Contacts of the helix formed by residues 224 - 246 (chain A) in PDB entry 2YPA
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 SER 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 4.4 3.3 - - - +
223A LEU* 1.3 77.1 - - - +
225A LYS* 1.3 69.8 + - - +
226A ASN* 3.6 13.1 + - - +
227A GLU* 2.8 33.1 + - - -
228A ILE* 3.1 22.7 + - - +
5E C 3.4 28.4 + - - -
6E C 3.3 21.3 + - - -
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Residues in contact with LYS 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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204A ASN* 3.5 33.9 + - - +
207A PHE* 3.7 44.7 - - + +
224A SER* 1.3 73.9 + - - +
226A ASN* 1.3 66.7 + - - +
228A ILE* 3.2 7.8 + - + +
229A LEU* 3.0 26.7 + - - +
558B ARG* 4.8 6.1 - - - +
562B ILE* 5.1 12.8 - - + -
6E C 3.1 38.8 + - - +
7E A 3.6 18.8 + - - -
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.6 10.8 + - - +
225A LYS* 1.3 79.0 - - - +
227A GLU* 1.3 59.3 + - + +
229A LEU* 3.3 11.3 + - - +
230A ARG* 2.4 61.5 + - - +
558B ARG* 4.9 2.0 + - - +
561B ASP* 4.0 16.4 - - - +
562B ILE* 4.0 29.7 - - + +
565B ALA* 4.5 1.9 - - - +
5E C 5.0 9.3 + - - +
6E C 4.8 0.6 + - - -
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Residues in contact with GLU 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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222A LYS 4.9 0.7 - - - +
223A LEU* 3.8 14.5 - - + +
224A SER* 2.8 42.4 + - - +
225A LYS 3.2 0.6 - - - -
226A ASN* 1.3 77.2 - - + +
228A ILE* 1.3 59.6 + - - +
230A ARG* 3.2 5.6 + - - +
231A LEU* 2.7 52.5 + - + +
5E C 5.8 2.9 - - - +
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Residues in contact with ILE 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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207A PHE* 3.9 44.2 - - + +
210A LEU* 3.9 26.9 - - + -
211A ARG* 4.3 17.5 - - + +
214A ILE* 4.7 4.6 - - + +
223A LEU* 3.8 32.9 - - + +
224A SER 3.1 23.2 + - - +
225A LYS* 3.4 7.4 - - + +
227A GLU* 1.3 75.7 - - - +
229A LEU* 1.3 63.1 + - - +
231A LEU* 3.9 4.5 - - - +
232A ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 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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207A PHE* 3.8 18.8 - - + -
210A LEU* 4.9 1.8 - - + -
225A LYS 3.0 18.5 + - - +
226A ASN* 3.4 8.7 - - - +
227A GLU 3.1 0.2 - - - -
228A ILE* 1.3 79.6 - - - +
230A ARG* 1.3 63.2 + - - +
232A ALA* 3.3 10.7 + - - +
233A MET* 3.4 20.4 + - - +
562B ILE* 3.8 10.1 - - + +
565B ALA* 3.6 29.6 - - + -
566B PHE* 3.6 36.1 - - + +
569B LEU* 3.6 27.0 - - + +
589B LEU* 3.9 13.7 - - + -
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Residues in contact with ARG 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 ASN* 2.4 54.7 + - - +
227A GLU* 4.0 5.4 - - - +
229A LEU* 1.3 75.0 - - - +
231A LEU* 1.3 59.3 + - + +
233A MET* 3.2 17.8 + - + +
234A LYS* 3.0 25.0 + - - +
561B ASP* 3.3 27.1 + - - +
564B GLU* 4.4 7.5 - - - +
565B ALA* 3.7 22.7 - - + +
568B GLU* 4.9 5.5 + - - -
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Residues in contact with LEU 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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214A ILE* 3.9 22.1 - - + +
215A PRO 5.7 0.4 - - - +
216A THR* 4.7 6.3 - - + -
223A LEU* 4.0 32.5 - - + -
227A GLU* 2.7 29.4 + - + +
228A ILE* 4.1 2.2 - - - +
230A ARG* 1.3 73.1 - - + +
