Contacts of the helix formed by residues 203 - 222 (chain B) in PDB entry 4CRU
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 TYR 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1601A GLN* 3.9 27.8 + - + +
1602A ALA* 3.8 31.6 - - - +
1603A TRP* 3.5 43.2 - + + +
202B THR* 1.3 73.7 - - - +
204B GLU* 1.3 58.8 + - - +
206B PHE* 4.5 8.0 - + - -
207B SER* 2.8 55.5 + - - -
248B ALA* 4.6 9.3 - - + +
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Residues in contact with GLU 204 (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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1601A GLN 4.5 7.8 + - - +
202B THR* 3.1 10.2 - - - +
203B TYR* 1.3 82.5 - - - +
205B ARG* 1.3 67.5 + - + +
207B SER* 3.3 6.7 + - - -
208B HIS* 3.2 24.1 + - + +
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Residues in contact with ARG 205 (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 TYR* 2.9 75.2 + - - -
199B ILE* 3.2 16.6 - - + +
201B GLN* 3.1 36.1 + - - +
202B THR* 3.0 24.2 + - - +
204B GLU* 1.3 81.0 - - + +
206B PHE* 1.3 62.6 + - - +
208B HIS* 3.4 5.2 + - - +
209B VAL* 3.3 26.3 + - + +
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Residues in contact with PHE 206 (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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1603A TRP* 3.6 33.7 - + + -
199B ILE* 3.2 14.8 + - - +
200B CYS* 4.4 3.1 - - - -
202B THR 3.2 6.3 + - - +
203B TYR* 3.9 7.0 - + - +
205B ARG* 1.3 79.0 - - - +
207B SER* 1.3 68.1 + - - +
209B VAL* 3.2 5.0 + - - +
210B ALA* 2.9 46.0 + - + +
239B LEU* 4.2 29.2 - - + -
245B ALA* 3.7 33.2 - - + -
248B ALA* 3.5 29.8 - - + -
249B LEU* 4.1 13.7 - - + -
252B CYS* 4.5 5.4 - - - -
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 2.8 47.7 + - - -
204B GLU* 3.3 9.4 + - - -
206B PHE* 1.3 87.1 - - - +
208B HIS* 1.3 59.8 + - - +
210B ALA* 3.7 2.3 - - - +
211B MET* 2.8 32.1 + - - +
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Residues in contact with HIS 208 (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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165B PRO* 5.7 5.6 - - + -
168B LEU* 3.6 32.7 - - + +
172B GLU* 5.2 3.6 + - - -
204B GLU* 3.2 15.2 + - + +
205B ARG* 3.8 6.1 - - - +
207B SER* 1.3 78.9 + - - +
209B VAL* 1.3 64.9 + - - +
211B MET* 3.4 28.0 + - + +
212B ILE* 3.2 32.5 + - + +
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Residues in contact with VAL 209 (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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164B ILE* 4.9 5.8 - - + -
168B LEU* 4.0 29.1 - - + +
186B LEU* 4.1 20.2 - - + -
190B LEU* 5.3 2.2 - - + -
199B ILE* 3.9 27.6 - - + -
205B ARG 3.3 12.3 + - - +
206B PHE 3.2 7.9 + - - +
208B HIS* 1.3 75.9 - - - +
210B ALA* 1.3 64.2 + - - +
212B ILE* 3.2 4.2 + - - +
213B LEU* 2.9 41.7 + - + +
239B LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 210 (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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206B PHE* 2.9 44.4 + - + +
207B SER* 3.8 4.5 - - - +
209B VAL* 1.3 78.8 - - - +
211B MET* 1.3 58.2 + - - +
213B LEU* 3.4 9.6 + - - +
214B GLY* 2.9 26.3 + - - -
236B TYR* 3.9 6.3 + - + -
239B LEU* 5.4 0.4 - - + -
249B LEU* 5.0 4.7 - - + -
252B CYS* 4.3 15.2 - - - -
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Residues in contact with MET 211 (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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172B GLU* 4.6 4.3 - - - +
207B SER 2.8 19.8 + - - +
208B HIS* 3.7 29.8 - - + +
210B ALA* 1.3 76.3 - - - +
212B ILE* 1.3 70.3 + - + +
214B GLY* 3.4 1.8 + - - -
215B LYS* 3.1 58.4 + - + +
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Residues in contact with ILE 212 (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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168B LEU* 4.0 30.3 - - + +
171B MET* 4.1 12.3 - - + -
172B GLU* 3.1 49.8 - - + +
208B HIS* 3.2 26.0 + - - +
209B VAL 3.2 7.4 + - - +
211B MET* 1.3 89.6 - - + +
213B LEU* 1.3 65.8 + - - +
215B LYS* 3.2 6.5 + - + +
216B MET* 2.9 38.6 + - + +
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Residues in contact with LEU 213 (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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171B MET* 3.9 24.9 - - + -
183B THR* 5.0 0.2 - - + -
