Contacts of the helix formed by residues 256 - 277 (chain C) in PDB entry 5AQM
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 ASN 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C ILE 3.1 10.0 + - - +
255C GLU* 1.3 76.4 - - - +
257C LYS* 1.3 60.1 + - - +
258C ARG* 3.3 3.8 + - - +
259C ALA* 2.9 23.5 + - + -
260C VAL* 3.0 26.2 + - - +
288C TYR* 3.8 28.0 - - + -
1383C TRS 2.8 42.8 + - - -
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Residues in contact with LYS 257 (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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254C SER 5.6 0.2 - - - -
255C GLU 3.4 9.9 + - - +
256C ASN* 1.3 72.5 + - - +
258C ARG* 1.3 58.4 + - + +
260C VAL* 3.5 6.5 + - - +
261C ARG* 2.9 28.6 + - - +
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ASN* 3.2 2.0 + - - +
257C LYS* 1.3 75.6 - - + +
259C ALA* 1.4 60.8 + - - +
261C ARG* 3.3 3.3 + - - +
262C ARG* 3.0 32.4 + - - +
1383C TRS 3.3 28.8 + - - +
211D ILE* 3.6 34.1 - - - +
215D MET* 3.7 34.6 - - + +
248D LEU* 3.8 28.1 - - - +
252D ASP* 2.7 42.4 + - - -
255D GLU* 5.0 2.0 + - - -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ILE* 4.3 18.4 - - + +
256C ASN* 2.9 29.9 + - + +
258C ARG* 1.4 73.1 - - - +
260C VAL* 1.3 66.1 + - - +
262C ARG* 3.3 1.6 + - - -
263C LEU* 3.0 20.8 + - - +
287C LEU* 3.4 38.6 - - + +
288C TYR* 4.5 1.3 - - + -
1383C TRS 3.4 8.9 - - - -
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Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL* 4.3 11.8 - - + +
242C ILE* 4.6 9.4 - - + -
253C ILE* 3.4 20.6 - - + +
254C SER* 3.7 21.8 - - - +
256C ASN 3.0 15.9 + - - +
257C LYS* 3.9 6.3 - - - +
259C ALA* 1.3 74.2 - - - +
261C ARG* 1.3 59.4 + - - +
263C LEU* 3.3 7.4 + - - +
264C ARG* 2.7 55.4 + - - +
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Residues in contact with ARG 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 4.3 11.1 - - - +
257C LYS 2.9 19.5 + - - +
258C ARG* 3.6 5.2 - - - +
259C ALA 3.2 0.2 - - - -
260C VAL* 1.3 76.8 - - - +
262C ARG* 1.4 56.7 + - - +
264C ARG* 3.2 8.2 + - + +
265C THR* 2.9 37.1 + - - +
212D GLU* 2.7 44.6 + - - -
215D MET* 3.8 33.1 - - + +
216D LYS* 4.0 5.7 - - - +
219D GLU* 2.8 38.2 + - - +
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Residues in contact with ARG 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ARG 3.0 17.8 + - - +
259C ALA 3.7 4.5 - - - +
261C ARG* 1.4 75.9 - - - +
263C LEU* 1.3 63.2 + - - +
265C THR* 3.5 5.4 + - - -
266C ALA* 3.0 23.9 + - - +
284C ILE* 3.3 15.0 - - + +
285C ASP 2.9 21.0 + - - +
286C SER 3.2 18.2 + - - -
287C LEU* 3.9 8.1 - - + +
1383C TRS 2.7 40.6 + - - -
215D MET* 4.1 12.3 - - + -
218D LEU* 3.9 29.4 - - + +
219D GLU* 4.9 6.9 - - + +
222D ASP* 2.8 46.3 + - - +
241D VAL* 4.0 13.3 - - - +
245D GLN* 3.3 9.9 - - - +
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL* 3.9 22.2 - - + +
241C PHE* 3.7 37.9 - - + -
242C ILE* 3.9 7.4 - - + +
253C ILE* 3.9 23.3 - - + -
259C ALA 3.0 17.5 + - - +
260C VAL* 3.6 3.8 - - - +
262C ARG* 1.3 77.0 - - - +
264C ARG* 1.4 56.8 + - - +
266C ALA* 3.2 3.5 + - + +
