Contacts of the helix formed by residues 227 - 241 (chain C) in PDB entry 5TIN
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 MET 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C PHE* 5.2 2.0 - - + -
222C TYR* 4.6 4.3 - - + +
223C TYR* 3.1 43.8 + - + +
225C ILE 3.5 1.2 - - - -
226C GLN* 1.3 99.5 - - + +
228C TYR* 1.3 64.1 + - + +
229C ILE 3.6 0.4 - - - -
230C PRO* 3.6 2.7 - - - +
231C SER* 2.9 28.2 + - - -
266C GLN* 4.1 6.5 + - - +
269C GLY 4.6 5.4 - - - +
270C SER* 3.9 36.3 - - - +
283C ILE* 4.0 18.6 - - + -
287C MET* 3.7 24.3 - - + +
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Residues in contact with TYR 228 (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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146C PRO* 3.4 19.9 - - + +
147C MET* 3.4 13.5 - - - +
220C MET* 3.4 25.4 - - + -
223C TYR* 2.9 33.8 + - + +
224C LEU* 4.1 14.4 - - + -
227C MET* 1.3 71.8 - - - +
229C ILE* 1.3 61.7 + - + +
231C SER* 2.7 17.8 + - - -
232C LEU* 2.9 17.1 + - - +
283C ILE* 3.6 19.2 - - + +
286C TRP* 3.4 49.9 - + + -
341C TYR* 2.7 24.0 + + - -
342C TRP* 3.8 24.0 - + + -
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 2.9 41.7 + - + +
225C ILE* 4.7 6.7 - - + +
228C TYR* 1.3 75.0 - - + +
230C PRO* 1.3 72.1 - - + +
232C LEU* 3.1 17.6 + - + +
233C LEU* 3.0 38.1 + - + +
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Residues in contact with PRO 230 (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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264B THR* 5.0 18.4 - - + +
271B ARG* 5.7 1.1 - - - +
291B LEU* 6.1 0.4 - - + -
224C LEU 3.7 1.8 - - - +
225C ILE 3.2 28.0 - - - +
226C GLN* 3.4 20.2 - - - +
227C MET 3.6 3.1 - - - +
229C ILE* 1.3 94.1 - - + +
231C SER* 1.3 61.6 + - - +
233C LEU* 3.3 12.4 + - + +
234C ILE* 3.2 26.9 + - - +
266C GLN* 3.8 17.0 - - - +
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Residues in contact with SER 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C MET 2.9 14.1 + - - -
228C TYR 2.7 19.6 + - - -
230C PRO* 1.3 75.6 - - - +
232C LEU* 1.3 64.0 + - - +
234C ILE* 3.3 8.1 + - - +
235C VAL* 3.2 26.9 + - - +
263C MET* 3.5 30.6 - - - +
266C GLN* 4.3 5.5 - - - +
286C TRP* 2.8 25.4 + - - -
287C MET* 4.1 5.8 - - - -
290C CYS* 4.4 2.2 - - - -
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Residues in contact with LEU 232 (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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228C TYR 2.9 14.3 + - - +
229C ILE* 3.1 24.0 + - + +
231C SER* 1.3 76.7 + - - +
233C LEU* 1.3 60.5 + - + +
235C VAL* 3.2 9.3 + - - +
236C ILE* 3.0 48.4 + - + +
286C TRP* 4.8 13.2 - - + -
334C PHE* 3.5 30.5 - - + -
338C ASN* 5.0 5.4 - - - +
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Residues in contact with LEU 233 (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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260B VAL* 6.0 2.9 - - + -
264B THR* 5.4 4.0 - - + -
291B LEU* 3.4 37.9 - - + -
295B PHE* 3.8 25.8 - - + -
229C ILE* 3.0 32.7 + - + +
230C PRO* 3.6 11.0 - - + +
231C SER 3.3 0.4 - - - -
232C LEU* 1.3 78.3 - - + +
234C ILE* 1.3 64.3 + - + +
236C ILE* 3.8 18.7 - - + +
237C LEU* 2.9 28.4 + - - +
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Residues in contact with ILE 234 (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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260B VAL* 5.3 3.1 - - + -
261B LEU* 3.5 31.2 - - + -
264B THR* 4.8 14.1 - - + -
230C PRO 3.2 17.1 + - - +
231C SER* 3.6 9.0 - - - +
232C LEU 3.3 0.4 - - - -
