Contacts of the helix formed by residues 226 - 247 (chain A) in PDB entry 3W0A
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 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PRO* 3.7 13.9 - - + -
157A VAL 3.4 32.8 - - - +
158A ARG* 3.7 35.9 - - + +
224A LEU 3.3 0.6 - - - -
225A SER* 1.3 76.7 + - - +
227A LEU* 1.3 59.6 + - - +
228A PRO* 3.5 1.1 - - - -
229A HIS* 3.5 9.0 + - + +
230A LEU* 2.9 45.9 + - + +
295A TYR* 4.2 7.2 - - + -
299A ASP* 3.5 38.6 - - + +
302A LYS* 3.3 24.2 + - + +
303A ALA* 4.1 3.1 - - + +
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Residues in contact with LEU 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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224A LEU* 3.1 27.4 + - + +
226A MET* 1.3 77.4 - - - +
228A PRO* 1.4 62.5 - - + +
231A ALA* 2.8 34.1 + - - +
303A ALA* 3.7 15.9 - - + +
404A LEU* 3.9 13.0 - - + -
410A CYS* 3.7 29.8 - - - -
413A LYS* 3.8 19.5 - - + -
414A LEU* 3.7 8.3 - - + -
501A DS5 3.1 48.7 - - - -
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Residues in contact with PRO 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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154A ARG* 3.5 36.7 + - + +
155A PRO 5.3 3.6 - - - +
224A LEU 3.5 13.0 - - - +
225A SER 3.9 7.9 - - - +
226A MET 3.7 2.5 - - - -
227A LEU* 1.4 88.8 - - + +
229A HIS* 1.4 55.2 + - - +
232A ASP* 3.0 34.1 + - - -
413A LYS* 3.4 33.6 - - + +
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Residues in contact with HIS 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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150A PHE* 4.1 1.6 - + - -
153A PHE* 3.7 27.5 - + + +
154A ARG 2.8 28.8 + - - +
155A PRO* 3.8 3.4 + - - +
156A PRO* 3.7 32.5 - - + +
226A MET* 3.5 8.4 + - + +
227A LEU 3.3 0.8 - - - -
228A PRO* 1.4 75.4 - - - +
230A LEU* 1.4 65.5 + - + +
232A ASP* 3.2 5.7 + - - +
233A LEU* 2.9 28.7 + - + +
293A TYR* 3.8 26.6 - + - -
295A TYR* 2.6 45.9 + + - -
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Residues in contact with LEU 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 MET* 2.9 26.5 + - + +
227A LEU 4.2 0.9 - - - +
229A HIS* 1.4 72.7 - - + +
231A ALA* 1.4 60.9 + - - +
233A LEU* 3.3 19.3 + - + +
234A VAL* 3.0 32.1 + - - +
295A TYR* 4.0 20.6 - - + -
299A ASP* 3.5 31.4 - - + +
300A VAL* 4.1 7.4 - - + -
303A ALA* 3.8 18.6 - - + -
501A DS5 3.9 46.7 - - + -
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Residues in contact with ALA 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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154A ARG* 4.4 0.7 - - - +
227A LEU 2.8 22.5 + - - +
228A PRO 3.9 1.3 - - - +
230A LEU* 1.4 72.6 - - - +
232A ASP* 1.4 57.5 + - - +
234A VAL* 4.0 0.2 - - - -
235A SER* 2.9 30.3 + - - -
413A LYS 3.5 17.5 - - - +
414A LEU* 3.9 22.4 - - + -
415A THR* 4.3 2.7 - - + +
418A VAL* 3.8 6.4 - - + +
501A DS5 3.6 23.1 - - - -
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Residues in contact with ASP 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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153A PHE* 3.6 25.1 - - + -
154A ARG* 2.7 62.2 + - - +
228A PRO 3.0 16.2 + - - +
229A HIS 3.2 5.1 + - - +
231A ALA* 1.4 75.0 - - - +
233A LEU* 1.3 57.7 + - - +
235A SER* 3.5 5.7 + - - -
236A TYR* 3.0 30.7 + - - +
