Contacts of the helix formed by residues 225 - 244 (chain B) in PDB entry 1IC8
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 SER 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASN* 2.7 25.0 + - - -
224B PRO* 1.3 75.0 - - - +
226B LYS* 1.3 50.3 + - - +
227B GLU* 2.7 27.8 + - - +
228B GLU* 2.2 58.7 + - - +
229B ARG 2.5 13.3 + - - -
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Residues in contact with LYS 226 (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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224B PRO 3.1 4.2 + - - -
225B SER* 1.3 69.8 - - - +
227B GLU* 1.3 65.2 + - + +
228B GLU 3.1 0.2 - - - -
229B ARG* 3.4 46.4 - - + +
230B GLU* 3.5 49.8 + - + +
261B GLU* 3.7 17.9 + - + -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 2.6 19.1 + - - +
226B LYS* 1.3 86.9 + - + +
228B GLU* 1.3 52.1 + - - +
230B GLU* 5.1 0.5 - - - +
231B THR* 2.4 26.5 + - - -
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA 5.7 0.3 - - - +
220B ARG* 6.0 1.4 - - - -
221B GLN* 4.4 10.6 - - - +
223B ASN* 2.5 40.9 + - - +
225B SER* 2.2 37.1 + - - +
227B GLU* 1.3 69.9 - - - +
229B ARG* 1.3 65.0 + - - +
231B THR* 3.1 14.0 - - + +
232B LEU* 3.1 27.5 + - + +
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 3.2 30.9 + - + +
225B SER 2.5 10.0 + - - +
226B LYS* 3.4 49.4 - - + +
227B GLU 3.6 0.4 - - - -
228B GLU* 1.3 67.8 - - - +
230B GLU* 1.3 57.6 + - + +
231B THR 2.7 4.3 + - - -
232B LEU* 2.6 32.6 + - - +
233B VAL* 2.9 10.4 + - - +
261B GLU* 3.1 22.9 + - - +
262B VAL* 4.2 2.6 - - - +
264B VAL* 3.7 28.1 - - + +
265B TYR* 3.1 56.5 - - - +
268B PHE* 5.6 5.4 - - + -
401F T 5.9 0.4 + - - -
402F C 5.2 1.8 + - - -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LYS* 3.5 32.4 + - + +
227B GLU 5.1 0.4 - - - +
229B ARG* 1.3 77.2 - - + +
231B THR* 1.3 57.4 + - - +
233B VAL* 2.9 29.3 - - + +
234B GLU* 3.6 16.3 - - - +
261B GLU* 2.7 46.0 - - + +
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Residues in contact with THR 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 GLU 2.4 29.0 + - - -
228B GLU* 3.1 18.6 - - + +
229B ARG 2.8 0.2 - - - -
230B GLU* 1.3 78.0 - - - +
232B LEU* 1.3 67.3 - - + +
234B GLU* 3.8 6.8 + - - +
235B GLU* 3.3 25.2 + - - +
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Residues in contact with LEU 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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213B ILE* 4.9 9.4 - - + -
214B LEU* 3.9 19.1 - - + -
217B ALA* 3.5 29.2 - - + -
220B ARG* 5.9 1.1 - - - +
223B ASN 6.0 0.2 - - - +
228B GLU* 3.1 18.1 + - + +
229B ARG* 2.6 15.4 + - - +
231B THR* 1.3 75.7 - - + +
233B VAL* 1.3 67.7 + - - +
234B GLU 3.1 2.0 - - - -
235B GLU* 2.6 30.8 + - + +
236B CYS* 2.8 16.5 + - - +
264B VAL* 4.5 5.6 - - + -
268B PHE* 3.4 34.5 - - + -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ARG 2.9 7.8 + - - +
230B GLU* 2.9 40.8 - - + +
232B LEU* 1.3 74.8 - - - +
234B GLU* 1.3 72.5 + - + +
237B ASN* 2.6 41.4 + - - +
258B LEU* 5.1 0.4 - - + -
259B VAL* 2.8 50.2 - - + +
260B THR* 3.6 16.8 - - - -
261B GLU* 4.1 2.2 - - - +
264B VAL* 4.3 3.9 - - + +
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Residues in contact with GLU 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 GLU 3.6 17.3 - - - +
231B THR* 4.1 7.5 - - - +
232B LEU 3.1 0.6 - - - -
233B VAL* 1.3 86.0 - - + +
235B GLU* 1.3 62.4 + - - +
237B ASN* 3.8 8.8 - - - +
238B ARG* 3.0 40.1 + - - +
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Residues in contact with GLU 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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213B ILE* 4.0 30.3 - - + +
216B GLN* 5.2 4.5 + - - -
231B THR* 3.3 18.3 + - - +
232B LEU* 2.6 29.6 + - + +
234B GLU* 1.3 71.9 - - - +
236B CYS* 1.3 61.4 + - - +
238B ARG* 3.1 27.5 - - - +
239B ALA* 3.4 7.1 + - - +
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Residues in contact with CYS 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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206B TRP* 4.3 3.1 - - + -
210B SER* 3.1 48.9 + - - +
213B ILE* 3.8 14.8 - - - -
214B LEU* 3.6 24.7 - - - -
232B LEU* 2.8 13.3 + - - +
233B VAL 4.1 0.4 - - - +