267C CYS* 2.8 44.1 + - - -
282C ILE* 5.3 3.8 - - + -
284C ILE* 4.0 17.9 - - + +
287C LEU* 4.6 5.4 - - + +
293C PHE* 4.1 15.3 - - + -
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Residues in contact with ARG 264 (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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231C GLU 5.0 0.2 + - - -
234C ASP* 4.9 6.4 - - + +
235C ASN* 2.7 34.1 + - - +
238C VAL* 3.6 35.9 - - + +
260C VAL* 2.7 43.7 + - - +
261C ARG* 3.7 7.3 - - - +
263C LEU* 1.4 72.4 - - - +
265C THR* 1.4 57.6 + - - +
267C CYS* 3.1 2.6 + - - +
268C GLU* 2.9 51.9 + - + +
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Residues in contact with THR 265 (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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261C ARG* 2.9 15.9 + - - +
262C ARG 3.8 3.4 - - - -
264C ARG* 1.4 75.3 - - - +
266C ALA* 1.3 62.4 + - - +
268C GLU* 3.3 21.1 + - - +
269C ARG* 3.2 22.4 + - + +
219D GLU* 2.6 51.4 + - + +
222D ASP* 6.5 0.4 - - + -
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Residues in contact with ALA 266 (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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262C ARG 3.0 17.7 + - - +
263C LEU* 3.6 4.7 - - + +
265C THR* 1.3 76.0 - - - +
267C CYS* 1.4 57.7 + - - +
269C ARG* 3.4 8.5 + - - +
270C ALA* 2.9 29.1 + - - +
282C ILE* 3.9 24.2 - - + +
284C ILE* 3.9 20.6 - - + -
222D ASP* 5.1 11.4 - - + +
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Residues in contact with CYS 267 (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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234C ASP* 4.4 4.0 - - - +
237C MET* 3.5 33.1 - - + +
238C VAL* 4.0 15.9 - - + -
241C PHE* 3.5 35.0 - - - -
263C LEU* 2.8 24.5 + - - -
264C ARG* 3.1 10.5 + - - +
266C ALA* 1.4 73.9 - - - +
268C GLU* 1.3 55.3 + - - +
270C ALA* 3.2 3.2 + - - -
271C LYS* 2.8 35.5 + - - +
282C ILE* 4.6 0.9 - - - -
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLU* 6.1 0.7 - - - +
234C ASP* 3.1 34.8 + - + +
264C ARG* 2.9 38.9 + - - +
265C THR* 3.3 21.1 + - - +
267C CYS* 1.3 73.4 - - - +
269C ARG* 1.3 62.3 + - - +
271C LYS* 3.3 7.7 + - - +
272C ARG* 3.2 32.3 + - - +
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Residues in contact with ARG 269 (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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265C THR* 3.2 10.5 + - + +
266C ALA* 3.7 10.5 - - - +
267C CYS 3.3 0.2 - - - -
268C GLU* 1.3 76.1 - - - +
270C ALA* 1.3 65.7 + - - +
272C ARG* 3.1 34.9 + - - +
273C THR* 3.0 31.4 + - - +
281C SER 5.0 9.3 + - - -
222D ASP 4.7 2.8 + - - -
223D THR* 3.3 58.6 + - - +
225D ILE* 5.5 5.1 - - - +
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Residues in contact with ALA 270 (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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237C MET* 3.9 13.0 - - + -
266C ALA 2.9 17.7 + - - +
267C CYS 3.2 4.5 + - - +
269C ARG* 1.3 71.9 - - - +
271C LYS* 1.3 67.5 + - - +
273C THR* 3.1 5.5 + - - -
274C LEU* 2.9 29.6 + - - +
280C ALA* 3.8 23.1 - - + +
281C SER 5.5 0.4 - - - +
