Contacts of the helix formed by residues 240 - 252 (chain B) in PDB entry 2I91
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 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B THR* 3.1 14.8 + - - +
239B LYS* 1.3 76.4 - - - +
241B GLU* 1.3 63.9 + - - +
242B LEU* 2.8 34.6 + - - +
243B GLU* 3.6 20.3 + - + +
244B ILE* 3.3 22.7 + - - +
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Residues in contact with GLU 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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239B LYS 3.3 6.8 + - - +
240B ASP* 1.3 72.3 + - - +
242B LEU* 1.3 73.9 + - + +
244B ILE* 3.0 14.1 + - + +
245B ILE* 2.9 30.3 + - + +
262B HIS* 5.3 5.8 - - + -
265B SER* 2.3 38.8 + - - -
267B GLU* 4.3 8.5 - - - +
268B ILE* 3.3 22.4 + - + +
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Residues in contact with LEU 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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240B ASP* 2.8 18.4 + - - +
241B GLU* 1.3 86.9 - - + +
243B GLU* 1.3 54.9 + - - +
245B ILE* 3.6 19.0 + - + +
246B HIS* 3.0 28.6 + - - +
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Residues in contact with GLU 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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234B ARG* 3.2 36.4 + - - +
238B THR* 2.7 32.9 + - - +
240B ASP* 3.4 22.1 + - - +
241B GLU 3.1 0.8 - - - -
242B LEU* 1.3 76.7 - - - +
244B ILE* 1.3 67.3 + - - +
246B HIS* 3.2 11.0 - - + +
247B LEU* 2.9 35.1 + - + +
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Residues in contact with ILE 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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235B VAL* 4.4 13.7 - - + +
238B THR* 3.7 19.1 - - + +
239B LYS 5.3 0.7 - - - +
240B ASP 3.4 16.2 - - - +
241B GLU* 3.0 14.5 + - - +
243B GLU* 1.3 76.8 - - - +
245B ILE* 1.3 65.0 + - - +
247B LEU* 3.0 9.6 + - - +
248B ILE* 2.9 40.4 + - + +
258B LEU* 4.3 12.8 - - + -
262B HIS* 3.4 46.4 - - + +
268B ILE* 3.7 19.5 - - + -
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Residues in contact with ILE 245 (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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241B GLU* 2.9 20.2 + - + +
242B LEU* 3.7 22.2 - - + +
244B ILE* 1.3 76.3 - - - +
246B HIS* 1.3 67.0 + - + +
248B ILE* 3.3 5.6 + - + +
249B ASP* 3.0 31.2 + - - +
267B GLU* 3.9 35.2 - - + +
268B ILE* 4.3 13.0 - - + -
271B SER* 4.0 28.9 - - - +
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Residues in contact with HIS 246 (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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242B LEU 3.0 15.5 + - - +
243B GLU* 3.2 17.6 - - + +
245B ILE* 1.3 78.8 - - + +
247B LEU* 1.3 59.8 + - + +
249B ASP* 3.1 11.4 + - + +
250B GLU* 2.9 34.9 + - - +
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Residues in contact with LEU 247 (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 ALA* 4.0 10.3 - - + +
234B ARG* 3.8 34.8 - - + -
235B VAL* 4.0 18.2 - - + +
238B THR* 5.5 0.2 - - + -
243B GLU* 2.9 32.3 + - + +
244B ILE* 3.6 6.1 - - - +
246B HIS* 1.3 72.6 - - + +
248B ILE* 1.3 59.0 + - - +
250B GLU* 4.4 6.3 - - - +
251B TYR* 2.8 62.0 + - + +
253B LEU* 4.0 15.1 - - + +
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Residues in contact with ILE 248 (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 VAL* 5.9 0.2 - - + -
244B ILE* 2.9 36.8 + - + +
245B ILE* 3.4 9.2 - - - +
247B LEU* 1.3 75.1 - - - +
249B ASP* 1.3 60.0 + - - +
252B ARG* 2.8 31.8 + - - +
253B LEU* 3.5 30.1 - - + +
258B LEU* 3.8 19.3 - - + -
268B ILE* 4.5 6.3 - - + -
271B SER* 3.5 31.9 - - - +
272B LEU* 3.7 25.1 - - + -
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Residues in contact with ASP 249 (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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220A PRO* 4.0 40.1 - - + +
224A LYS* 5.8 2.4 + - - +
245B ILE* 3.0 23.6 + - - +
246B HIS* 3.1 14.5 + - + +
248B ILE* 1.3 80.2 - - - +
250B GLU* 1.3 60.8 + - - +
251B TYR 3.6 0.2 + - - -
252B ARG* 4.0 6.9 + - - +
271B SER* 4.1 10.7 + - - +
274B GLN* 4.0 16.6 + - - -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LYS* 4.1 21.6 + - - +
227B LYS* 5.4 1.7 + - - -
246B HIS* 2.9 21.9 + - - +
247B LEU* 3.2 5.6 + - - +
249B ASP* 1.3 78.6 - - - +
251B TYR* 1.3 101.4 + - + +
252B ARG 3.6 0.2 - - - -
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Residues in contact with TYR 251 (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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224A LYS* 5.8 1.1 - - - +
166B MET* 5.6 1.2 - - - +
224B LYS* 5.5 1.3 - - + -
227B LYS* 3.7 47.1 + - + +
228B TYR* 3.5 44.4 - + + -
230B GLU* 5.5 0.3 + - - -
231B ALA* 3.3 25.6 - - + -
247B LEU* 2.8 39.7 + - + +
250B GLU* 1.3 109.5 + - + +
252B ARG* 1.3 72.7 + - - +
253B LEU* 3.0 11.8 + - + -
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Residues in contact with ARG 252 (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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221A GLU* 3.1 50.3 + - + +
224A LYS* 5.8 5.4 - - - +
166B MET* 5.9 5.7 - - - +
228B TYR* 5.1 1.9 + - - -
248B ILE* 2.8 15.0 + - - +
249B ASP 4.0 5.5 + - - +
250B GLU 3.6 1.8 + - - -
251B TYR* 1.3 79.1 - - - +
253B LEU* 1.3 62.9 + - - +
254B VAL* 3.7 11.2 + - - +
257B HIS* 4.8 1.9 + - - -
275B ASP* 3.7 22.9 + - + +
14F A 2.8 74.2 + - + +
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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