Contacts of the helix formed by residues 227 - 241 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A PHE* 5.2 2.2 - - + -
222A TYR* 4.6 4.3 - - + +
223A TYR* 3.1 42.3 + - + +
225A ILE 3.5 1.0 - - - -
226A GLN* 1.3 99.9 - - + +
228A TYR* 1.3 62.5 + - - +
229A ILE 3.6 0.9 - - - -
230A PRO* 3.6 3.2 - - - +
231A SER* 2.9 28.8 + - - -
266A GLN* 4.1 6.4 + - - +
269A GLY 4.6 6.1 - - - +
270A SER* 4.0 37.0 - - - +
283A ILE* 4.0 18.2 - - + -
287A MET* 3.7 25.2 - - + +
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Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PRO* 3.4 20.0 - - + +
147A MET* 3.4 12.8 - - - +
220A MET* 3.4 24.5 - - + -
223A TYR* 2.9 34.4 + - + +
224A LEU* 4.1 13.5 - - + -
227A MET* 1.3 70.7 - - - +
229A ILE* 1.3 62.2 + - + +
231A SER* 2.7 18.5 + - - -
232A LEU* 2.9 16.2 + - - +
283A ILE* 3.6 19.8 - - + +
286A TRP* 3.5 49.9 - + + -
341A TYR* 2.7 23.4 + + - -
342A TRP* 3.8 24.9 - + + -
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.0 41.2 + - + +
225A ILE* 4.7 7.0 - - + +
228A TYR* 1.3 75.0 - - + +
230A PRO* 1.3 72.7 - - + +
232A LEU* 3.1 18.0 + - + +
233A LEU* 3.0 37.2 + - + +
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Residues in contact with PRO 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU 3.7 1.6 - - - +
225A ILE 3.2 28.3 - - - +
226A GLN* 3.4 20.2 - - - +
227A MET 3.6 3.4 - - - +
229A ILE* 1.3 95.6 - - + +
231A SER* 1.3 61.0 + - - +
233A LEU* 3.3 11.9 + - + +
234A ILE* 3.2 27.2 + - - +
266A GLN* 3.8 16.8 - - - +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A MET 2.9 14.0 + - - -
228A TYR 2.7 19.8 + - - -
230A PRO* 1.3 74.9 - - - +
232A LEU* 1.3 63.0 + - - +
234A ILE* 3.3 9.3 + - - +
235A VAL* 3.2 27.5 + - - +
263A MET* 3.5 29.3 - - - +
266A GLN* 4.3 4.9 - - - +
286A TRP* 2.8 25.9 + - - -
287A MET* 4.1 5.8 - - - -
290A CYS* 4.4 2.5 - - - -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A TYR 2.9 14.5 + - - +
229A ILE* 3.3 23.3 - - + +
231A SER* 1.3 77.6 + - - +
233A LEU* 1.3 61.0 + - + +
235A VAL* 3.2 9.3 + - - +
236A ILE* 3.0 48.7 + - + +
286A TRP* 4.8 13.9 - - + -
334A PHE* 3.5 30.7 - - + -
338A ASN* 4.8 4.0 - - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 3.0 31.0 + - + +
230A PRO* 3.6 12.3 - - + +
231A SER 3.3 0.2 - - - -
232A LEU* 1.3 78.3 - - + +
234A ILE* 1.3 63.6 + - + +
236A ILE* 3.4 20.9 + - + +
237A LEU* 2.9 29.0 + - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO 3.2 16.7 + - - +
231A SER* 3.7 9.6 - - - +
232A LEU 3.3 0.4 - - - -
233A LEU* 1.3 74.7 - - + +
235A VAL* 1.3 65.0 + - - +
237A LEU* 3.3 19.4 - - + +
238A SER* 3.1 18.2 + - - -
259A THR* 3.6 40.7 - - + +
262A THR* 3.7 29.4 - - + +
263A MET* 4.0 16.6 - - - -
266A GLN* 4.8 4.0 - - - +
294A VAL* 4.3 2.7 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A SER 3.2 15.0 + - - +
232A LEU 3.2 7.8 + - - +
234A ILE* 1.3 74.5 - - - +
236A ILE* 1.3 64.4 + - - +
238A SER* 2.6 24.6 + - - +
239A TRP* 3.4 36.7 + - + +
263A MET* 5.1 0.9 - - - -
290A CYS* 3.8 39.9 - - + +
293A PHE* 4.5 9.2 - - + -
294A VAL* 3.9 9.6 - - + -
334A PHE* 4.1 24.9 - - + -
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 3.0 43.2 + - + +
233A LEU* 3.8 20.0 - - + +
235A VAL* 1.3 75.4 - - + +
237A LEU* 1.3 63.9 + - - +
239A TRP* 3.0 48.5 + - + +
240A VAL* 3.6 11.0 + - + +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU 2.9 14.7 + - - +
234A ILE* 3.3 25.1 - - + +
236A ILE* 1.3 76.3 - - - +
238A SER* 1.3 63.1 + - - +
239A TRP 3.2 0.5 + - - -
240A VAL* 3.2 28.2 + - + +
255A LEU* 3.2 26.5 - - + +
258A THR* 5.3 5.4 - - - +
259A THR* 3.9 15.7 - - + -
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE 3.1 2.9 + - - -
235A VAL* 2.6 21.3 + - - +
237A LEU* 1.3 79.3 - - - +
239A TRP* 1.3 69.1 + - - +
241A SER* 3.2 21.8 - - - -
242A PHE* 4.7 1.0 - - - -
255A LEU* 5.0 5.4 - - - -
256A GLY* 6.1 0.7 - - - -
259A THR* 3.9 17.2 - - - +
293A PHE 4.6 0.7 + - - -
294A VAL* 3.7 27.8 - - - +
297A ALA* 4.0 23.3 - - - +
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Residues in contact with TRP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A VAL* 3.5 34.5 + - + +
236A ILE* 3.0 36.6 + - + +
238A SER* 1.3 83.2 + - - +
240A VAL* 1.3 64.8 + - - +
241A SER 3.0 2.5 - - - -
242A PHE* 3.0 46.6 + + + -
243A TRP* 3.3 19.6 - + + -
293A PHE* 4.8 3.2 + + - +
330A PHE* 3.7 19.7 - + + +
331A PRO* 3.6 42.8 - - + -
334A PHE* 3.7 31.9 - + + -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ILE* 3.8 12.6 - - + +
237A LEU* 3.2 28.1 + - + +
239A TRP* 1.3 76.6 - - - +
241A SER* 1.3 66.4 + - - +
243A TRP* 3.0 25.3 + - + +
244A ILE* 3.4 18.8 + - + +
255A LEU* 3.6 22.2 - - + -
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A SER 3.2 17.6 + - - -
240A VAL* 1.3 81.2 - - - +
242A PHE* 1.3 61.3 + - - +
244A ILE* 3.0 19.0 + - - +
252A ARG* 3.0 59.1 + - - +
255A LEU* 3.7 22.9 - - - +
256A GLY 5.9 0.2 - - - -
297A ALA* 5.2 4.9 + - - -
301A 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