B ALA* 1.3 77.2 - - - +
233B GLY* 1.3 56.4 + - - +
235B THR* 3.3 4.2 + - - -
236B GLU* 2.9 40.7 + - - +
404B MET* 3.6 26.2 - - + -
406B ILE* 3.9 22.0 - - + -
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PRO* 4.3 16.1 - - - +
217B GLY* 6.2 3.4 - - - -
229B SER 3.1 13.8 + - - -
230B ASN 3.2 2.2 + - - -
232B VAL* 1.3 77.1 - - - +
234B ILE* 1.3 57.7 + - - +
236B GLU* 3.3 1.6 + - - +
237B ALA* 2.9 29.3 + - - +
250B VAL* 3.9 13.4 - - - +
251B GLY 5.7 4.5 - - - -
268B LEU* 4.7 7.9 - - - -
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ASN* 2.9 26.0 + - + +
231B ALA 4.1 2.7 - - - +
233B GLY* 1.3 71.9 - - - +
235B THR* 1.3 67.2 + - - +
237B ALA* 3.2 5.3 + - - +
238B LEU* 2.9 30.5 + - + +
268B LEU* 4.2 7.2 - - + +
271B GLN* 3.8 27.8 - - + +
272B THR* 3.5 27.4 - - - +
275B TYR* 3.9 27.1 - - + -
376B THR* 3.8 22.4 - - + -
380B LEU* 3.9 20.6 - - + -
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ILE* 4.0 14.1 - - + -
231B ALA 2.9 22.6 + - - -
232B VAL 3.5 4.5 - - - -
234B ILE* 1.3 77.6 - - - +
236B GLU* 1.3 58.1 + - - +
238B LEU* 3.2 3.4 + - - +
239B LEU* 2.9 45.8 + - + +
380B LEU* 3.5 10.6 - - - +
383B MET* 3.4 17.8 - - + +
391B LEU* 3.9 21.8 - - + +
395B THR* 3.6 24.2 - - - +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLY* 3.1 15.7 - - - -
174B GLY 4.6 2.0 - - - +
175B ILE* 2.8 24.6 + - + +
176B SER* 2.7 50.6 + - - -
191B LEU* 6.2 0.4 - - + -
198B ASP* 4.7 1.0 - - - +
213B ARG* 5.7 2.3 + - - +
215B PRO* 3.3 33.1 - - + +
232B VAL* 2.9 28.9 + - + +
233B GLY 4.0 0.2 - - - +
235B THR* 1.3 75.5 - - + +
237B ALA* 1.3 58.4 + - - +
239B LEU* 3.9 9.3 - - + +
240B ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PRO* 4.3 1.9 - - - +
233B GLY 2.9 18.6 + - - +
234B ILE 3.5 4.7 - - - +
236B GLU* 1.3 78.1 - - - +
238B LEU* 1.3 56.8 + - + +
240B ALA* 3.3 0.8 + - - -
241B ALA* 2.9 30.5 + - - +
248B ILE* 3.7 27.3 - - + +
250B VAL* 4.1 9.0 - - + -
272B THR* 4.0 26.2 - - + -
276B LEU* 4.1 6.0 - - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN* 4.6 3.8 + - - +
234B ILE* 2.9 26.4 + - + +
235B THR* 3.5 4.0 - - - +
237B ALA* 1.3 76.0 - - + +
239B LEU* 1.3 64.0 + - - +
241B ALA* 3.4 2.6 + - - +
242B GLU* 3.2 21.8 + - - +
275B TYR* 3.8 54.1 - - + +
276B LEU* 4.0 15.9 - - + +
279B TYR* 4.3 7.6 - - + -
281B TYR* 4.1 21.5 + - + -
380B LEU* 5.8 1.1 - - + -
384B PHE* 4.3 10.1 - - + -
391B LEU* 3.6 26.7 - - + -
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN* 3.5 31.9 + - - +
191B LEU* 3.8 29.8 - - + -
195B GLN* 5.4 11.0 + - + +
198B ASP* 4.1 5.6 - - - +
235B THR* 2.9 37.9 + - + +
236B GLU* 3.9 9.2 - - + +
238B LEU* 1.3 75.3 - - - +
240B ALA* 1.3 62.0 + - - +
242B GLU* 3.6 9.7 + - - +
243B GLN* 3.7 17.0 + - - +
391B LEU* 4.4 7.6 - - + -
392B ALA* 4.0 28.9 - - + +
395B THR* 4.8 0.9 - - - +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ASP* 3.3 31.8 + - - +
213B ARG* 4.9 6.5 - - + +
236B GLU 2.9 19.2 + - - +
237B ALA* 3.7 4.0 - - - +
239B LEU* 1.3 75.0 - - - +
241B ALA* 1.3 65.7 + - - +
243B GLN* 3.1 12.1 + - - +
245B VAL* 3.2 32.6 + - + +
248B ILE* 4.3 9.0 - - + -
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA 2.9 17.4 + - - +
238B LEU 3.4 3.8 + - - +
240B ALA* 1.3 76.0 - - - +
242B GLU* 1.3 63.1 + - - +
244B GLY* 3.0 14.0 + - - -
245B VAL* 3.7 17.9 + - - +
246B LYS* 5.4 3.3 + - - -
248B ILE* 4.4 2.2 - - + +
276B LEU* 3.5 25.1 - - + -
281B TYR* 3.7 27.0 - - + -
284B VAL* 4.3 4.3 - - + -
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN* 3.3 40.8 - - - +
6B LYS* 3.4 7.9 - - - +
7B LYS* 2.9 52.0 + - - +
238B LEU 3.2 7.2 + - - +
239B LEU 3.8 6.5 - - - +
240B ALA 3.1 1.0 - - - -
241B ALA* 1.3 78.7 - - - +
243B GLN* 1.3 59.6 + - - +
244B GLY 3.2 1.0 + - - -
281B TYR* 2.5 38.6 + - - +
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Residues in contact with GLN 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN* 5.1 0.2 - - - +
6B LYS 3.1 27.7 + - - -
7B LYS* 3.7 11.1 - - - +
8B TRP* 3.0 31.1 + - - -
195B GLN* 3.7 43.1 - - + +
198B ASP* 3.7 12.8 - - + -
199B ARG* 3.4 42.0 - - - +
202B GLY* 3.5 14.9 - - - -
239B LEU 3.7 12.2 + - - +
240B ALA 3.1 3.0 + - - +
242B GLU* 1.3 81.0 - - - +
244B GLY* 1.4 57.7 + - - +
245B VAL 3.7 1.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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