Contacts of the helix formed by residues 223 - 241 (chain B) in PDB entry 2IAG
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 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B SER 3.8 1.8 + - - -
222B LEU* 1.3 78.1 - - - +
224B VAL* 1.3 63.8 + - - +
225B GLY* 3.7 4.6 + - - -
226B ASP* 3.0 33.7 + - - +
227B LYS* 2.9 21.7 + - - +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU 3.8 0.8 + - - +
223B SER* 1.3 72.4 - - - +
225B GLY* 1.3 57.7 + - - +
227B LYS* 3.2 16.2 + - + +
228B ASP* 2.9 29.6 + - + +
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Residues in contact with GLY 225 (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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223B SER* 3.2 5.2 + - - -
224B VAL* 1.3 78.1 - - - +
226B ASP* 1.3 57.7 + - - +
228B ASP* 3.2 8.8 + - - +
229B HIS* 2.9 25.7 + - - +
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Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 4.2 13.8 - - + +
222B LEU* 3.9 28.8 - - + +
223B SER* 3.0 26.8 + - - +
225B GLY* 1.3 73.2 - - - +
227B LYS* 1.3 60.1 + - - +
229B HIS* 3.2 14.6 + - - +
230B MET* 2.9 28.1 + - - +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 5.3 10.8 - - + -
220B GLY* 5.3 10.8 + - - -
222B LEU* 3.5 38.8 + - + +
223B SER 2.9 13.0 + - - +
224B VAL* 3.4 18.4 - - + +
226B ASP* 1.3 74.9 - - - +
228B ASP* 1.3 57.9 + - - +
230B MET* 3.3 8.4 + - - +
231B CYS* 3.0 33.0 + - - -
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Residues in contact with ASP 228 (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 VAL* 2.9 13.8 + - + +
225B GLY* 3.4 11.0 - - - +
227B LYS* 1.3 75.5 - - - +
229B HIS* 1.3 62.6 + - - +
231B CYS* 3.4 13.3 + - - +
232B SER* 2.9 28.5 + - - -
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Residues in contact with HIS 229 (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 GLN* 3.2 31.3 + - + -
213B LEU* 3.6 21.8 - - + +
225B GLY 2.9 13.3 + - - +
226B ASP* 3.2 17.8 + - - +
228B ASP* 1.3 76.2 - - - +
230B MET* 1.3 61.8 + - - +
232B SER* 3.2 10.2 + - - -
233B VAL* 3.1 30.2 + - + +
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Residues in contact with MET 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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107B ILE* 5.4 0.7 - - + +
210B LEU* 3.6 54.1 - - + +
213B LEU* 3.9 26.0 - - + +
214B LEU* 3.9 11.7 - - + +
217B LEU* 3.5 37.9 - - + -
222B LEU* 4.6 4.5 - - + -
226B ASP 2.9 16.3 + - - +
227B LYS* 3.6 8.7 - - - +
228B ASP 3.3 0.4 - - - -
229B HIS* 1.3 77.0 - - - +
231B CYS* 1.3 61.6 + - - +
233B VAL* 3.3 3.1 + - - +
234B LYS* 3.0 38.0 + - - +
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Residues in contact with CYS 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 LYS* 3.0 21.1 + - - -
228B ASP* 3.7 17.5 - - - +
229B HIS 3.3 0.4 - - - -
230B MET* 1.3 75.3 - - - +
232B SER* 1.3 56.6 + - - +
234B LYS* 3.3 10.6 + - - +
235B SER* 2.8 35.5 + - - +
238B TRP* 5.3 1.4 - - - -
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Residues in contact with SER 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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228B ASP* 2.9 15.9 + - - -
229B HIS* 3.2 14.2 + - - -
231B CYS* 1.3 75.1 - - - +
233B VAL* 1.3 61.6 + - - +
235B SER* 3.7 6.0 - - - -
236B ARG* 3.0 29.8 + - - +
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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
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206B THR* 3.3 34.4 - - + +
209B GLN* 3.8 19.7 - - + +
210B LEU* 3.4 28.9 - - + +
213B LEU* 5.1 0.4 - - + -
229B HIS* 3.1 38.1 + - + +
230B MET* 3.7 10.5 - - - +
232B SER* 1.3 74.3 - - - +
234B LYS* 1.3 63.9 + - - +
236B ARG* 3.4 4.0 + - - +
237B LEU* 3.1 25.3 + - + +