282C ILE* 4.0 19.5 - - + -
297C ILE* 4.4 2.9 - - + -
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Residues in contact with LYS 271 (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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230C GLY* 3.4 25.3 + - - -
233C PHE* 4.4 8.3 - - + -
234C ASP* 2.8 29.5 + - - +
237C MET* 3.8 15.2 - - - +
267C CYS 2.8 13.4 + - - +
268C GLU* 3.4 13.6 - - - +
270C ALA* 1.3 73.4 - - - +
272C ARG* 1.3 65.7 + - - +
274C LEU* 3.2 18.3 + - - +
275C PHE* 3.5 26.2 + - + -
302C PHE* 3.7 29.9 - - + -
343C ILE* 4.8 5.8 - - + -
1384C GOL 4.0 24.5 + - - -
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Residues in contact with ARG 272 (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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268C GLU* 3.2 14.3 + - - +
269C ARG* 3.1 44.4 + - - +
271C LYS* 1.3 79.6 - - - +
273C THR* 1.3 63.4 + - - +
275C PHE* 3.1 48.3 + - + +
276C SER* 4.3 2.1 + - - -
1384C GOL 5.1 6.7 - - - +
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Residues in contact with THR 273 (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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269C ARG* 3.0 23.7 + - - +
270C ALA* 3.4 9.3 - - - -
272C ARG* 1.3 75.4 - - - +
274C LEU* 1.3 58.0 + - - +
275C PHE 3.1 1.2 + - - -
276C SER* 3.2 6.5 + - - -
277C SER* 2.9 34.4 + - - +
279C GLN 3.9 21.1 - - - +
280C ALA* 3.9 11.7 - - + -
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Residues in contact with LEU 274 (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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237C MET* 4.5 0.9 - - + -
270C ALA 2.9 21.3 + - - +
271C LYS* 3.2 9.8 + - - +
273C THR* 1.3 73.4 - - - +
275C PHE* 1.3 65.1 + - + +
276C SER 3.2 0.4 - - - -
277C SER 3.3 10.3 - - - +
279C GLN* 3.7 30.5 - - - -
280C ALA* 3.8 4.9 - - + +
297C ILE* 3.8 16.2 - - + +
298C THR 4.1 5.4 - - - +
299C ARG* 3.0 51.1 + - + +
302C PHE* 3.5 44.2 - - + -
344C PRO* 4.1 3.3 - - - +
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Residues in contact with PHE 275 (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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271C LYS* 3.5 22.4 - - + -
272C ARG* 3.1 43.0 + - + +
274C LEU* 1.3 78.5 - - - +
276C SER* 1.3 60.5 + - - +
299C ARG* 3.4 2.5 + - - -
302C PHE* 6.2 0.4 - + - -
339C GLY 4.2 2.0 - - - -
342C ARG* 3.7 53.3 - - + +
343C ILE* 3.5 30.1 - - + -
344C PRO* 3.4 26.4 - - + +
1384C GOL 3.5 23.3 - - - -
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Residues in contact with SER 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG 4.9 1.9 + - - -
273C THR* 3.2 6.2 + - - -
275C PHE* 1.3 81.3 - - - +
277C SER* 1.3 61.4 + - - +
278C THR* 5.8 0.2 - - - +
299C ARG* 3.4 10.1 + - - +
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C THR* 2.9 22.7 + - - +
274C LEU* 3.2 17.8 - - - +
276C SER* 1.3 82.9 + - - +
278C THR* 1.3 62.2 + - - +
279C GLN 3.3 18.4 - - - -
299C ARG* 3.1 15.6 + - - -
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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