Contacts of the helix formed by residues 224 - 243 (chain A) in PDB entry 1TYI
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 ASP 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLY 3.3 5.2 + - - +
223A ILE* 1.3 73.9 - - - +
225A ASP* 1.3 63.3 + - - +
226A GLU* 3.4 13.0 + - + +
227A SER* 2.8 26.3 + - - -
228A TYR* 3.0 16.8 + - - +
266A ASN* 4.1 10.3 - - + +
267A LEU* 3.2 10.4 - - - +
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Residues in contact with ASP 225 (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 ASP* 1.3 74.1 - - - +
226A GLU* 1.3 70.1 + - + +
228A TYR* 3.1 3.3 + - - +
229A GLU* 2.9 30.7 + - - +
266A ASN 4.6 2.7 + - - +
267A LEU* 3.3 15.1 - - - +
268A THR* 2.8 56.2 + - - +
271A GLY* 4.4 11.0 - - - -
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Residues in contact with GLU 226 (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 ASP* 3.3 13.4 - - + +
225A ASP* 1.3 80.4 - - + +
227A SER* 1.3 59.6 + - - +
229A GLU* 3.2 22.8 - - - +
230A ALA* 2.9 29.9 + - - +
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Residues in contact with SER 227 (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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220A ARG* 2.7 31.9 + - - -
223A ILE* 2.8 22.6 - - - +
224A ASP* 2.8 18.6 + - - -
226A GLU* 1.3 78.3 - - - +
228A TYR* 1.3 65.0 + - - +
230A ALA* 3.1 7.1 + - - +
231A ILE* 3.0 25.5 + - - +
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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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166A ILE* 2.8 50.4 + - + +
189A PHE* 4.1 26.6 - + + +
219A LEU* 4.2 16.6 - - + -
223A ILE* 4.2 7.4 - - + +
224A ASP 3.0 5.8 + - - +
225A ASP 3.6 2.2 - - - +
227A SER* 1.3 76.9 - - - +
229A GLU* 1.3 67.6 + - + +
231A ILE* 3.1 18.8 + - - +
232A PHE* 3.2 12.7 + + - +
256A SER* 4.9 4.3 - - - -
265A PHE* 5.1 3.4 - + - -
267A LEU* 3.4 46.4 - - + -
271A GLY 5.2 5.4 - - - -
272A HIS* 5.8 2.5 - - - -
275A CYS* 3.3 32.2 - - + -
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Residues in contact with GLU 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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225A ASP* 2.9 19.6 + - - +
226A GLU* 3.2 35.1 - - - +
228A TYR* 1.3 81.8 - - + +
230A ALA* 1.3 62.4 + - - +
232A PHE* 3.1 8.5 + - - +
233A LYS* 3.0 48.7 + - - +
271A GLY* 5.1 8.6 - - - +
274A LYS* 4.1 14.0 + - - +
275A CYS* 6.0 1.3 - - - -
278A PHE* 3.9 26.2 - - + -
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Residues in contact with ALA 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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226A GLU 2.9 20.1 + - - +
227A SER* 3.1 9.8 + - - +
229A GLU* 1.3 78.7 - - - +
231A ILE* 1.3 59.2 + - + +
233A LYS* 4.2 9.2 - - - +
234A PRO* 2.8 36.1 - - + +
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Residues in contact with ILE 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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189A PHE* 3.7 17.3 - - + -
217A TYR* 3.6 34.5 - - + -
219A LEU* 2.9 37.7 - - + -
220A ARG* 3.5 19.7 - - - +
223A ILE* 4.7 1.3 - - + -
227A SER* 3.0 27.2 + - - +
228A TYR* 3.1 6.9 + - - +
230A ALA* 1.3 78.2 - - + +
232A PHE* 1.3 51.8 + - - +
234A PRO* 4.0 2.5 - - - +
235A VAL* 2.6 37.9 + - - +
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Residues in contact with PHE 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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164A ILE* 4.2 3.8 - - + -
166A ILE* 3.8 11.9 - - + -
189A PHE* 3.0 45.7 - + - -
228A TYR* 3.2 13.2 + + + +
229A GLU* 3.1 14.3 + - - +
231A ILE* 1.3 73.3 - - - +
233A LYS* 1.3 65.8 + - + +
235A VAL* 2.7 18.2 - - - +
236A MET* 2.9 44.0 + - + +
275A CYS* 3.0 52.9 - - - -
278A PHE* 3.8 13.7 - + + -
279A VAL* 3.6 25.8 - - + -
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Residues in contact with LYS 233 (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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229A GLU* 3.0 48.7 + - - +
230A ALA* 4.2 6.5 - - - +
232A PHE* 1.3 76.2 - - - +
234A PRO* 1.3 78.3 - - + +
236A MET* 3.3 8.4 + - + +
237A SER* 3.1 21.8 + - - -
240A MET* 4.4 3.0 - - - +
278A PHE* 3.9 45.8 - - + -
