Contacts of the helix formed by residues 227 - 241 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE* 5.2 2.5 - - + -
222B TYR* 4.6 4.9 - - + +
223B TYR* 3.1 42.5 + - + +
225B ILE 3.5 1.4 - - - -
226B GLN* 1.3 100.1 - - + +
228B TYR* 1.3 64.5 + - + +
229B ILE 3.6 0.7 - - - -
230B PRO* 4.0 2.5 - - - +
231B SER* 2.9 28.2 + - - -
266B GLN* 4.1 6.7 + - - +
269B GLY 4.5 5.8 - - - +
270B SER* 3.9 36.1 - - - +
283B ILE* 4.0 18.2 - - + -
287B MET* 3.7 24.9 - - + +
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PRO* 3.4 20.9 - - + +
147B MET* 3.4 13.0 - - - +
220B MET* 3.4 24.0 - - + -
223B TYR* 2.9 34.2 + - + +
224B LEU* 4.1 13.7 - - + -
227B MET* 1.3 71.3 - - - +
229B ILE* 1.3 62.5 + - + +
231B SER* 2.7 17.4 + - - -
232B LEU* 2.9 16.5 + - - +
283B ILE* 3.6 18.4 - - + +
286B TRP* 3.4 50.4 - + + -
341B TYR* 2.7 24.8 + + - -
342B TRP* 3.8 23.1 - + + -
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.0 41.8 + - + +
225B ILE* 4.7 6.7 - - + +
228B TYR* 1.3 75.8 - - + +
230B PRO* 1.3 71.2 - - + +
232B LEU* 3.1 16.7 + - + +
233B LEU* 3.0 38.1 + - + +
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Residues in contact with PRO 230 (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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264A THR* 5.1 18.3 - - + +
271A ARG* 5.7 1.1 - - - +
291A LEU* 6.1 0.7 - - + -
224B LEU 3.7 1.6 - - - +
225B ILE 3.2 27.8 - - - +
226B GLN 3.3 20.6 - - - +
227B MET 3.6 3.6 - - - +
229B ILE* 1.3 95.2 - - + +
231B SER* 1.3 61.7 + - - +
233B LEU* 3.3 12.7 + - + +
234B ILE* 3.2 26.3 + - - +
266B GLN* 3.8 16.6 - - - +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B MET 2.9 14.4 + - - -
228B TYR 2.7 19.8 + - - -
230B PRO* 1.3 75.1 - - - +
232B LEU* 1.3 63.6 + - - +
234B ILE* 3.3 8.7 + - - +
235B VAL* 3.2 26.9 + - - +
263B MET* 3.5 29.9 - - - +
266B GLN* 4.3 4.8 - - - +
286B TRP* 2.8 25.9 + - - -
287B MET* 4.1 5.8 - - - -
290B CYS* 4.4 2.5 - - - -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR 2.9 15.3 + - - +
229B ILE* 3.3 22.9 - - + +
231B SER* 1.3 77.2 + - - +
233B LEU* 1.3 60.9 + - + +
235B VAL* 3.2 9.0 + - - +
236B ILE* 3.0 47.9 + - + +
286B TRP* 4.8 13.2 - - + -
334B PHE* 3.5 30.7 - - + -
338B ASN* 4.8 4.3 - - - +
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Residues in contact with LEU 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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260A VAL* 6.0 2.7 - - + -
264A THR* 5.4 4.5 - - + -
291A LEU* 3.4 37.7 - - + -
295A PHE* 3.8 27.3 - - + -
229B ILE* 3.0 31.2 + - + +
230B PRO* 3.6 11.7 - - + +
231B SER 3.3 0.4 - - - -
232B LEU* 1.3 78.9 - - + +
234B ILE* 1.3 64.5 + - + +
236B ILE* 3.4 16.9 + - + +
237B LEU* 2.9 28.3 + - - +
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Residues in contact with ILE 234 (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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260A VAL* 5.3 2.5 - - + -
261A LEU* 3.6 31.0 - - + -
264A THR* 4.8 14.1 - - + -
230B PRO 3.2 17.8 + - - +
231B SER* 3.7 9.4 - - - +
232B LEU 3.3 0.4 - - - -
233B LEU* 1.3 74.9 - - + +
235B VAL* 1.3 65.3 + - - +
237B LEU* 3.3 11.5 - - + +
238B SER* 3.1 18.5 + - - -
259B THR* 3.6 39.5 - - + +
262B THR* 3.7 18.2 - - + -
263B MET* 4.0 16.4 - - - -
266B GLN* 4.8 4.7 - - - +
294B VAL* 3.9 2.4 - - + +
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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
