Contacts of the helix formed by residues 201 - 220 (chain B) in PDB entry 1IL5
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 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B GLU* 3.1 24.3 - - - +
191B ARG* 4.7 2.4 + - - -
199B ALA 3.5 4.1 + - - +
200B PRO* 1.3 76.9 - - - +
202B PRO* 1.3 78.5 - - + -
203B SER* 2.7 21.2 + - - -
204B VAL* 2.8 20.6 + - - +
205B ILE* 3.5 3.9 + - - -
235B ARG* 3.1 37.5 + - + +
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Residues in contact with PRO 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PRO 4.7 0.9 - - - +
201B ASP* 1.3 87.0 - - + -
203B SER* 1.3 62.4 + - - +
204B VAL 2.9 1.7 + - - -
205B ILE* 3.2 9.6 + - + +
206B THR* 2.9 31.1 + - - +
233B GLN* 4.0 14.8 - - + +
234B ARG 3.5 13.2 - - - +
235B ARG 3.6 13.9 - - - +
236B ASN 4.8 0.9 - - - -
237B GLY* 3.9 19.1 - - - -
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 2.9 30.7 + - - -
201B ASP* 2.7 26.4 + - - -
202B PRO* 1.3 77.1 - - - +
204B VAL* 1.3 57.8 + - - +
206B THR* 4.5 1.6 - - - -
207B LEU* 3.2 30.8 + - - +
233B GLN 3.3 23.4 - - - +
234B ARG* 3.6 13.8 + - - -
235B ARG* 3.7 2.7 + - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 5.9 0.7 - - + -
173B GLN* 4.7 0.4 - - - +
183B TYR* 4.2 5.8 - - + -
184B ILE* 3.7 23.3 - - + +
187B GLU* 3.6 37.0 - - + +
188B MET* 5.6 3.6 - - + -
191B ARG* 5.8 0.4 - - - +
200B PRO* 4.0 17.9 - - + -
201B ASP* 2.8 22.4 + - - +
203B SER* 1.3 82.1 - - - +
205B ILE* 1.3 65.0 + - - +
207B LEU* 3.2 8.7 + - - +
208B GLU* 3.1 44.4 + - - +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 3.6 23.1 - - + +
135B GLU* 3.3 46.7 - - + +
200B PRO* 3.7 34.3 - - + +
201B ASP 3.5 4.7 + - - +
202B PRO* 3.2 9.7 + - + +
204B VAL* 1.3 75.1 - - - +
206B THR* 1.3 65.1 + - - +
208B GLU* 3.1 15.8 + - - +
209B ASN* 2.9 38.5 + - - +
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PRO* 2.9 17.5 + - - +
203B SER 4.7 2.9 - - - -
205B ILE* 1.3 77.6 - - - +
207B LEU* 1.3 58.1 + - - +
209B ASN* 3.4 6.0 + - - +
210B SER* 2.9 42.9 + - - +
231B GLN 4.4 4.7 - - - +
232B LEU* 4.2 15.3 - - + -
233B GLN* 2.8 54.4 + - + +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 3.1 29.5 - - + -
183B TYR* 3.6 28.9 - - + -
184B ILE* 4.9 2.0 - - + -
203B SER 3.2 20.4 - - - +
204B VAL* 3.2 8.6 + - - +
206B THR* 1.3 78.7 - - - +
208B GLU* 1.3 64.1 + - - +
210B SER* 3.0 5.5 + - - -
211B TRP 2.9 20.6 + - - -
214B LEU* 4.3 17.0 - - + +
232B LEU* 3.7 32.5 - - + -
248B LEU* 5.5 0.4 - - + -
251B ILE* 4.1 24.9 - - + -
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Residues in contact with GLU 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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123B TYR* 4.2 2.4 + - + -
134B ARG* 2.9 28.7 + - - +
173B GLN* 3.0 37.3 - - - +
177B GLU* 3.4 33.8 - - - +
180B ARG* 4.8 2.6 + - - -
181B PHE* 3.9 8.1 - - - -
184B ILE* 3.6 17.4 - - + +
204B VAL* 3.1 27.3 - - - +
205B ILE* 3.1 11.0 + - - +
207B LEU* 1.3 79.1 - - - +
209B ASN* 1.3 63.8 + - - +
210B SER 3.4 0.2 + - - -
211B TRP* 3.4 14.6 + - - +
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Residues in contact with ASN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 4.4 7.9 - - - +
134B ARG* 3.1 30.3 + - - +
205B ILE* 2.9 34.6 + - - +
206B THR* 3.8 5.9 + - - +
208B GLU* 1.3 75.8 - - - +
210B SER* 1.3 61.4 + - - +
211B TRP 3.7 0.5 + - - -
212B GLY 4.8 2.3 + - - -
213B ARG* 5.4 0.7 + - - +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 2.9 28.5 + - - +
207B LEU* 3.0 5.4 + - - -
209B ASN* 1.3 78.0 - - - +
211B TRP* 1.3 63.7 + - - +
212B GLY 3.3 2.9 - - - -
213B ARG* 3.1 22.3 + - - -
214B LEU* 2.8 38.0 + - - +
230B ILE* 5.4 1.4 - - - +
231B GLN 5.1 1.9 + - - -
232B LEU* 5.0 7.7 - - - +
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Residues in contact with TRP 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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45B LEU* 4.5 6.1 - - + -
78B ASN* 3.6 29.2 - - + -
79B ALA* 5.8 0.2 - - + -
180B ARG* 3.5 53.8 - - + +
181B PHE* 3.3 37.2 - + + -
207B LEU 2.9 7.5 + - - -
208B GLU 3.4 12.1 + - - +
209B ASN 3.4 2.2 - - - -