233C LEU* 1.3 75.0 - - + +
235C VAL* 1.3 65.1 + - - +
237C LEU* 3.3 11.6 - - + +
238C SER* 3.1 18.4 + - - -
259C THR* 3.6 40.8 - - + +
262C THR* 3.7 18.4 - - + -
263C MET* 4.0 16.8 - - - -
266C GLN* 4.8 4.0 - - - +
294C VAL* 3.9 2.6 - - + +
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Residues in contact with VAL 235 (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 SER 3.2 15.9 + - - +
232C LEU 3.2 8.0 + - - +
234C ILE* 1.3 76.6 - - - +
236C ILE* 1.3 62.6 + - + +
238C SER* 2.6 24.4 + - - +
239C TRP* 3.4 35.8 + - + +
263C MET* 5.1 0.9 - - - -
290C CYS* 3.8 39.0 - - + +
293C PHE* 4.5 8.7 - - + -
294C VAL* 3.9 9.4 - - + -
334C PHE* 4.1 25.4 - - + -
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Residues in contact with ILE 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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295B PHE* 3.8 21.3 - - + -
299B LEU* 6.1 1.1 - - + -
232C LEU* 3.0 41.9 + - + +
233C LEU* 3.8 16.4 - - + +
235C VAL* 1.3 75.1 - - + +
237C LEU* 1.3 63.8 + - - +
239C TRP* 3.0 48.0 + - + +
240C VAL* 3.6 8.8 + - + +
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Residues in contact with LEU 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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257B ILE* 4.7 11.2 - - + -
260B VAL* 4.1 20.9 - - + -
261B LEU* 4.2 19.5 - - + -
295B PHE* 4.0 18.8 - - + -
298B LEU* 3.5 25.8 - - + -
233C LEU 2.9 14.3 + - - +
234C ILE* 3.3 14.1 - - + +
236C ILE* 1.3 76.9 - - - +
238C SER* 1.3 61.6 + - - +
239C TRP 3.2 1.2 + - - -
240C VAL* 3.2 19.7 + - + +
255C LEU* 3.2 27.2 - - + +
258C THR* 5.3 0.2 - - - +
259C THR* 3.9 15.9 - - + -
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Residues in contact with SER 238 (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 ILE 3.1 2.3 + - - -
235C VAL* 2.6 21.0 + - - +
237C LEU* 1.3 79.4 - - - +
239C TRP* 1.3 70.6 + - - +
241C SER* 3.2 22.0 - - - -
242C PHE* 4.7 0.5 - - - -
255C LEU* 5.0 6.0 - - - +
256C GLY* 6.1 0.7 - - - -
259C THR* 3.9 16.4 - - - -
293C PHE 4.6 0.7 + - - -
294C VAL* 3.7 28.5 - - - +
297C ALA* 4.0 23.9 - - - +
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Residues in contact with TRP 239 (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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235C VAL* 3.4 34.3 + - + +
236C ILE* 3.0 36.4 + - + +
238C SER* 1.3 84.9 + - - +
240C VAL* 1.3 64.7 + - - +
241C SER 3.0 2.7 - - - -
242C PHE* 3.0 46.5 + + + -
243C TRP* 3.3 20.1 - + + -
293C PHE* 4.8 2.8 + + - +
330C PHE* 3.7 19.5 - + + +
331C PRO* 3.6 43.7 - - + -
334C PHE* 3.7 31.0 - + + -
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Residues in contact with VAL 240 (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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295B PHE* 5.0 4.3 - - + -
298B LEU* 4.5 22.7 - - + -
299B LEU* 4.1 23.8 - - + -
302B ALA* 4.8 13.1 - - + +
236C ILE* 3.8 10.5 - - + +
237C LEU* 3.2 24.1 + - + +
239C TRP* 1.3 76.8 - - - +
241C SER* 1.3 66.7 + - - +
243C TRP* 3.0 24.0 + - - +
244C ILE* 3.4 18.0 + - + +
255C LEU* 3.6 23.3 - - + -
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Residues in contact with SER 241 (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 SER 3.2 17.8 + - - -
240C VAL* 1.3 81.3 - - - +
242C PHE* 1.3 61.6 + - - -
244C ILE* 3.0 19.3 + - - +
252C ARG* 3.0 60.1 + - - +
255C LEU* 3.7 22.6 - - - +
297C ALA* 5.2 5.0 + - - -
301C TYR* 4.9 1.7 - - - +
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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