186B LEU* 4.9 0.9 - - + -
209B VAL* 2.9 39.0 + - + +
210B ALA* 3.8 2.2 - - - +
212B ILE* 1.3 74.8 - - - +
214B GLY* 1.3 56.8 + - - +
216B MET* 3.2 10.7 + - - +
217B VAL* 2.9 32.6 + - - +
232B VAL* 4.3 20.2 - - + +
235B CYS* 4.2 27.1 - - + -
236B TYR* 3.3 31.0 - - + +
239B LEU* 3.9 19.5 - - + -
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Residues in contact with GLY 214 (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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210B ALA 2.9 15.0 + - - -
211B MET* 3.8 2.2 - - - -
213B LEU* 1.3 77.8 - - - +
215B LYS* 1.3 61.1 + - - +
217B VAL* 3.3 4.5 + - - +
218B LEU* 3.2 21.1 + - - +
236B TYR* 3.1 12.7 + - - -
254B PRO* 4.0 15.2 - - - +
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Residues in contact with LYS 215 (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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172B GLU* 3.0 37.0 + - + +
211B MET* 3.1 39.5 + - + +
212B ILE* 3.2 9.2 + - + +
214B GLY* 1.3 75.7 - - - +
216B MET* 1.3 63.0 + - + +
218B LEU* 3.3 10.7 + - + +
219B GLN* 3.1 33.2 + - + +
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Residues in contact with MET 216 (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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171B MET* 3.6 53.2 - - + +
172B GLU* 5.3 1.3 - - - -
179B LYS* 4.7 2.5 - - + -
183B THR* 3.3 24.5 - - - +
212B ILE* 2.9 21.4 + - + +
213B LEU* 3.2 15.7 + - - +
215B LYS* 1.3 75.2 - - + +
217B VAL* 1.3 59.2 + - - +
219B GLN* 3.2 15.4 + - - +
220B LEU* 2.8 37.3 + - + +
228B LEU* 3.7 26.2 - - + -
232B VAL* 3.9 15.3 - - + -
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Residues in contact with VAL 217 (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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213B LEU 2.9 18.7 + - - +
214B GLY 3.3 7.4 + - - +
216B MET* 1.3 70.5 - - - +
218B LEU* 1.3 68.4 + - - +
220B LEU* 3.2 11.4 + - + +
221B SER* 3.0 19.2 + - - -
229B LEU* 5.7 0.9 - - + -
232B VAL* 3.8 21.1 - - + -
236B TYR* 3.9 16.6 - - + +
254B PRO* 3.9 15.9 - - + -
256B GLN* 3.7 30.1 - - + +
257B LEU* 3.9 15.0 - - + -
262B PHE* 3.7 14.0 - - + -
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Residues in contact with LEU 218 (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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214B GLY 3.2 10.4 + - - +
215B LYS* 3.6 12.3 - - - +
217B VAL* 1.3 79.0 - - - +
219B GLN* 1.3 63.7 + - + +
221B SER* 2.6 28.8 + - - +
222B LYS* 3.6 34.4 + - - +
256B GLN* 3.6 26.7 - - - +
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Residues in contact with GLN 219 (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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172B GLU* 3.6 20.6 + - - +
179B LYS* 3.3 29.5 + - - +
215B LYS* 3.1 23.0 + - + +
216B MET* 3.2 23.2 + - - +
218B LEU* 1.3 77.5 - - + +
220B LEU* 1.3 59.4 + - + +
222B LYS* 3.1 14.1 + - - +
223B GLU* 2.9 30.4 + - + +
228B LEU* 5.9 1.0 - - - +
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Residues in contact with LEU 220 (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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216B MET* 2.8 25.1 + - + +
217B VAL* 3.2 8.5 + - - +
219B GLN* 1.3 71.9 - - + +
221B SER* 1.3 63.1 + - - +
222B LYS 3.0 5.6 + - - -
223B GLU 3.7 6.3 - - - +
224B PRO* 3.6 22.4 - - + +
225B SER* 3.7 44.2 - - - +
228B LEU* 4.0 17.5 - - + -
229B LEU* 3.8 33.9 - - + +
232B VAL* 4.2 15.0 - - + -
262B PHE* 3.9 17.5 - - + -
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Residues in contact with SER 221 (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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217B VAL 3.0 12.1 + - - -
218B LEU* 2.6 28.6 + - - +
220B LEU* 1.3 76.2 - - - +
222B LYS* 1.3 63.7 + - - +
224B PRO* 5.2 1.5 - - - +
256B GLN* 4.4 10.1 + - - -
261B THR* 3.8 25.4 - - - +
262B PHE* 3.8 9.8 - - - -
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Residues in contact with LYS 222 (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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218B LEU* 3.7 45.1 - - - +
219B GLN* 3.1 11.3 + - - +
221B SER* 1.3 85.1 - - - +
223B GLU* 1.3 67.3 + - + +
224B PRO* 3.6 9.0 - - - +
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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