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231B SER 3.2 15.5 + - - +
232B LEU 3.2 7.6 + - - +
234B ILE* 1.3 74.3 - - - +
236B ILE* 1.3 63.5 + - + +
238B SER* 2.6 24.1 + - - +
239B TRP* 3.4 37.3 + - + +
263B MET* 5.1 0.9 - - - -
290B CYS* 3.8 40.8 - - + +
293B PHE* 4.5 8.7 - - + -
294B VAL* 3.9 10.1 - - + -
334B PHE* 4.1 24.2 - - + -
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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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295A PHE* 3.7 22.9 - - + -
299A LEU* 6.0 1.8 - - + -
232B LEU* 3.0 43.0 + - + +
233B LEU* 3.8 16.8 - - + +
234B ILE 3.4 0.2 - - - -
235B VAL* 1.3 76.0 - - + +
237B LEU* 1.3 63.5 + - - +
239B TRP* 3.0 50.0 + - + +
240B VAL* 3.6 7.9 + - + +
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Residues in contact with LEU 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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257A ILE* 4.7 11.0 - - + -
260A VAL* 4.1 20.2 - - + -
261A LEU* 4.3 19.3 - - + -
295A PHE* 4.0 18.8 - - + -
298A LEU* 3.5 26.0 - - + -
233B LEU 2.9 14.0 + - - +
234B ILE* 3.3 14.8 - - + +
236B ILE* 1.3 76.9 - - - +
238B SER* 1.3 62.8 + - - +
239B TRP 3.2 1.0 + - - -
240B VAL* 3.2 18.5 + - + +
255B LEU* 3.2 27.0 - - + +
258B THR* 5.3 0.2 - - - +
259B THR* 3.9 15.5 - - + -
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Residues in contact with SER 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 ILE 3.1 3.0 + - - -
235B VAL* 2.6 21.2 + - - +
237B LEU* 1.3 79.6 - - - +
239B TRP* 1.3 70.1 + - - +
241B SER* 3.2 22.4 - - - -
242B PHE* 4.7 0.7 - - - -
255B LEU* 5.0 5.8 - - - -
256B GLY* 6.1 0.7 - - - -
259B THR* 3.9 16.6 - - - +
293B PHE 4.6 0.7 + - - -
294B VAL* 3.7 27.5 - - - +
297B ALA* 4.0 25.0 - - - +
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Residues in contact with TRP 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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235B VAL* 3.4 34.3 + - + +
236B ILE* 3.0 36.8 + - + +
238B SER* 1.3 85.2 + - - +
240B VAL* 1.3 64.0 + - - +
241B SER 3.0 2.7 - - - -
242B PHE* 3.0 46.7 + + + -
243B TRP* 3.3 19.6 - + + -
293B PHE* 4.8 3.4 - + - +
330B PHE* 3.7 19.4 - + + +
331B PRO* 3.6 42.0 - - + -
334B PHE* 3.7 31.9 - + + -
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Residues in contact with VAL 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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253A VAL* 6.3 0.2 - - + -
295A PHE* 5.0 4.3 - - + -
298A LEU* 4.5 22.9 - - + -
299A LEU* 4.0 24.5 - - + -
302A ALA* 4.7 13.5 - - + +
236B ILE* 3.8 10.5 - - + +
237B LEU* 3.2 24.3 + - + +
239B TRP* 1.3 78.3 - - - +
241B SER* 1.3 67.1 + - - +
243B TRP* 3.0 24.0 + - - +
244B ILE* 3.4 17.2 + - + +
255B LEU* 3.6 22.9 - - + -
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Residues in contact with SER 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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238B SER 3.2 18.7 + - - -
240B VAL* 1.3 81.0 - - - +
242B PHE* 1.3 61.1 + - - +
244B ILE* 3.0 18.6 + - - +
252B ARG* 3.0 59.1 + - - +
255B LEU* 3.7 23.3 - - - +
256B GLY 6.0 0.2 - - - -
297B ALA* 5.2 5.6 + - - -
301B TYR* 4.9 2.1 - - - +
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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