Contacts of the helix formed by residues 229 - 250 (chain C) in PDB entry 5AQP
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 GLY 229 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU* 4.5 11.4 - - - -
201C GLY* 5.6 3.4 - - - -
203C GLY* 4.4 15.2 - - - -
204C THR 5.2 0.4 - - - -
228C LEU* 1.3 77.1 - - - +
230C GLY* 1.3 64.6 + - - -
231C GLU* 3.2 3.4 - - - -
232C ASP* 3.1 26.8 + - - +
233C PHE* 3.7 14.8 - - - -
340C SER* 4.8 0.9 - - - -
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Residues in contact with GLY 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLY* 6.0 0.8 - - - -
203C GLY 5.6 1.6 - - - +
229C GLY* 1.3 70.3 - - - -
231C GLU* 1.3 55.8 + - - +
233C PHE* 3.0 15.6 + - - +
234C ASP* 3.0 25.0 + - - -
271C LYS* 3.2 28.3 + - - -
340C SER* 3.5 14.5 + - - -
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C GLY* 6.6 0.2 - - - -
229C GLY* 3.2 2.1 + - - -
230C GLY* 1.3 74.8 - - - +
232C ASP* 1.3 59.2 + - - +
234C ASP* 3.2 13.9 + - - +
235C ASN* 2.9 40.6 + - - +
264C ARG* 5.3 4.9 - - - +
268C GLU* 6.0 1.6 - - - +
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Residues in contact with ASP 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C HIS 3.4 17.6 - - - +
228C LEU* 3.4 10.0 - - + -
229C GLY 3.1 31.3 + - - +
231C GLU* 1.3 74.7 - - - +
233C PHE* 1.3 67.0 + - + +
235C ASN* 3.5 15.4 + - - +
236C ARG* 3.3 26.7 + - - +
309C LEU* 3.9 20.0 - - + +
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 4.2 15.3 - - + -
228C LEU* 4.4 12.3 - - + -
229C GLY* 3.7 17.3 - - - -
230C GLY* 3.0 19.2 + - - +
232C ASP* 1.3 77.7 - - - +
234C ASP* 1.3 64.6 + - - +
236C ARG* 3.4 5.2 + - - +
237C MET* 3.3 19.2 + - - +
271C LYS* 4.2 5.4 - - + -
302C PHE* 4.2 15.4 - - + -
306C ASN* 3.2 29.8 + - - +
309C LEU* 4.0 20.4 - - + -
310C PHE* 3.5 30.5 - + - -
313C THR* 5.8 0.9 - - + -
340C SER* 3.8 22.2 - - - -
343C ILE* 3.8 23.3 - - + -
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Residues in contact with ASP 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLY 3.0 17.4 + - - +
231C GLU* 3.2 17.6 + - + +
233C PHE* 1.3 75.5 - - - +
235C ASN* 1.3 59.4 + - - +
237C MET* 3.1 9.3 + - - +
238C VAL* 2.9 33.3 + - - +
264C ARG* 4.1 13.2 - - + +
267C CYS* 4.4 4.4 - - + +
268C GLU* 3.5 39.0 - - + +
271C LYS* 3.0 36.9 + - - +
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Residues in contact with ASN 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLU* 2.9 23.8 + - - +
232C ASP* 3.6 16.7 + - - +
233C PHE 3.3 0.4 - - - -
234C ASP* 1.3 76.4 - - - +
236C ARG* 1.3 59.0 + - + +
238C VAL* 3.2 2.1 + - - +
239C ASN* 2.9 39.1 + - - +
264C ARG* 2.4 52.6 + - - +
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Residues in contact with ARG 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ASP 3.3 10.2 + - - +
233C PHE 3.6 2.2 - - - +
234C ASP 3.2 0.4 - - - -
235C ASN* 1.3 77.5 - - + +
237C MET* 1.3 63.2 + - - +
239C ASN* 3.3 13.0 + - - +
240C HIS* 3.0 23.2 + - - +
305C LEU* 2.8 44.4 + - + +
306C ASN* 3.2 31.8 - - - +
308C ASP* 2.8 41.8 + - - -
309C LEU* 3.7 26.0 - - + +
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Residues in contact with MET 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C PHE 3.3 7.1 + - - +
234C ASP* 3.1 11.1 + - - +
236C ARG* 1.3 79.6 - - - +
238C VAL* 1.3 56.3 + - - +
240C HIS* 3.2 6.4 + - - +
241C PHE* 3.0 59.2 + - + -
267C CYS* 3.5 39.3 - - + +
270C ALA* 4.2 12.3 - - - -
271C LYS* 3.7 13.7 - - + +
274C LEU* 4.9 1.6 - - + -
297C ILE* 3.9 22.0 - - + -
302C PHE* 3.4 37.2 - - + -
305C LEU* 4.5 3.8 - - - +
306C ASN* 5.2 0.2 - - - +
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ASP 2.9 19.2 + - - +
235C ASN 3.2 7.8 + - - +
237C MET* 1.3 76.8 - - - +
239C ASN* 1.3 59.9 + - - +
241C PHE* 3.3 2.1 + - - +
242C ILE* 2.9 47.1 + - + +
260C VAL* 4.6 13.9 - - + +
263C LEU* 4.0 12.3 - - + +
264C ARG* 3.8 51.6 - - + +
267C CYS* 4.0 14.1 - - + -
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Residues in contact with ASN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASN* 2.9 27.5 + - - +
