Contacts of the helix formed by residues 220 - 241 (chain G) in PDB entry 4BOG
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 TYR 220 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219G PHE* 1.3 92.8 - + + +
221G ILE* 1.3 61.8 + - + +
222G VAL 2.7 11.4 + - - -
223G TYR* 2.8 44.2 + + + +
224G THR* 2.9 24.7 + - - +
273G THR* 6.3 3.6 - - + -
279H PRO* 2.8 41.2 + - + +
282H ALA* 3.8 4.5 - - + +
283H LEU* 3.1 42.5 + - + +
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Residues in contact with ILE 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G PHE* 6.0 6.7 - - + -
217G PRO 3.9 6.5 - - - +
218G LEU* 3.0 51.8 - - + -
219G PHE 3.9 2.9 - - - +
220G TYR* 1.3 73.0 - - + +
222G VAL* 1.3 55.3 + - - +
224G THR* 3.2 16.2 - - + +
225G ILE* 2.9 34.7 + - + +
283G TYR* 4.9 25.1 - - + -
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Residues in contact with VAL 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G LEU* 3.5 28.7 - - + +
219G PHE* 2.9 25.1 - - - +
220G TYR 2.7 0.4 - - - -
221G ILE* 1.3 78.3 - - - +
223G TYR* 1.3 63.1 + - + +
225G ILE* 3.2 27.6 + - + +
226G VAL* 3.3 10.3 + - + +
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Residues in contact with TYR 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G PHE 4.6 3.1 - - - -
220G TYR* 2.8 68.8 + + + +
222G VAL* 1.3 80.5 - - + +
224G THR* 1.3 56.5 + - - +
226G VAL* 2.6 21.8 - - + +
227G PRO* 2.3 34.0 - - + +
266G LEU* 5.9 2.0 - - + -
269G LYS* 5.2 11.8 + - - +
275H SER* 5.3 7.6 - - - -
276H GLN* 4.1 28.8 + - - -
279H PRO* 4.1 14.8 - - + +
296H MET* 6.0 13.5 - - + -
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Residues in contact with THR 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G TYR* 2.9 19.7 + - - +
221G ILE* 3.2 21.0 - - + +
223G TYR* 1.3 78.5 - - - +
225G ILE* 1.3 57.3 + - + +
227G PRO* 2.5 35.4 - - + +
228G CYS* 3.2 16.6 + - - +
266G LEU* 6.1 0.4 - - + -
269G LYS* 3.8 24.7 + - - +
287G ILE* 6.0 7.2 - - + -
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Residues in contact with ILE 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G ILE* 2.9 15.0 + - + +
222G VAL* 3.2 17.0 - - + +
224G THR* 1.3 74.9 - - - +
226G VAL* 1.3 72.8 + - + +
228G CYS* 3.1 9.5 + - - +
229G ILE* 2.8 45.9 + - + +
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Residues in contact with VAL 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G VAL* 3.3 12.7 + - + +
223G TYR* 2.6 37.2 - - + +
225G ILE* 1.3 83.5 - - + +
227G PRO* 1.3 56.9 - - + +
229G ILE* 4.6 1.8 - - - -
230G LEU* 2.3 76.0 + - + +
300H THR* 5.5 7.4 - - + +
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Residues in contact with PRO 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G TYR* 2.3 34.3 - - + +
224G THR* 2.5 28.3 - - + +
226G VAL* 1.3 75.0 - - + +
228G CYS* 1.3 64.0 + - - +
230G LEU* 4.5 2.0 - - + -
231G ILE* 2.4 58.8 + - + +
266G LEU* 4.1 30.3 - - + -
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Residues in contact with CYS 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G THR* 3.2 17.5 + - - +
