Contacts of the helix formed by residues 260 - 274 (chain C) in PDB entry 5AO3
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 ILE 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C ARG* 3.5 40.2 - - - +
258C GLY 4.4 4.9 - - - +
259C LEU* 1.3 73.2 - - - +
261C PRO* 1.3 68.7 - - + -
262C GLU* 4.3 7.0 - - + +
263C GLU* 3.0 17.0 + - + +
264C ASP* 3.0 30.9 + - - +
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Residues in contact with PRO 261 (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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251C LYS* 4.0 30.1 - - + +
254C MET* 4.4 12.3 - - + -
255C GLU* 3.4 36.6 - - + +
259C LEU 3.1 12.5 - - - +
260C ILE* 1.3 86.4 - - + -
262C GLU* 1.3 63.3 + - - +
264C ASP* 5.1 0.4 - - + -
265C ILE* 3.0 50.2 + - + +
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Residues in contact with GLU 262 (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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251C LYS* 5.7 0.4 - - - +
260C ILE* 3.1 8.3 + - + +
261C PRO* 1.3 80.4 - - - +
263C GLU* 1.3 64.8 + - - +
265C ILE* 4.6 1.3 - - - +
266C CYS* 3.7 16.1 + - - +
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Residues in contact with GLU 263 (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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194C ARG* 4.2 17.5 - - - +
260C ILE* 3.0 14.3 + - + +
262C GLU* 1.3 78.7 - - - +
264C ASP* 1.3 61.1 + - - +
266C CYS* 3.4 8.8 - - - +
267C PHE* 3.2 20.6 + - - +
288C LYS 5.9 1.8 - - - +
289C GLY* 3.9 15.9 - - - +
290C ARG* 5.0 0.2 - - - +
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Residues in contact with ASP 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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194C ARG* 2.8 36.2 + - - +
198C CYS* 3.7 15.0 - - - -
254C MET* 6.0 1.1 - - - -
259C LEU* 3.6 12.5 - - + +
260C ILE 3.0 24.8 + - - +
261C PRO* 5.0 0.9 - - + -
263C GLU* 1.3 74.5 - - - +
265C ILE* 1.3 61.2 + - + +
266C CYS 3.1 2.0 - - - -
267C PHE* 2.9 6.6 + - - +
268C ILE* 2.8 34.3 + - + +
290C ARG* 2.7 42.7 + - - -
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Residues in contact with ILE 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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241C PHE* 4.3 5.6 - - + -
242C GLU* 6.1 0.4 - - + -
245C ILE* 3.5 30.5 - - + -
251C LYS* 4.0 14.1 - - + -
254C MET* 3.8 32.1 - - + -
261C PRO* 3.0 34.6 + - + +
262C GLU* 4.6 1.6 - - - +
264C ASP* 1.3 77.1 - - - +
266C CYS* 1.3 60.8 - - - +
268C ILE* 3.6 8.1 + - - +
269C LYS* 3.1 48.5 + - - +
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Residues in contact with CYS 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 GLU 3.7 12.2 + - - +
263C GLU* 3.4 13.0 + - - +
264C ASP 3.1 0.2 - - - -
265C ILE* 1.3 77.8 - - - +
267C PHE* 1.3 62.1 + - - +
269C LYS* 3.1 11.3 + - - +
270C GLU* 3.0 48.9 + - - +
276C LEU* 4.5 13.5 - - - -
288C LYS* 4.1 13.0 - - - -
289C GLY* 4.0 11.2 - - - -
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Residues in contact with PHE 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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195C ASP* 4.5 3.4 - - - -
198C CYS* 3.6 29.8 - - + -
199C VAL* 4.3 7.0 - - + -
263C GLU 3.2 10.3 + - - +
264C ASP* 2.9 10.9 + - - +
266C CYS* 1.3 79.9 - - - +
268C ILE* 1.3 59.7 + - - +
270C GLU* 3.4 7.7 + - - +
271C GLN* 3.0 52.7 + - + -
289C GLY* 4.1 4.6 - - - -
290C ARG* 3.5 46.7 - - + +
297C LEU* 4.0 24.0 - - + -
298C TYR* 3.4 37.7 - + - -
