Contacts of the helix formed by residues 225 - 243 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D LEU 3.3 8.9 - - - +
224D VAL* 1.3 86.0 - - + +
226D PRO* 1.3 75.2 - - + +
227D SER 4.5 0.4 - - - +
228D MET* 3.0 12.8 + - + +
229D SER* 3.1 10.2 + - - -
375D GLU* 5.5 0.2 - - - +
407D PRO* 4.1 1.8 - - + -
418D MET* 3.8 24.2 - - + -
420D PRO* 4.1 8.1 - - + -
428D VAL* 3.8 18.4 - - + +
429D ARG 4.4 2.2 - - - +
430D TYR* 3.5 46.0 - - + +
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Residues in contact with PRO 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D VAL 3.3 4.7 - - - +
225D PRO* 1.3 84.8 - - + +
227D SER* 1.3 57.0 + - - +
229D SER* 3.4 1.7 + - - -
230D ASN* 2.8 37.4 + - - +
252D TYR* 3.6 31.9 - - + +
255D CYS* 4.3 4.3 - - - -
260D GLN* 3.7 36.6 - - + +
264D ALA* 3.8 19.3 - - + -
372D ILE* 3.9 17.9 - - + -
428D VAL 4.3 3.4 - - - +
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D PRO 3.1 0.2 + - - -
226D PRO* 1.3 80.5 - - - +
228D MET* 1.3 60.5 + - - +
231D ALA* 3.1 23.2 + - - +
372D ILE* 4.0 7.3 - - - +
375D GLU* 2.6 50.8 + - - +
376D THR* 3.4 23.7 + - - -
379D ILE* 3.9 5.2 - - - +
430D TYR* 2.8 23.8 + - - -
438D PHE* 4.0 0.5 - - - -
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Residues in contact with MET 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D VAL* 4.6 4.5 - - + -
225D PRO* 3.0 11.1 + - + +
227D SER* 1.3 77.7 + - - +
229D SER* 1.3 66.1 + - - +
231D ALA* 3.3 3.3 + - - +
232D VAL* 3.2 26.6 + - - +
379D ILE* 3.8 24.5 - - + -
403D VAL 3.9 3.8 - - - +
404D MET* 3.9 18.8 - - - -
405D ASP 3.5 40.4 - - - +
406D ILE* 3.8 13.0 - - + -
418D MET* 4.4 11.9 - - + -
430D TYR* 3.5 12.5 + - - +
436D VAL* 3.7 32.3 - - + -
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D GLY* 3.0 29.6 + - - +
218D PRO* 5.0 0.3 - - - +
219D LEU* 4.3 7.9 - - - -
224D VAL* 3.9 19.1 - - - +
225D PRO 3.1 11.9 + - - -
226D PRO* 3.6 11.4 - - - -
228D MET* 1.3 77.7 - - - +
230D ASN* 1.3 65.1 + - - +
232D VAL* 3.1 6.4 + - - +
233D GLY* 3.1 18.0 + - - -
251D GLY 4.6 4.2 + - - +
252D TYR* 4.4 15.2 - - - -
253D GLY 5.0 0.7 + - - -
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Residues in contact with ASN 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PRO* 2.8 23.4 + - - +
229D SER* 1.3 72.7 + - - +
231D ALA* 1.3 61.2 + - - +
234D ILE* 2.8 41.2 + - + +
251D GLY 4.9 0.3 - - - +
252D TYR* 4.2 13.7 - - - +
264D ALA* 3.1 25.9 + - - +
267D CYS* 4.1 1.4 - - - +
268D LEU* 3.6 42.5 - - + +
271D GLN* 5.4 0.6 + - - +
372D ILE* 3.9 18.6 - - - +
376D THR* 4.1 14.3 + - + +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D SER 3.1 19.7 + - - +
228D MET* 3.6 6.1 - - - +
229D SER 3.3 0.2 - - - -
230D ASN* 1.3 77.6 - - - +
232D VAL* 1.3 60.1 + - - +
234D ILE* 3.7 0.8 + - - -
235D THR* 2.8 30.8 + - - -
376D THR* 4.1 13.8 - - + +
379D ILE* 3.8 23.1 - - + -
380D LEU* 3.8 12.8 - - + +
404D MET* 3.8 15.7 - - + -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.8 24.5 - - + -
176D SER* 4.4 1.1 - - - -
216D PHE 5.4 1.6 - - - +
217D GLY* 6.4 0.4 - - - -
219D LEU* 4.0 22.2 - - + -
228D MET 3.2 13.2 + - - +
229D SER 3.1 8.4 + - - +
231D ALA* 1.3 77.2 - - - +
233D GLY* 1.3 57.6 + - - +
235D THR* 3.3 4.4 + - - -
236D GLU* 2.9 46.1 + - - +
404D MET* 3.9 25.8 - - + -
406D ILE* 3.9 20.6 - - + -
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Residues in contact with GLY 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PRO* 4.4 15.9 - - - +
217D GLY* 6.2 3.6 - - - -
229D SER 3.1 12.9 + - - -
230D ASN 3.2 2.4 + - - -
232D VAL* 1.3 74.5 - - - +
234D ILE* 1.3 60.6 + - - +
236D GLU* 3.3 1.2 + - - +
237D ALA* 2.9 30.0 + - - +
250D VAL* 3.9 13.2 - - - +
251D GLY 5.7 4.0 - - - -
268D LEU* 4.8 7.6 - - - -
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Residues in contact with ILE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ASN* 2.8 30.8 + - + +
231D ALA 4.1 2.5 - - - +
233D GLY* 1.3 70.6 - - - -
235D THR* 1.3 64.3 + - - +