225G ILE* 3.1 11.4 + - - +
227G PRO* 1.3 81.5 - - - +
229G ILE* 1.3 55.1 + - + +
231G ILE* 4.0 4.0 - - - +
232G SER* 2.5 32.6 + - - -
263G LEU* 6.4 2.9 - - - -
287G ILE* 5.1 19.1 - - - -
290G LEU* 5.2 16.2 - - + -
294G SER* 5.3 2.1 + - - -
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Residues in contact with ILE 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ILE* 2.8 45.8 + - + +
226G VAL* 4.0 2.9 - - - +
227G PRO 2.8 1.2 + - - -
228G CYS* 1.3 73.1 - - + +
230G LEU* 1.3 58.0 + - + +
231G ILE 3.3 1.3 - - - -
232G SER* 2.8 12.3 - - - -
233G ILE* 2.7 33.8 + - + +
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Residues in contact with LEU 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G VAL* 2.3 76.1 + - + +
227G PRO* 4.5 1.8 - - + -
229G ILE* 1.3 68.7 - - + +
231G ILE* 1.3 58.9 + - + +
232G SER 2.9 1.3 - - - -
233G ILE* 2.7 56.2 + - + +
234G LEU* 3.1 11.9 + - + +
300H THR* 5.0 19.1 - - + +
303H VAL* 4.2 27.6 - - + -
304H VAL* 5.6 3.4 - - + -
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Residues in contact with ILE 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G PRO* 2.4 62.9 + - + +
228G CYS* 3.9 4.0 - - - +
230G LEU* 1.3 69.5 - - + +
232G SER* 1.3 48.8 + - - +
234G LEU* 3.2 12.8 + - + +
235G ALA* 2.6 32.4 + - + +
259G LEU* 3.2 38.7 - - + +
262G PHE* 4.7 26.0 - - + -
263G LEU* 4.0 12.6 - - + -
266G LEU* 5.3 4.9 - - + -
294G SER* 5.4 5.2 - - - +
272H LEU* 5.6 4.9 - - + -
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Residues in contact with SER 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G CYS 2.5 19.0 + - - -
229G ILE* 2.8 19.4 - - - -
231G ILE* 1.3 78.9 - - - +
233G ILE* 1.4 58.9 + - - +
235G ALA* 3.3 11.0 - - - +
236G ILE* 2.4 39.2 + - - +
294G SER* 4.8 7.0 + - - -
446G MET* 4.8 16.6 - - - +
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Residues in contact with ILE 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G ILE* 2.7 14.0 + - + +
230G LEU* 2.7 66.6 + - + +
232G SER* 1.4 70.0 - - - +
234G LEU* 1.3 51.8 + - + +
236G ILE* 3.1 11.5 - - + +
237G LEU* 2.6 57.5 + - + +
303H VAL* 5.6 4.7 - - + +
304H VAL* 5.4 14.8 - - + +
307H GLY* 4.4 13.0 - - - -
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Residues in contact with LEU 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G LEU* 3.1 13.5 + - + +
231G ILE* 3.8 10.8 - - + +
233G ILE* 1.3 80.4 - - + +
235G ALA* 1.3 54.4 + - - +
237G LEU* 2.9 13.9 - - + +
238G VAL* 2.5 44.1 + - + +
255G ALA* 6.0 4.3 - - + +
258G ALA* 6.2 0.2 - - + -
259G LEU* 4.9 12.1 - - + +
262G PHE* 4.9 19.7 - - + -
264H LEU* 3.9 19.3 - - + -
265H LEU* 5.3 8.3 - - + -
268H ALA* 4.9 6.1 - - + -
303H VAL* 5.5 8.3 - - + +
306H CYS* 5.7 0.7 - - + -
307H GLY* 4.5 7.0 - - - +
310H LEU* 3.8 25.4 - - + -
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Residues in contact with ALA 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G ILE* 2.6 22.6 + - + +
232G SER* 2.8 15.0 + - - +
234G LEU* 1.3 68.0 - - - +
236G ILE* 1.3 52.4 + - - +
237G LEU 2.7 3.6 - - - -