236C ARG* 3.7 12.4 - - - +
238C VAL* 1.3 78.5 - - - +
240C HIS* 1.3 63.9 + - - +
242C ILE* 3.3 14.6 + - - +
243C ALA* 3.0 24.8 + - - +
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Residues in contact with HIS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ARG 3.0 14.5 + - - +
237C MET 3.2 7.4 + - - +
239C ASN* 1.3 78.3 - - - +
241C PHE* 1.3 79.2 + + - +
243C ALA* 3.4 6.6 + - - +
244C GLU* 3.0 46.7 + - - +
247C ARG* 4.7 13.8 + - - -
296C SER 5.2 2.0 + - - -
297C ILE* 3.8 25.2 - - + +
301C ARG* 4.1 23.5 - - + +
305C LEU* 3.6 27.3 - - + +
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Residues in contact with PHE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C MET* 3.0 48.8 + - + +
240C HIS* 1.3 92.1 - + - +
242C ILE* 1.3 59.6 + - - +
244C GLU* 3.2 8.9 + - - +
245C PHE* 2.9 30.3 + - - +
263C LEU* 3.7 28.0 - - + -
267C CYS* 3.4 19.5 - - - -
282C ILE* 4.0 15.3 - - + -
293C PHE* 3.8 21.8 - + + -
295C THR* 3.5 25.1 - - + -
296C SER 4.3 4.9 - - - -
297C ILE* 3.9 25.1 - - + -
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C VAL* 2.9 36.6 + - + +
239C ASN* 3.8 12.6 - - - +
241C PHE* 1.3 75.5 - - - +
243C ALA* 1.3 64.4 + - - +
245C PHE* 3.4 7.1 + - - +
246C LYS* 3.1 42.0 + - - +
251C LYS 4.9 0.2 - - - +
252C ASP* 4.5 2.2 - - - +
253C ILE* 4.1 15.4 - - + +
254C SER* 4.1 31.2 - - - -
260C VAL* 4.7 9.4 - - + -
263C LEU* 3.9 15.3 - - + -
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ASN 3.0 16.4 + - - +
240C HIS* 3.6 6.3 - - - +
242C ILE* 1.3 76.4 - - - +
244C GLU* 1.3 58.1 + - - +
246C LYS* 3.2 13.6 + - - +
247C ARG* 2.9 47.0 + - + +
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Residues in contact with GLU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C HIS* 3.0 39.1 + - + +
241C PHE* 3.2 14.7 + - - +
243C ALA* 1.3 76.1 - - - +
245C PHE* 1.3 57.0 + - - +
247C ARG* 3.3 26.1 + - - +
248C LYS* 2.9 60.3 + - + +
293C PHE* 3.6 7.7 - - + -
295C THR* 2.7 32.0 + - - -
296C SER 4.8 2.3 - - - +
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Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE 2.9 16.3 + - - +
242C ILE* 3.7 7.6 - - - +
244C GLU* 1.3 72.5 - - - +
246C LYS* 1.3 61.1 + - - +
249C HIS* 2.8 48.0 + + + +
250C LYS 3.6 0.7 + - - -
251C LYS* 3.6 25.4 - - + +
253C ILE* 3.5 31.6 - - + -
287C LEU* 3.9 20.4 - - + -
288C TYR* 4.2 13.5 - + + -
291C ILE* 3.9 33.9 - - + -
293C PHE* 3.4 40.1 - + + -
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ILE* 3.1 28.1 + - - +
243C ALA* 3.2 13.4 + - - +
245C PHE* 1.3 76.7 - - - +
247C ARG* 1.4 59.7 + - + +
250C LYS* 2.7 31.3 + - - +
251C LYS 3.5 20.2 - - - +
252C ASP* 3.5 38.0 + - - +
254C SER* 5.2 1.0 + - - -
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C HIS* 4.7 12.5 + - - -
243C ALA* 2.9 36.3 + - + +
244C GLU* 3.3 37.4 + - - +
246C LYS* 1.4 77.9 - - + +
248C LYS* 1.3 63.0 + - + +
250C LYS* 4.6 1.0 + - - +
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Residues in contact with LYS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C GLU* 2.9 54.2 + - + +
247C ARG* 1.3 79.2 - - + +
249C HIS* 1.3 84.8 + - + +
293C PHE* 4.8 6.0 - - + -
294C TYR 4.3 11.7 + - - -
295C THR* 3.9 7.9 + - - +
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Residues in contact with HIS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C PHE* 2.8 58.2 + + + +
248C LYS* 1.3 97.6 + - + +
250C LYS* 1.3 70.5 + - - +
251C LYS* 3.2 12.0 + - + +
291C ILE* 3.5 38.3 - - + +
292C ASP 4.5 6.3 + - - -
293C PHE* 4.6 5.2 - + - -
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C PHE 3.6 0.2 + - - -
246C LYS* 2.7 27.3 + - - +
247C ARG 4.6 1.0 + - - +
248C LYS 3.8 0.8 - - - -
249C HIS* 1.3 74.6 - - - +
251C LYS* 1.3 61.2 + - - +
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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
------------------------------------------------------------
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