415A THR* 3.4 10.1 - - - +
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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
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150A PHE* 3.5 33.0 - - + -
153A PHE* 3.8 18.1 - - + -
229A HIS* 2.9 17.4 + - + +
230A LEU* 3.5 22.9 - - + +
231A ALA 3.2 0.2 - - - -
232A ASP* 1.3 78.6 - - - +
234A VAL* 1.3 57.6 + - - +
236A TYR* 3.4 3.0 + - + +
237A SER* 2.8 31.8 + - - +
295A TYR* 3.9 21.5 - - + -
501A DS5 3.6 53.8 - - + +
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Residues in contact with VAL 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 LEU 3.0 10.7 + - - +
231A ALA 4.0 0.7 - - - +
233A LEU* 1.3 75.1 - - - +
235A SER* 1.3 54.5 + - - +
237A SER* 3.2 7.6 + - - -
238A ILE* 2.8 52.0 + - + +
268A ILE* 4.9 1.3 - - + -
271A ILE* 3.8 16.4 - - + -
418A VAL* 4.1 2.2 - - + -
422A PHE* 4.1 4.3 - - + -
501A DS5 3.4 83.7 - - + -
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Residues in contact with SER 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 ALA 2.9 19.6 + - - -
232A ASP* 3.7 3.8 - - - -
234A VAL* 1.3 77.1 - - - +
236A TYR* 1.3 60.9 - - - +
238A ILE* 3.2 3.6 + - - -
239A GLN* 3.0 25.3 + - - +
415A THR* 2.8 36.0 + - - +
417A LEU* 3.5 28.1 - - - +
418A VAL* 3.9 7.4 - - - -
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Residues in contact with TYR 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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144A ASP* 4.5 16.4 + - + +
149A ASP* 2.7 45.5 + - + +
150A PHE* 4.6 6.7 - + - -
153A PHE* 3.5 29.8 - + + -
232A ASP 3.0 19.3 + - - +
233A LEU* 3.5 3.6 - - + +
235A SER* 1.3 73.7 - - - +
237A SER* 1.3 70.4 + - - +
239A GLN* 3.2 20.6 + - + +
240A LYS* 3.2 55.7 + - + +
501A DS5 4.0 23.1 - - + -
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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 LEU* 2.8 18.8 + - - +
234A VAL 3.6 3.8 - - - -
236A TYR* 1.3 74.7 - - - +
238A ILE* 1.4 60.2 + - - +
240A LYS* 3.1 4.7 + - - +
241A VAL* 2.9 32.9 + - - +
271A ILE* 3.8 12.3 - - - -
274A ARG* 4.4 1.5 + - - -
501A DS5 3.1 58.5 + - - +
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Residues in contact with ILE 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 VAL* 2.8 40.0 + - + +
235A SER* 3.2 7.4 + - - +
237A SER* 1.4 72.7 - - - +
239A GLN* 1.3 57.4 + - - +
241A VAL* 3.2 9.8 + - + +
242A ILE* 2.8 43.4 + - + +
263A LEU* 6.0 0.7 - - + +
267A ALA* 4.3 11.4 - - + -
271A ILE* 3.5 15.7 - - + -
417A LEU* 3.8 22.2 - - + -
418A VAL* 4.6 7.9 - - + -
421A VAL* 4.2 23.8 - - + -
422A PHE* 3.9 18.8 - - + -
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Residues in contact with GLN 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 SER* 3.0 24.4 + - - +
236A TYR* 3.2 20.5 + - + +
238A ILE* 1.3 74.4 - - - +
240A LYS* 1.4 61.7 + - + +
242A ILE* 3.2 13.4 + - + +
243A GLY* 3.0 23.6 + - - -
417A LEU* 3.7 15.0 - - + +
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Residues in contact with LYS 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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141A LYS 5.6 2.4 + - - -
142A THR* 3.2 41.3 - - + +
144A ASP 6.3 0.7 - - - +
149A ASP* 4.7 3.8 + - - -
236A TYR* 3.2 53.1 + - + +
237A SER 3.1 7.9 + - - +
239A GLN* 1.4 77.6 - - + +
241A VAL* 1.4 51.4 + - - +