232A ALA* 1.3 60.1 + - - +
233A MET 3.2 0.2 - - - -
234A LYS* 3.4 36.3 - - + +
235A TYR* 2.8 29.3 + - - +
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Residues in contact with ALA 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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210A LEU* 4.0 24.2 - - + -
214A ILE* 3.8 21.3 - - + +
228A ILE 3.0 19.4 + - - +
229A LEU* 3.5 6.7 - - - +
230A ARG 3.2 0.2 - - - -
231A LEU* 1.3 76.6 - - - +
233A MET* 1.3 59.5 - - - +
235A TYR* 3.9 2.1 - - - +
236A ILE* 3.1 34.7 + - + +
569B LEU* 4.7 8.3 - - + -
592B ALA* 5.3 0.9 - - + -
596B ILE* 4.5 2.5 - - + +
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Residues in contact with MET 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 LEU 3.4 16.6 + - - +
230A ARG* 3.2 18.6 + - + +
231A LEU 3.2 0.4 - - - -
232A ALA* 1.3 72.3 - - - +
234A LYS* 1.3 66.9 + - - +
235A TYR 3.0 1.8 - - - -
236A ILE* 3.0 1.9 + - - -
237A ASN* 2.9 33.2 + - - +
565B ALA* 3.1 40.2 - - + +
568B GLU* 3.8 18.2 - - + -
569B LEU* 3.7 25.6 - - + +
572B MET* 3.5 31.0 - - - +
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Residues in contact with LYS 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 ARG 3.0 10.7 + - - +
231A LEU* 3.4 33.7 - - + +
233A MET* 1.3 80.0 - - - +
235A TYR* 1.3 58.8 + - - +
237A ASN* 4.1 6.7 - - - +
238A PHE* 3.2 21.1 + - - +
58C ASP 5.7 3.8 - - - -
59C LEU 4.7 14.9 + - - -
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Residues in contact with TYR 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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213A LEU 3.5 17.9 - - - -
214A ILE* 4.5 4.9 - - + -
215A PRO* 3.8 23.6 - - + -
231A LEU 2.8 17.2 + - - +
232A ALA* 3.9 6.7 - - - +
233A MET 3.0 0.2 - - - -
234A LYS* 1.3 76.3 - - - +
236A ILE* 1.3 65.2 + - - +
238A PHE* 3.3 3.2 + + - +
239A LEU* 3.0 45.1 + - + +
596B ILE* 3.6 32.3 - - + -
600B GLU* 2.5 32.4 + - - +
59C LEU* 3.6 35.2 - - + -
86C ARG* 3.8 13.0 - - - -
87C LEU* 3.9 3.6 - - - +
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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 ALA 3.1 18.7 + - - +
233A MET 3.0 1.6 + - - -
235A TYR* 1.3 71.8 - - - +
237A ASN* 1.3 61.9 + - - +
239A LEU* 3.4 7.4 + - - +
240A ALA* 2.8 27.9 + - - +
569B LEU* 4.5 15.0 - - + -
572B MET* 3.3 29.8 - - + -
573B CYS* 4.9 4.0 - - - -
576B HIS* 3.9 19.7 - - + +
592B ALA* 4.5 8.5 - - + +
595B VAL* 3.8 29.4 - - + -
596B ILE* 3.7 26.7 - - + -
599B LEU* 4.0 7.1 - - + +
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Residues in contact with ASN 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 MET* 2.9 24.7 + - - +
234A LYS* 4.1 6.2 - - - +
236A ILE* 1.3 75.1 - - - +
238A PHE* 1.3 64.1 + - - +
240A ALA* 3.1 5.7 + - - +
241A LYS* 2.9 42.5 + - - +
572B MET* 3.4 21.7 - - - +
576B HIS* 5.4 2.3 + - - -
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Residues in contact with PHE 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 LYS 3.2 14.9 + - - +
235A TYR* 3.3 11.2 - + - +
237A ASN* 1.3 80.0 - - - +
239A LEU* 1.3 74.4 + - + +
241A LYS* 3.5 6.4 + - - +
242A LEU* 3.1 31.4 + - + +
58C ASP* 4.2 23.1 - - + -
59C LEU* 3.6 40.2 - - + -
77C ARG* 3.9 37.3 + - + -
79C LEU* 4.7 2.9 - - + -
87C LEU* 4.0 21.3 - - + -
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Residues in contact with LEU 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 TYR* 3.0 50.2 + - + +