237D ALA* 3.3 4.1 + - - +
238D LEU* 3.0 30.1 + - + +
268D LEU* 4.2 6.9 - - + +
271D GLN* 3.8 27.8 - - + +
272D THR* 3.5 27.6 - - - +
275D TYR* 3.9 27.8 - - + -
376D THR* 3.8 22.0 - - + -
380D LEU* 3.9 20.0 - - + -
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.9 14.4 - - + -
231D ALA 2.8 23.0 + - - -
232D VAL 3.5 4.9 - - - -
233D GLY 3.2 0.2 - - - -
234D ILE* 1.3 79.0 - - - +
236D GLU* 1.3 57.7 + - - +
238D LEU* 3.2 3.0 + - - +
239D LEU* 2.9 49.4 + - + +
380D LEU* 3.5 9.8 - - - +
383D MET* 3.4 17.7 - - + +
391D LEU* 3.9 20.6 - - + +
395D THR* 3.5 24.2 - - - +
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Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLY 5.4 0.2 - - - +
173D GLY* 3.2 16.6 - - - -
174D GLY 4.6 1.8 - - - +
175D ILE* 2.8 23.5 + - + +
176D SER* 2.7 52.7 + - - -
191D LEU* 6.2 0.4 - - + -
198D ASP* 4.8 1.2 - - - +
213D ARG* 5.7 2.2 + - - +
215D PRO* 3.3 29.6 - - + +
216D PHE 5.0 0.2 - - - +
232D VAL* 2.9 28.0 + - + +
233D GLY 3.9 3.4 - - - +
235D THR* 1.3 77.0 - - + +
237D ALA* 1.3 61.8 + - - +
239D LEU* 3.4 9.1 + - + +
240D ALA* 3.0 25.5 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PRO* 4.3 2.3 - - - +
233D GLY 2.9 17.4 + - - +
234D ILE 3.6 4.7 - - - +
236D GLU* 1.3 76.8 - - - +
238D LEU* 1.3 55.6 + - - +
240D ALA* 3.3 1.4 + - - -
241D ALA* 2.9 30.1 + - - +
248D ILE* 3.6 27.0 - - + +
250D VAL* 4.1 9.0 - - + -
272D THR* 3.9 27.4 - - + -
276D LEU* 4.0 6.5 - - + +
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Residues in contact with LEU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 4.6 3.4 + - - +
234D ILE* 3.0 25.4 + - + +
235D THR* 3.6 4.3 - - - +
237D ALA* 1.3 75.2 - - + +
239D LEU* 1.3 63.3 + - + +
241D ALA* 3.3 2.3 + - - +
242D GLU* 3.1 22.9 + - - +
275D TYR* 3.8 57.2 - - + +
276D LEU* 4.1 18.4 - - + +
279D TYR* 4.3 6.5 - - + -
281D TYR* 4.1 18.9 + - + -
380D LEU* 5.8 1.1 - - + -
384D PHE* 4.4 8.7 - - + -
391D LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 3.5 33.7 + - - +
191D LEU* 3.8 28.9 - - + -
195D GLN* 5.5 11.2 + - + +
198D ASP* 4.1 6.2 - - - +
235D THR* 2.9 40.5 + - + +
236D GLU* 4.0 8.7 - - + +
238D LEU* 1.3 73.0 - - - +
240D ALA* 1.3 61.8 + - - +
242D GLU* 3.6 8.5 + - - +
243D GLN* 3.7 17.2 + - - +
391D LEU* 4.4 8.5 - - + -
392D ALA* 4.1 28.5 - - + +
395D THR* 4.7 0.9 - - - +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ASP* 3.3 31.6 + - - +
213D ARG* 4.8 6.1 - - + +
236D GLU 3.0 18.6 + - - +
237D ALA* 3.7 4.5 - - - +
239D LEU* 1.3 75.4 - - - +
241D ALA* 1.3 64.9 + - - +
243D GLN* 3.0 12.6 + - - +
244D GLY 3.3 0.2 + - - -
245D VAL* 3.2 33.8 + - + +
248D ILE* 4.3 8.7 - - + -
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Residues in contact with ALA 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ALA 2.9 17.4 + - - +
238D LEU 3.3 3.8 + - - +
240D ALA* 1.3 75.6 - - - +
242D GLU* 1.3 63.8 + - - +
244D GLY* 3.0 15.4 + - - -
245D VAL* 3.8 17.2 + - - +
246D LYS* 5.4 2.9 + - - -
248D ILE* 4.5 2.7 - - + +
276D LEU* 3.6 23.1 - - + -
281D TYR* 3.7 27.8 - - + -
284D VAL* 4.4 4.5 - - + -
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 3.3 40.3 - - - +
6D LYS* 3.4 9.7 - - - +
7D LYS* 2.8 51.8 + - - +
238D LEU 3.1 9.4 + - - +
239D LEU 3.8 2.9 - - - +
240D ALA 3.1 0.6 - - - -
241D ALA* 1.3 80.1 - - - +
243D GLN* 1.3 59.0 + - - +
244D GLY 3.2 0.7 + - - -
281D TYR* 2.6 38.9 + - - +
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Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 5.0 0.4 - - - +
6D LYS 3.1 29.1 + - - -
7D LYS* 3.7 10.5 - - - +
8D TRP* 3.0 30.6 + - - -
195D GLN* 3.6 41.7 - - + +
198D ASP* 3.7 7.0 - - + -
199D ARG* 3.4 41.0 - - - +
202D GLY* 3.6 15.8 - - - -
239D LEU 3.7 13.1 + - - +
240D ALA 3.0 9.3 + - - +
242D GLU* 1.3 81.7 - - - +
244D GLY* 1.3 55.3 + - - +
245D 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
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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