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Residues in contact with LYS 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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106B ARG 4.8 0.8 + - - -
107B ILE* 2.8 29.6 + - - +
108B PHE* 4.5 5.4 - - + +
109B ASP* 2.8 33.2 + - - +
210B LEU* 3.8 24.2 - - + -
217B LEU* 3.6 16.3 - - - +
230B MET* 3.0 38.6 + - + +
231B CYS* 3.6 8.9 - - - +
233B VAL* 1.3 76.6 - - - +
235B SER* 1.3 57.0 + - - +
237B LEU* 3.3 3.5 + - - +
238B TRP* 2.8 59.6 + - + +
278B VAL* 5.7 0.2 - - - -
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Residues in contact with SER 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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231B CYS* 2.8 21.5 + - - +
232B SER* 3.7 7.9 - - - -
234B LYS* 1.3 76.5 - - - +
236B ARG* 1.3 63.0 + - - +
238B TRP* 3.3 22.9 + - - +
239B LYS* 3.1 27.5 + - - +
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Residues in contact with ARG 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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202B ASP* 2.5 45.7 + - - -
206B THR* 2.8 35.5 + - + -
232B SER 3.0 17.7 + - - +
233B VAL* 3.7 5.2 - - - +
234B LYS 3.3 0.2 - - - -
235B SER* 1.3 74.6 - - - +
237B LEU* 1.3 58.2 + - - +
239B LYS* 3.2 8.5 + - - +
240B LEU* 2.9 47.6 + - + +
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Residues in contact with LEU 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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203B VAL* 4.2 24.9 - - + +
206B THR* 3.7 19.3 - - + +
207B PHE* 4.0 26.0 - - + +
210B LEU* 4.0 23.6 - - + -
233B VAL* 3.1 17.7 + - + +
234B LYS 3.7 4.5 - - - +
236B ARG* 1.3 75.8 - - - +
238B TRP* 1.3 56.6 + - - +
240B LEU* 3.3 10.9 + - + +
241B LEU* 2.9 32.5 + - + +
278B VAL* 3.5 27.9 - - + +
281B LEU* 4.2 19.5 - - + -
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Residues in contact with TRP 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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108B PHE* 3.8 10.2 + - - -
109B ASP* 3.7 23.1 - - + -
231B CYS* 5.3 0.7 - - - -
234B LYS* 2.8 47.2 + - + +
235B SER* 3.8 24.0 - - - +
236B ARG 3.3 0.2 - - - -
237B LEU* 1.3 75.3 - - - +
239B LYS* 1.3 63.1 + - + +
241B LEU 4.7 0.2 - - - +
242B SER* 3.3 18.9 + - - -
271B GLU 5.6 0.4 - - - +
274B ALA* 3.4 21.5 - - + +
275B ARG* 3.5 66.9 + - + +
278B VAL* 3.4 32.7 - - + +
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Residues in contact with LYS 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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235B SER 3.1 17.0 + - - +
236B ARG* 3.4 9.9 - - + +
238B TRP* 1.3 77.8 - - + +
240B LEU* 1.3 69.2 + - + +
242B SER* 3.1 23.0 + - - -
245B ARG* 3.7 16.2 + - - +
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Residues in contact with LEU 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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177B TYR* 4.5 6.9 + - - -
199B HIS* 4.5 16.0 - - + +
202B ASP* 3.9 16.8 - - - +
203B VAL* 4.4 14.1 - - + -
206B THR* 4.6 3.8 - - - +
236B ARG* 2.9 60.1 + - + +
237B LEU* 3.8 13.9 - - + +
239B LYS* 1.3 80.4 - - + +
241B LEU* 1.3 68.9 + - + +
242B SER 3.5 0.2 - - - -
245B ARG* 3.4 44.4 - - - +
246B LEU* 4.6 2.1 - - - +
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Residues in contact with LEU 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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177B TYR* 3.9 26.7 - - + +
181B TYR* 3.8 20.6 - - + -
203B VAL* 4.5 9.4 - - + -
237B LEU* 2.9 26.0 + - + +
238B TRP 3.9 3.1 - - - -
240B LEU* 1.3 89.4 - - + +
242B SER* 1.3 66.6 + - - +
246B LEU* 3.6 10.0 - - + +
274B ALA* 4.1 3.4 - - - -
277B LEU* 3.3 47.7 - - + +
278B VAL* 4.0 14.1 - - + -
281B LEU* 4.0 23.3 - - + -
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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