Contacts of the helix formed by residues 232 - 254 (chain B) in PDB entry 2N5T
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 THR 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B PRO* 1.3 80.0 - - - +
233B ASN* 1.3 79.5 + - + +
234B GLU* 3.1 25.4 + - + +
235B VAL* 3.3 15.4 + - - +
236B ILE* 3.5 11.2 + - - +
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Residues in contact with ASN 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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231B PRO 5.6 0.8 + - - -
232B THR* 1.3 81.6 - - + +
234B GLU* 1.3 62.6 + - - +
236B ILE* 3.3 20.1 + - - +
237B ASP* 3.0 37.9 + - - +
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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
----------------------------------------------------------
232B THR* 3.7 17.9 - - + +
233B ASN* 1.3 79.1 - - - +
235B VAL* 1.3 66.9 + - + +
237B ASP* 3.2 8.7 + - - +
238B LYS* 3.0 53.6 + - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ILE* 5.6 0.2 - - + -
228B TYR* 2.8 65.5 - - + -
231B PRO* 3.8 12.3 - - + -
232B THR* 3.3 14.3 + - - +
234B GLU* 1.3 77.7 - - + +
236B ILE* 1.3 69.5 + - - +
237B ASP 3.2 0.2 + - - -
238B LYS* 3.2 11.2 + - + +
239B MET* 2.8 28.8 + - + +
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Residues in contact with ILE 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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13B PHE* 4.3 18.7 - - + -
217B TYR* 4.0 26.9 - - + +
219B ILE* 4.1 16.6 - - + -
231B PRO* 4.1 13.5 - - + +
232B THR 3.7 15.5 - - - +
233B ASN* 3.3 23.3 + - - +
234B GLU 3.3 0.4 - - - -
235B VAL* 1.3 76.2 - - - +
237B ASP* 1.3 56.5 + - - +
239B MET* 3.0 10.3 + - - +
240B ARG* 2.6 36.7 + - + +
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Residues in contact with ASP 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 ASN* 3.0 30.2 + - - +
234B GLU* 3.5 7.6 - - - +
236B ILE* 1.3 78.9 - - - +
238B LYS* 1.3 66.7 + - - +
240B ARG* 2.9 9.5 + - - +
241B ALA* 2.8 22.7 + - - +
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Residues in contact with LYS 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 43.3 + - + +
235B VAL* 3.5 11.5 - - + +
237B ASP* 1.3 74.7 - - + +
239B MET* 1.3 74.5 + - + +
241B ALA* 3.0 10.5 + - - +
242B VAL* 3.0 29.4 + - + +
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Residues in contact with MET 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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11B ILE* 3.3 16.2 - - + +
13B PHE* 3.9 2.2 - - + -
219B ILE* 3.6 27.1 - - + -
221B ASP* 2.7 45.3 - - + +
223B VAL* 4.6 1.6 - - + -
224B ASN* 3.5 13.0 - - - +
228B TYR* 3.7 22.0 - - + +
235B VAL* 2.8 18.6 + - - +
236B ILE 3.3 7.0 - - - +
238B LYS* 1.3 87.1 - - + +
240B ARG* 1.3 60.8 + - - +
241B ALA 3.3 0.2 - - - -
242B VAL* 3.4 25.9 + - + +
243B GLN 2.9 20.4 + - - -
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Residues in contact with ARG 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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13B PHE* 3.6 33.5 - - + -
236B ILE* 2.6 20.4 + - + +
237B ASP* 2.9 13.4 + - - +
239B MET* 1.3 73.3 - - - +
241B ALA* 1.3 64.5 + - - +
243B GLN* 3.2 24.3 + - - +
244B GLU* 3.1 27.6 + - + +
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Residues in contact with ALA 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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237B ASP 2.8 11.5 + - - +
238B LYS* 3.4 11.4 - - - +
240B ARG* 1.3 74.6 - - - +
242B VAL* 1.3 65.6 + - + +
244B GLU* 3.3 12.8 + - - +
245B GLN* 3.0 24.3 + - - +
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Residues in contact with VAL 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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11B ILE* 3.7 5.4 - - + -
221B ASP* 4.7 0.4 - - - +
223B VAL* 3.1 45.3 - - + -
238B LYS* 3.0 15.7 + - + +
239B MET* 3.7 26.7 - - + +
240B ARG 3.2 0.4 - - - -
241B ALA* 1.3 78.7 - - + +
243B GLN* 1.3 63.2 + - - +
245B GLN* 3.1 7.4 + - + +
246B VAL* 3.1 27.6 + - + +
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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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11B ILE* 2.5 48.9 - - + +
13B PHE* 3.4 12.0 - - + -
239B MET 2.9 10.3 + - - +