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Residues in contact with ILE 268 (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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198C CYS* 3.6 31.6 - - + +
201C ILE* 3.9 30.7 - - + +
202C ALA* 4.2 12.6 - - - -
241C PHE* 3.6 36.6 - - + -
254C MET* 4.7 6.1 - - + -
259C LEU* 5.0 2.5 - - + -
264C ASP* 2.8 26.0 + - + +
265C ILE* 3.9 6.3 - - - +
267C PHE* 1.3 72.2 - - - +
269C LYS* 1.3 64.0 + - - +
270C GLU 3.4 0.2 + - - -
271C GLN* 3.4 14.7 + - - +
272C ILE* 3.2 29.7 + - + +
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Residues in contact with LYS 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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238C VAL* 3.6 34.7 - - + +
241C PHE* 4.3 13.5 - - + -
242C GLU* 3.5 41.1 + - - +
265C ILE* 3.1 35.1 + - + +
266C CYS* 3.1 10.6 + - - +
268C ILE* 1.3 76.8 - - - +
270C GLU* 1.3 57.2 + - - +
272C ILE* 3.0 12.3 + - - +
273C VAL* 2.8 31.8 + - - +
276C LEU* 4.9 14.4 - - + -
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Residues in contact with GLU 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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266C CYS* 3.0 22.3 + - - +
267C PHE* 3.8 2.1 - - - +
268C ILE 3.2 0.4 - - - -
269C LYS* 1.3 71.6 - - - +
271C GLN* 1.3 58.1 + - - +
272C ILE 3.0 4.7 - - - -
274C GLY* 3.0 41.6 + - - +
275C PRO* 4.8 1.0 - - - +
276C LEU* 3.6 29.5 - - + +
286C PRO 4.4 0.7 - - - +
287C TYR* 3.6 23.6 + - + -
288C LYS 3.0 18.9 + - - -
289C GLY* 3.0 27.3 + - - -
298C TYR* 3.1 27.7 + - + -
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Residues in contact with GLN 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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198C CYS 3.7 13.1 + - - -
199C VAL* 3.3 30.3 - - - +
202C ALA* 3.5 15.5 - - + +
267C PHE* 3.0 62.7 + - + +
268C ILE* 3.6 8.9 - - - +
270C GLU* 1.3 76.6 - - - +
272C ILE* 1.3 58.6 + - - +
297C LEU 3.9 10.4 - - - +
298C TYR* 4.2 16.2 - - + -
301C VAL* 4.1 15.2 - - + +
302C SER* 3.9 24.5 + - - +
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Residues in contact with ILE 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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202C ALA* 4.3 11.0 - - + +
205C CYS* 4.2 24.2 - - + +
206C HIS* 4.2 20.4 - - + +
234C GLU* 3.6 26.3 - - + +
237C SER* 3.7 32.3 - - - +
238C VAL* 4.0 6.5 - - + -
241C PHE* 5.2 4.9 - - + -
268C ILE* 3.2 32.3 - - + +
269C LYS* 3.0 10.9 + - - +
271C GLN* 1.3 83.5 - - - +
273C VAL* 1.3 59.6 + - - +
274C GLY 3.6 0.4 - - - -
301C VAL* 5.8 0.2 - - + -
302C SER* 5.6 3.0 - - - -
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Residues in contact with VAL 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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232C THR* 5.4 0.4 - - - +
234C GLU* 4.1 6.1 - - + +
235C GLN* 4.0 36.1 - - + +
238C VAL* 3.5 27.1 - - + -
269C LYS* 2.8 16.0 + - + +
272C ILE* 1.3 74.1 - - - +
274C GLY* 1.3 72.5 + - - +
275C PRO 4.6 3.3 - - - +
276C LEU* 4.8 11.4 - - + -
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Residues in contact with GLY 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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270C GLU* 3.0 30.6 + - - +
272C ILE 3.6 0.8 - - - -
273C VAL* 1.3 94.7 - - - +
275C PRO* 1.3 77.7 - - - +
276C LEU* 3.5 2.4 + - - +
287C TYR* 4.1 5.6 - - - -
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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