210B SER* 1.3 75.5 - - - +
212B GLY* 1.3 72.2 + - - +
214B LEU* 3.3 4.2 + - - +
215B SER* 3.0 26.8 + - - -
252B ILE* 4.1 6.6 - - + +
254B LEU 3.0 26.7 + - - -
255B MET* 4.0 2.4 - - - +
256B VAL* 3.4 47.6 - - + -
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASN 4.8 2.6 + - - -
210B SER 3.3 0.4 - - - -
211B TRP* 1.3 84.5 - - - +
213B ARG* 1.3 62.7 + - - +
215B SER* 3.2 9.0 + - - -
216B THR* 3.0 25.7 + - - -
256B VAL* 4.6 6.3 - - - -
258B ARG* 4.3 19.2 + - - -
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Residues in contact with ARG 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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209B ASN 5.6 0.2 - - - +
210B SER* 3.1 22.2 + - - +
212B GLY* 1.3 75.3 - - - +
214B LEU* 1.3 62.2 + - - +
216B THR* 3.2 8.6 + - - -
217B ALA* 2.9 29.7 + - - +
228B SER* 5.0 11.1 + - - -
229B PRO 4.5 10.5 + - - -
230B ILE* 3.2 47.8 - - - +
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Residues in contact with LEU 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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181B PHE* 4.1 26.5 - - + -
207B LEU* 4.3 17.0 - - + +
210B SER* 2.8 27.1 + - - +
211B TRP 3.6 3.8 - - - +
213B ARG* 1.3 76.5 - - - +
215B SER* 1.3 63.4 + - - +
217B ALA* 3.3 0.9 + - - +
218B ILE* 2.9 41.6 + - + +
230B ILE* 3.7 37.2 - - + -
232B LEU* 4.5 10.3 - - + -
242B VAL* 6.4 1.1 - - + -
248B LEU* 4.0 26.7 - - + -
251B ILE* 6.4 0.2 - - + -
252B ILE* 4.9 9.4 - - + -
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Residues in contact with SER 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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211B TRP* 3.0 19.8 + - - -
212B GLY 3.3 9.9 - - - -
214B LEU* 1.3 77.8 - - - +
216B THR* 1.3 64.3 + - - +
218B ILE* 3.6 0.4 + - - -
219B GLN* 2.9 32.3 + - - +
252B ILE* 4.9 1.8 - - - +
255B MET* 3.3 33.8 - - - +
256B VAL* 3.4 31.2 + - - +
258B ARG* 4.8 0.9 - - - -
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Residues in contact with THR 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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212B GLY 3.0 13.4 + - - -
213B ARG* 3.2 10.4 + - - -
215B SER* 1.3 74.6 - - - +
217B ALA* 1.3 65.6 + - - +
219B GLN* 2.9 14.9 + - - +
220B GLU* 2.9 30.6 + - + +
258B ARG* 3.4 33.2 + - + +
259B CYS* 5.7 2.9 - - - -
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Residues in contact with ALA 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 ARG* 2.9 16.3 + - - +
214B LEU 3.8 2.0 - - - +
216B THR* 1.3 77.4 - - - +
218B ILE* 1.3 55.9 + - - +
220B GLU* 3.4 15.8 - - - +
221B SER* 3.1 31.5 + - - -
226B PHE* 3.5 18.4 - - + -
228B SER 5.3 0.9 - - - +
230B ILE* 3.4 34.3 - - + -
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Residues in contact with ILE 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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39B ARG* 5.2 1.7 - - + +
40B HIS* 3.9 26.4 + - + -
42B ILE* 4.2 20.4 - - + -
214B LEU* 2.9 27.8 + - + +
217B ALA* 1.3 75.8 - - - +
219B GLN* 1.3 58.8 + - - +
221B SER* 2.8 20.5 + - - -
226B PHE* 3.7 24.2 - - + -
245B VAL* 3.9 11.2 - - + -
248B LEU* 3.9 20.9 - - + -
252B ILE* 4.7 7.9 - - + -
255B MET* 3.9 32.5 - - + -
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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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39B ARG* 2.8 38.9 + - + +
44B VAL* 5.1 1.6 - - - -
215B SER 2.9 23.2 + - - +
216B THR 2.9 4.7 + - - +
218B ILE* 1.3 78.8 - - - +
220B GLU* 1.3 57.3 + - - +
221B SER 3.3 2.6 + - - +
255B MET* 3.7 23.3 - - + +
256B VAL 2.7 27.2 + - - +
257B TYR* 3.9 1.4 - - - -
258B ARG* 2.9 31.5 + - + +
259B CYS* 2.9 25.6 + - + +
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Residues in contact with GLU 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 THR* 2.9 35.8 + - + +
217B ALA* 3.4 17.2 - - - +
219B GLN* 1.3 75.5 - - - +
221B SER* 1.3 61.1 + - - +
222B ASN* 3.5 9.2 + - - +
227B ALA* 3.7 29.7 + - - +
259B CYS* 4.7 12.3 - - - -
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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