236A ILE* 3.7 8.3 - - - +
238A PHE* 1.3 81.8 - - + +
240A ALA* 1.3 60.1 + - - +
242A LEU* 3.0 7.6 + - + +
243A LEU* 2.8 31.7 + - - +
596B ILE* 4.2 10.1 - - + +
599B LEU* 3.9 29.2 - - + -
600B GLU* 4.0 23.8 - - + -
603B VAL* 4.6 13.1 - - + +
87C LEU* 3.7 24.2 - - + -
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Residues in contact with ALA 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 2.8 21.6 + - - +
237A ASN* 3.7 6.3 - - - +
239A LEU* 1.3 73.1 - - - +
241A LYS* 1.3 64.7 + - + +
243A LEU* 3.5 8.0 + - - +
244A ASN* 3.4 21.0 + - - +
576B HIS* 3.8 28.3 - - + +
599B LEU* 4.2 9.6 - - + +
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Residues in contact with LYS 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 ASN* 2.9 32.1 + - - +
238A PHE* 3.7 6.3 - - - +
240A ALA* 1.3 76.8 - - + +
242A LEU* 1.3 62.3 + - - +
244A ASN* 3.1 11.4 + - - +
245A ASP* 3.0 27.4 + - - +
77C ARG* 3.7 12.3 - - - +
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Residues in contact with LEU 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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238A PHE* 3.1 32.8 + - + +
239A LEU* 3.0 9.7 + - - +
241A LYS* 1.3 79.2 - - - +
243A LEU* 1.3 58.5 + - - +
245A ASP* 3.2 0.9 + - + -
246A GLN* 2.9 30.1 + - + +
603B VAL* 4.3 26.7 - - + -
74C LYS* 5.1 1.1 - - + +
75C LEU* 4.0 22.9 - - + -
77C ARG* 3.2 42.8 - - + +
87C LEU* 4.3 15.3 - - + -
88C PHE* 4.5 8.5 - - + -
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Residues in contact with LEU 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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239A LEU 2.8 18.5 + - - +
240A ALA* 3.8 7.9 - - - +
241A LYS 3.3 0.2 - - - -
242A LEU* 1.3 73.1 - - - +
244A ASN* 1.3 60.3 + - - +
246A GLN* 3.5 13.8 + - - +
247A GLU* 3.3 17.4 - - - +
599B LEU* 4.0 25.6 - - + +
602B GLN* 3.6 29.4 - - + +
603B VAL* 3.6 40.3 - - + +
606B ARG* 3.3 33.9 + - - +
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Residues in contact with ASN 244 (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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240A ALA 3.4 10.2 + - - +
241A LYS* 3.1 12.4 + - - +
243A LEU* 1.3 80.3 - - - +
245A ASP* 1.3 73.1 + - - +
247A GLU* 3.5 30.8 + - - +
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Residues in contact with ASP 245 (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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241A LYS* 3.0 17.2 + - - +
242A LEU* 3.2 5.1 + - + +
244A ASN* 1.3 83.8 + - - +
246A GLN* 1.3 56.3 + - - +
247A GLU 3.0 12.6 + - - +
248A GLU* 3.4 24.6 - - - +
75C LEU* 3.9 11.4 - - + +
77C ARG* 3.5 31.9 + - - +
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Residues in contact with GLN 246 (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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242A LEU* 2.9 16.4 + - - +
243A LEU* 3.7 10.8 - - - +
244A ASN 3.3 1.0 - - - -
245A ASP* 1.3 74.3 - - - +
247A GLU* 1.3 63.3 + - - +
248A GLU* 4.0 3.9 + - - -
603B VAL* 3.3 36.1 + - - +
606B ARG* 3.5 28.1 - - + +
607B ASN* 3.2 40.6 + - - +
610B PRO 5.5 2.6 - - - +
74C LYS* 4.7 3.6 - - - +
75C LEU* 4.4 21.2 - - + +
88C PHE* 4.0 8.5 - - - -
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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