238G VAL* 2.6 22.8 + - - -
239G PHE* 2.6 50.3 + - + -
259G LEU* 4.3 12.1 - - + +
294G SER* 4.8 9.9 - - - +
446G MET* 5.9 0.4 - - - -
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Residues in contact with ILE 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G SER* 2.4 41.6 + - - +
233G ILE* 3.1 16.6 - - + +
235G ALA* 1.3 68.9 - - - +
237G LEU* 1.3 52.2 + - + +
239G PHE* 3.1 16.1 - - + +
240G TYR* 2.5 62.3 + - + +
439G PHE* 4.8 15.4 - - + -
442G ILE* 5.7 0.7 - - + -
446G MET* 3.7 29.5 - - + -
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Residues in contact with LEU 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G ILE* 2.6 47.7 + - + +
234G LEU* 2.9 17.3 - - + +
235G ALA 2.7 0.4 + - - -
236G ILE* 1.3 78.8 - - + +
238G VAL* 1.3 49.8 + - + -
239G PHE 3.1 4.3 - - - -
240G TYR* 3.8 7.6 - - + -
241G LEU* 2.3 42.7 + - - +
307H GLY* 3.9 8.3 - - - +
310H LEU* 3.2 45.3 - - + -
311H ASN* 3.8 25.6 - - + +
314H PHE* 4.3 3.0 - - + -
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Residues in contact with VAL 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G LEU* 2.5 28.5 + - + +
235G ALA* 2.6 8.5 + - - +
237G LEU* 1.3 73.2 - - + +
239G PHE* 1.3 68.4 + - + +
240G TYR 3.3 0.2 - - - -
241G LEU* 4.0 4.7 - - + -
242G PRO* 2.8 22.3 - - - +
248G LYS* 2.7 30.4 + - - +
252G SER* 4.6 6.5 - - - +
255G ALA* 3.2 33.7 - - + -
256G LEU* 4.8 14.1 - - + -
259G LEU* 5.4 2.2 - - + -
301G VAL* 5.2 1.8 - - + -
305G HIS* 4.1 15.4 + - + +
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Residues in contact with PHE 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G ALA* 2.6 52.0 + - + -
236G ILE* 3.1 12.8 - - - +
238G VAL* 1.3 96.2 - - + +
240G TYR* 1.3 58.0 + - - +
242G PRO* 2.9 22.9 - - - +
243G PRO* 3.8 1.6 - - - +
256G LEU* 5.1 0.4 - - + -
259G LEU* 5.1 1.3 - - + -
294G SER* 5.5 4.5 - - - -
297G LEU* 4.9 9.9 - - + -
298G SER* 4.4 18.6 - - - -
301G VAL* 4.3 27.6 - - + -
305G HIS* 5.9 0.4 - - - -
439G PHE* 3.6 22.6 - - + +
442G ILE* 3.9 35.4 - - + -
446G MET* 4.4 11.7 - - + -
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Residues in contact with TYR 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G ILE* 2.5 41.5 + - + +
237G LEU* 3.5 9.4 - - + +
239G PHE* 1.3 74.5 - - - +
241G LEU* 1.3 54.6 + - - +
242G PRO* 3.2 3.2 - - - -
243G PRO* 3.4 9.0 - - + +
244G ASP* 2.8 49.7 + - + +
439G PHE* 4.6 27.1 - + + -
311H ASN* 4.3 18.7 + - - +
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Residues in contact with LEU 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G LEU 2.3 31.5 + - - +
238G VAL* 4.8 4.5 - - + -
240G TYR* 1.3 67.9 - - - +
242G PRO* 1.4 56.3 - - - +
244G ASP* 3.4 5.8 - - - -
245G ALA* 2.4 46.7 + - + -
248G LYS* 3.2 35.0 - - + +
251G LEU* 3.2 40.8 - - + -
310H LEU* 5.0 6.1 - - + -
314H PHE* 2.9 56.5 - - + -
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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
------------------------------------------------------------
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