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Residues in contact with PRO 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 ALA* 2.8 29.2 - - + +
231A ILE* 4.0 2.7 - - - +
232A PHE 3.3 0.4 - - - -
233A LYS* 1.3 96.4 - - + +
235A VAL* 1.3 62.2 + - - +
237A SER* 2.6 26.8 + - - +
238A LYS* 3.5 12.7 + - - +
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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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187A VAL* 3.3 22.2 - - + -
189A PHE* 2.9 27.8 - - + -
215A VAL* 4.8 0.2 - - + -
217A TYR* 2.8 52.4 - - + +
231A ILE 2.6 26.5 + - - +
232A PHE 2.7 25.6 - - - +
234A PRO* 1.3 68.7 - - - +
236A MET* 1.3 71.8 + - + +
238A LYS* 2.9 16.4 + - - +
239A VAL* 3.2 8.5 + - + -
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Residues in contact with MET 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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164A ILE* 5.1 7.2 - - + -
189A PHE* 5.7 0.4 - - + -
232A PHE* 2.9 61.8 + - + +
233A LYS* 3.6 7.6 - - + +
235A VAL* 1.3 81.7 - - + +
237A SER* 1.3 61.4 + - - +
239A VAL* 2.7 34.2 - - + +
240A MET* 2.9 14.1 - - + +
278A PHE* 4.0 5.6 - - + +
279A VAL* 3.8 23.3 - - + +
282A PHE* 3.3 44.0 - - + -
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Residues in contact with SER 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 LYS 3.1 12.5 + - - -
234A PRO* 2.6 23.5 + - - +
235A VAL 3.1 0.2 - - - -
236A MET* 1.3 76.5 - - - +
238A LYS* 1.3 65.6 + - - +
240A MET* 3.0 31.1 + - - +
241A GLU* 3.2 21.1 + - - +
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Residues in contact with LYS 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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185A MET* 6.0 0.4 - - - -
202A LEU* 5.6 7.3 - - - +
215A VAL* 4.9 11.5 - - + +
217A TYR* 3.2 38.7 - - - +
234A PRO* 3.8 16.1 - - - +
235A VAL* 2.9 5.6 + - - +
237A SER* 1.3 84.5 + - - +
239A VAL* 1.3 62.4 + - - +
241A GLU* 3.6 15.2 + - - +
242A MET* 3.3 22.7 + - - +
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Residues in contact with VAL 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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162A LEU* 4.0 23.1 - - + -
185A MET* 3.5 28.5 - - + -
187A VAL* 3.9 25.1 - - + -
215A VAL* 6.3 0.4 - - + -
235A VAL* 3.2 6.7 + - + +
236A MET* 2.7 30.9 + - + +
238A LYS* 1.3 80.0 - - - +
240A MET* 1.3 55.9 + - - +
242A MET* 3.1 4.2 + - - -
243A PHE* 2.6 43.8 + - + +
245A PRO* 6.1 0.4 - - + -
282A PHE* 4.0 15.5 - - + -
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Residues in contact with MET 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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233A LYS 4.4 3.1 - - - +
236A MET* 2.9 17.9 - - + +
237A SER* 3.0 38.5 + - - +
239A VAL* 1.3 83.4 - - - +
241A GLU* 1.3 67.4 + - + +
242A MET 3.3 0.3 + - - -
243A PHE 3.3 13.5 - - - +
244A GLN* 3.5 7.6 - - - +
282A PHE* 2.9 58.8 - - + -
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Residues in contact with GLU 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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237A SER* 3.2 18.7 + - - +
238A LYS* 3.8 15.4 - - - +
240A MET* 1.3 83.7 - - + +
242A MET* 1.3 60.1 + - - +
244A GLN* 3.6 8.0 - - - +
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Residues in contact with MET 242 (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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185A MET* 3.4 33.9 - - + +
211A LYS 4.8 0.2 - - - +
212A TYR* 3.7 25.4 - - + +
213A TYR* 3.2 46.0 + - + +
238A LYS 3.3 16.4 + - - +
239A VAL 3.5 2.2 - - - +
241A GLU* 1.3 80.0 - - - +
243A PHE* 1.4 56.3 + - - +
244A GLN* 4.0 6.6 + - - +
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Residues in contact with PHE 243 (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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160A ARG* 3.1 43.3 - - + -
161A VAL 3.1 35.7 - - - -
162A LEU* 3.5 15.0 - - + -
182A ASP 3.9 10.1 - - - -
183A ARG 3.6 6.3 - - - -
185A MET* 3.3 34.8 - - + -
213A TYR* 3.8 18.4 - + - -
239A VAL* 2.6 22.3 + - + +
240A MET* 3.3 13.7 + - - +
242A MET* 1.4 73.4 - - - +
244A GLN* 1.4 64.4 + - - +
245A PRO* 3.0 37.3 - - + +
282A PHE* 5.2 1.2 - - - -
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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