243A GLY* 3.1 3.8 + - - +
244A PHE* 2.8 33.6 + - - +
274A ARG* 3.5 11.4 - - - +
501A DS5 3.6 12.1 - - - +
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Residues in contact with VAL 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 2.9 21.6 + - - +
238A ILE* 3.6 12.1 - - + +
240A LYS* 1.4 73.1 - - - +
242A ILE* 1.4 59.1 + - + +
244A PHE* 3.3 6.5 + - - +
245A ALA* 2.9 28.1 + - - +
263A LEU* 4.0 13.7 - - + -
266A SER* 5.3 1.3 - - - +
267A ALA* 5.1 8.5 - - - +
270A VAL* 3.7 32.3 - - + -
271A ILE* 4.8 6.5 - - + -
274A ARG* 3.7 28.0 - - - +
338A ILE* 4.0 13.5 - - + -
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Residues in contact with ILE 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 ILE* 2.8 42.0 + - + +
239A GLN* 3.5 12.6 - - + +
241A VAL* 1.4 71.0 - - - +
243A GLY* 1.3 63.4 + - - +
245A ALA* 3.3 2.3 + - - +
246A LYS* 3.2 41.0 + - + +
260A ILE* 6.5 0.2 - - + -
263A LEU* 4.0 36.2 - - + +
417A LEU* 4.4 14.8 - - + -
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Residues in contact with GLY 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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142A THR* 3.9 12.8 - - - -
239A GLN 3.0 13.2 + - - -
240A LYS* 3.1 4.6 + - - -
242A ILE* 1.3 78.4 - - - +
244A PHE* 1.3 60.2 + - - +
246A LYS* 3.5 20.3 + - - +
247A MET* 3.3 15.8 + - - +
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Residues in contact with PHE 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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135A LEU* 3.8 33.4 - - + -
138A ALA* 3.8 18.1 - - + +
139A HIS* 3.9 17.5 - + + -
142A THR* 3.8 16.0 - - - +
240A LYS 2.8 18.3 + - - +
241A VAL* 3.6 7.6 - - - +
243A GLY* 1.3 70.7 - - - +
245A ALA* 1.3 65.5 + - - +
247A MET* 3.0 19.7 + - - +
248A ILE* 3.4 17.9 + - + +
270A VAL* 5.6 0.7 - - + -
274A ARG* 4.8 7.9 - - - +
331A VAL* 3.6 22.2 - - + -
334A MET* 3.9 32.3 - - + -
335A ALA 4.0 9.6 - - - -
338A ILE* 3.8 18.2 - - + -
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Residues in contact with ALA 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 VAL 2.9 17.4 + - - +
242A ILE 3.7 4.9 - - - +
244A PHE* 1.3 76.2 - - - +
246A LYS* 1.3 56.1 + - - +
248A ILE* 2.9 29.2 + - - +
251A PHE* 3.3 36.9 - - + +
263A LEU* 3.7 21.3 - - + -
338A ILE* 4.2 14.1 - - + -
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Residues in contact with LYS 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 ILE* 3.2 29.4 + - + +
243A GLY* 3.6 13.7 - - - +
245A ALA* 1.3 74.8 - - - +
247A MET* 1.3 59.8 + - + +
248A ILE 3.7 3.3 + - - +
251A PHE* 4.2 12.7 - - + +
252A ARG* 3.0 61.5 + - + +
259A GLN* 5.1 11.1 - - - +
263A LEU* 6.1 0.7 - - + -
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Residues in contact with MET 247 (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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134A ILE* 3.2 28.1 - - + +
135A LEU* 4.7 2.2 - - - +
137A ASP* 5.0 2.0 - - - +
138A ALA* 3.6 39.0 - - + +
141A LYS* 4.3 23.8 - - + -
142A THR* 3.7 20.9 - - + -
243A GLY* 3.3 21.1 - - - +
244A PHE* 3.0 8.7 + - - +
246A LYS* 1.3 78.3 - - + +
248A ILE* 1.3 61.6 + - - +
249A PRO* 3.3 1.0 - - - +
252A ARG* 4.4 15.7 - - - +
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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