235B GLU* 1.3 72.2 - - - +
237B ASN* 1.3 57.0 + - - +
238B ARG 2.6 15.3 + - - -
239B ALA* 2.8 18.3 + - - +
240B GLU* 2.8 13.9 + - - +
259B VAL* 4.0 12.8 - - + -
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Residues in contact with ASN 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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233B VAL* 2.6 32.4 + - - +
234B GLU* 3.8 9.4 - - - +
235B GLU 3.4 0.2 - - - -
236B CYS* 1.3 75.8 - - - +
238B ARG* 1.3 61.6 + - - +
240B GLU* 4.1 3.4 - - - -
241B CYS* 3.5 24.4 + - - -
249B SER* 5.6 2.6 - - - +
254B LEU* 3.0 26.2 - - + +
258B LEU* 2.9 24.7 - - - +
259B VAL* 2.6 39.8 + - - +
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Residues in contact with ARG 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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234B GLU* 3.0 31.6 + - - +
235B GLU* 3.1 17.1 - - - +
236B CYS 2.6 4.9 + - - -
237B ASN* 1.3 72.5 - - - +
239B ALA* 1.3 66.9 + - - +
241B CYS* 2.8 9.8 + - - +
242B ILE* 2.8 36.9 + - + +
249B SER* 3.7 30.9 + - - -
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Residues in contact with ALA 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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209B ALA* 3.7 26.9 - - + +
210B SER 4.6 0.2 - - - +
213B ILE* 3.9 25.4 - - + -
235B GLU 3.4 2.1 + - - +
236B CYS 2.8 10.4 + - - +
238B ARG* 1.3 74.7 - - - +
240B GLU* 1.3 52.9 + - - +
242B ILE* 3.1 10.8 + - - +
243B GLN* 2.5 40.1 + - - +
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Residues in contact with GLU 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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127B ASN* 4.9 0.2 + - - -
205B LYS 5.5 0.6 - - - +
206B TRP* 6.1 0.2 - - - -
207B GLY* 3.7 22.0 + - - -
209B ALA* 4.2 0.3 - - - +
210B SER* 2.3 44.7 + - - +
236B CYS 2.8 18.1 + - - +
237B ASN 4.0 0.9 - - - +
239B ALA* 1.3 75.5 - - - +
241B CYS* 1.3 61.9 + - - +
243B GLN* 3.6 10.8 - - - +
244B ARG* 2.3 66.0 + - - +
254B LEU* 3.6 27.8 - - + -
257B ASN* 5.0 5.0 - - - +
259B VAL* 4.5 9.4 - - + -
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Residues in contact with CYS 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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176B GLN* 5.2 4.0 - - - -
237B ASN 3.5 13.4 + - - +
238B ARG* 2.8 10.4 + - - +
240B GLU* 1.3 75.7 - - - +
242B ILE* 1.3 62.7 + - + +
244B ARG* 3.0 19.5 - - - +
245B GLY 2.8 18.1 - - - +
246B VAL* 3.1 19.5 - - - +
247B SER* 3.7 11.9 - - - +
248B PRO* 4.6 6.3 - - - -
249B SER* 4.5 20.2 - - - -
251B ALA 4.7 8.7 - - - -
254B LEU* 4.1 21.1 - - - +
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Residues in contact with ILE 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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238B ARG* 2.8 33.7 + - + +
239B ALA* 3.5 11.0 - - - +
241B CYS* 1.3 75.0 - - + +
243B GLN* 1.3 64.6 + - - +
244B ARG 3.1 1.0 + - - -
245B GLY* 3.2 11.1 + - - +
247B SER* 3.7 23.3 + - - +
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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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124B GLN 4.5 1.4 + - - -
125B GLN* 2.9 63.6 + - - +
207B GLY* 5.7 0.4 - - - -
208B PRO* 3.8 23.9 - - - +
209B ALA* 3.6 24.9 + - + +
239B ALA 2.5 21.0 + - - +
240B GLU* 3.6 14.4 - - - +
242B ILE* 1.3 75.4 - - - +
244B ARG* 1.3 57.7 + - - +
245B GLY 3.5 2.8 + - - -
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Residues in contact with ARG 244 (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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125B GLN* 3.4 29.0 + - - +
126B HIS* 3.6 53.4 + - + +
127B ASN* 3.9 16.6 - - - +
176B GLN* 4.5 8.0 + - - -
207B GLY* 5.0 0.8 - - - -
240B GLU* 2.3 57.0 + - - +
241B CYS* 3.0 11.2 - - - +
242B ILE 3.0 0.4 - - - -
243B GLN* 1.3 80.2 - - - +
245B GLY* 1.3 62.3 + - - +
246B VAL* 3.0 15.2 + - + +
254B LEU* 3.2 33.1 + - - +
257B ASN* 4.2 15.4 + - - +
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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
------------------------------------------------------------
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