240B ARG* 3.2 41.9 + - - +
241B ALA 3.2 0.2 - - - -
242B VAL* 1.3 76.4 - - - +
244B GLU* 1.3 64.3 + - - +
246B VAL* 3.4 6.8 - - - +
247B ALA* 3.3 20.8 + - - +
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Residues in contact with GLU 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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240B ARG* 3.1 20.3 + - + +
241B ALA* 3.6 10.9 - - - +
242B VAL 3.2 0.2 - - - -
243B GLN* 1.3 81.5 - - - +
245B GLN* 1.3 60.7 + - - +
246B VAL 3.2 0.7 - - - -
247B ALA* 3.2 9.7 + - + +
248B SER* 3.0 29.9 + - - +
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Residues in contact with GLN 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 ALA 3.0 17.1 + - - +
242B VAL* 3.5 9.4 - - + +
244B GLU* 1.3 74.3 - - - +
246B VAL* 1.3 67.0 + - + +
248B SER* 3.3 17.0 + - - +
249B GLU* 3.3 36.3 + - - +
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Residues in contact with VAL 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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9B PRO 4.9 3.8 - - - +
10B GLY* 4.2 19.1 - - - +
11B ILE* 4.0 14.1 - - + -
223B VAL* 4.2 19.5 - - + -
242B VAL* 3.1 14.8 + - + +
243B GLN 3.4 9.6 - - - +
244B GLU 3.2 0.2 - - - -
245B GLN* 1.3 77.6 - - + +
247B ALA* 1.3 62.2 + - - +
249B GLU* 3.2 20.7 + - - +
250B LYS* 3.2 38.3 + - + +
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Residues in contact with ALA 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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243B GLN* 3.3 12.9 + - - +
244B GLU* 3.2 14.4 + - + +
246B VAL* 1.3 79.3 - - - +
248B SER* 1.3 62.3 + - - +
250B LYS* 3.2 20.0 + - + +
251B ALA* 3.0 21.9 + - - +
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Residues in contact with SER 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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244B GLU* 3.0 17.2 + - - +
245B GLN* 3.3 22.9 + - - -
247B ALA* 1.3 74.9 - - - +
249B GLU* 1.3 57.1 + - - +
251B ALA* 3.1 11.2 + - - +
252B GLU* 2.9 34.0 + - - +
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Residues in contact with GLU 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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245B GLN* 3.3 24.7 + - - +
246B VAL* 3.2 22.2 + - - +
248B SER* 1.3 73.5 - - - +
250B LYS* 1.3 67.2 + - - +
251B ALA 3.0 0.3 + - - -
252B GLU* 3.1 7.4 + - - +
253B LEU* 2.7 43.9 + - + +
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Residues in contact with LYS 250 (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 GLU* 5.9 9.0 + - - -
246B VAL* 3.2 26.8 + - + +
247B ALA* 3.2 17.9 + - + +
249B GLU* 1.3 77.2 - - - +
251B ALA* 1.3 58.6 + - - +
253B LEU* 3.3 7.8 + - - +
254B ALA* 2.8 33.0 + - - +
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Residues in contact with ALA 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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247B ALA 3.0 11.9 + - - +
248B SER* 3.3 11.7 - - - +
249B GLU 3.0 0.6 - - - -
250B LYS* 1.3 79.3 - - - +
252B GLU* 1.3 65.5 + - + +
254B ALA* 3.2 16.9 + - - +
255B LYS* 3.7 4.0 + - - +
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Residues in contact with GLU 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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248B SER* 2.9 21.4 + - - +
249B GLU* 3.7 8.3 - - - +
251B ALA* 1.3 75.1 - - - +
253B LEU* 1.3 64.0 + - + +
255B LYS* 3.4 20.3 + - - +
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Residues in contact with LEU 253 (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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249B GLU* 2.7 38.4 + - + +
250B LYS* 3.8 6.3 - - - +
252B GLU* 1.3 70.8 - - + +
254B ALA* 1.3 60.7 + - - +
255B LYS 3.0 14.3 + - - +
531B PRO* 4.4 30.5 - - + +
532B ARG* 5.6 17.3 - - + +
535B LYS* 5.9 9.4 - - + +
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Residues in contact with ALA 254 (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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250B LYS 2.8 18.8 + - - +
251B ALA* 3.2 10.3 + - - +
253B LEU* 1.3 75.2 - - - +
255B LYS* 1.3 64.5 - - - +
256B LEU* 3.4 6.9 + - - +
286B ARG 5.6 3.3 - - - +
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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