Contacts of the helix formed by residues 247 - 267 (chain F) in PDB entry 6CAJ
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 GLU 247 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242F THR* 5.4 1.6 - - - -
243F PRO* 6.3 0.4 - - - -
245F ASN 5.0 3.0 - - - +
246F GLU* 1.3 87.0 + - - +
248F LEU* 1.3 64.3 + - - +
249F SER* 4.1 10.8 - - - +
250F ARG* 4.3 26.1 + - + +
251F ASP* 3.2 26.9 + - - +
289F SER* 5.2 15.5 - - - -
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Residues in contact with LEU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F TYR* 3.6 41.3 - - + -
242F THR* 4.3 15.3 - - + +
246F GLU 4.1 0.8 + - - -
247F GLU* 1.3 72.8 - - - +
249F SER* 1.3 62.5 + - - +
250F ARG 3.1 0.7 - - - -
252F LEU* 3.0 57.4 + - + +
284F ILE 5.2 1.6 - - - +
287F VAL* 4.8 17.3 - - + -
292F ARG 5.3 0.4 - - - +
293F GLU* 4.7 12.3 - - + +
296F ALA* 4.4 17.5 - - + -
297F LYS* 5.1 6.1 - - + +
300F LEU* 4.1 16.8 - - + -
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Residues in contact with SER 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F GLU* 3.3 7.2 - - - +
248F LEU* 1.3 78.5 - - - +
250F ARG* 1.3 57.3 + - - +
253F VAL* 3.3 22.2 - - - +
284F ILE* 3.2 26.0 + - - +
285F THR* 4.0 14.8 + - - +
287F VAL* 3.0 34.3 + - - +
288F GLY 5.1 0.2 + - - -
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Residues in contact with ARG 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F GLU* 5.3 10.0 + - - +
247F GLU* 3.7 27.7 + - + +
248F LEU 3.1 0.2 - - - -
249F SER* 1.3 79.2 - - - +
251F ASP* 1.3 60.0 + - - +
252F LEU 3.3 1.3 - - - -
253F VAL* 3.3 5.7 + - + +
254F ASN* 2.9 46.7 + - - +
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Residues in contact with ASP 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F TYR* 3.4 15.7 + - - +
243F PRO* 3.3 31.9 - - + +
246F GLU* 5.1 10.2 + - + +
247F GLU 3.2 18.2 + - - +
250F ARG* 1.3 76.7 - - - +
252F LEU* 1.3 60.3 + - - +
254F ASN* 3.3 8.6 + - - +
255F LYS* 2.9 33.6 + - - +
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Residues in contact with LEU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236F VAL* 5.1 3.6 - - + -
237F ILE* 4.4 18.8 - - + -
240F TYR* 3.7 36.2 + - + +
248F LEU* 3.0 35.3 + - + +
251F ASP* 1.3 75.0 - - - +
253F VAL* 1.3 60.3 + - - +
255F LYS* 4.4 7.4 - - - +
256F LEU* 2.9 55.9 + - + +
284F ILE* 3.8 37.7 - - + -
300F LEU* 4.1 8.5 - - + -
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Residues in contact with VAL 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LEU 4.5 0.2 + - - -
249F SER 3.3 22.7 - - - +
250F ARG* 3.3 10.2 + - + +
252F LEU* 1.3 78.6 - - - +
254F ASN* 1.3 64.1 + - - +
255F LYS 3.4 0.5 + - - -
256F LEU* 4.4 2.6 - - - +
257F LYS* 3.3 43.3 + - - +
281F ASN* 3.4 31.2 - - - +
284F ILE* 3.7 19.3 - - + -
285F THR* 4.3 5.6 - - - +
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Residues in contact with ASN 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ARG* 2.9 41.3 + - - +
251F ASP* 3.9 9.5 - - - +
253F VAL* 1.3 80.5 - - - +
255F LYS* 1.3 59.4 + - - +
257F LYS* 4.2 12.2 + - - +
258F PRO* 3.5 16.3 - - - +
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Residues in contact with LYS 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F HIS* 6.2 1.4 - - - -
236F VAL* 5.0 5.9 + - - +
239F ASP 4.8 4.2 + - - -
240F TYR* 3.3 42.8 - - + +
241F THR* 5.1 3.2 + - - +
251F ASP* 2.9 23.4 + - - +
252F LEU* 4.1 8.3 - - - +
253F VAL 3.2 0.2 - - - -
254F ASN* 1.3 77.0 - - - +
256F LEU* 1.3 63.9 + - - +
257F LYS 3.2 2.0 - - - -
258F PRO* 3.3 13.3 - - - +
259F TYR* 3.8 44.8 + - + +
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Residues in contact with LEU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F LEU* 4.0 17.5 - - + -
236F VAL* 3.9 19.7 - - + -
237F ILE* 5.6 2.0 - - + -
252F LEU* 2.9 42.6 + - + +
253F VAL* 4.5 2.9 - - - +
254F ASN 3.6 0.4 - - - -
255F LYS* 1.3 74.1 - - + +
257F LYS* 1.3 59.9 + - + +
258F PRO 3.6 0.2 - - - -
259F TYR* 3.4 26.0 + - + +
260F MET* 3.1 37.2 + - + +
280F LEU* 4.1 22.0 - - + -
284F ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F VAL* 3.3 34.5 + - - +
254F ASN* 4.4 11.9 - - - +
255F LYS 3.2 1.8 - - - -
256F LEU* 1.3 75.0 - - + +
258F PRO* 1.4 66.5 - - + +
260F MET* 3.4 5.8 + - - +
261F SER* 2.9 27.6 + - - -
281F ASN* 4.2 17.6 - - - +
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Residues in contact with PRO 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F VAL* 5.8 1.0 - - + +
202F VAL* 5.9 4.7 - - + +
203F ILE* 4.0 9.3 - - + +
254F ASN 3.5 15.5 - - - +
255F LYS* 3.3 14.4 - - - +
257F LYS* 1.4 88.5 - - + +
259F TYR* 1.3 63.5 + - + +
261F SER* 3.6 8.0 - - - -
262F PHE* 2.9 29.3 + - - +
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Residues in contact with TYR 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F SER 5.1 2.3 + - - -
202F VAL 3.3 25.1 + - - -
203F ILE* 4.1 13.4 - - + -
204F HIS* 3.3 35.6 + - + +
207F MET* 4.1 18.9 - - + +
236F VAL* 3.9 21.8 - - + -
255F LYS* 3.8 43.5 + - + +
256F LEU* 3.4 26.9 + - + +
257F LYS 3.2 0.8 - - - -
258F PRO* 1.3 79.5 - - + +
260F MET* 1.3 70.9 + - + +
262F PHE* 3.3 7.5 + - - +
263F LEU* 3.0 31.1 + - - +
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Residues in contact with MET 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F MET* 3.8 17.7 - - + -
229F LEU* 4.2 8.3 - - + -
233F LEU* 4.1 14.8 - - + -
256F LEU* 3.1 21.1 + - + +
257F LYS* 4.0 5.4 - - - +
258F PRO 3.4 0.2 - - - -
259F TYR* 1.3 90.5 - - + +
261F SER* 1.3 55.4 + - - +
263F LEU* 3.7 27.3 - - + +
264F THR* 2.6 40.2 + - - +
269F LEU* 4.5 2.3 - - + +
273F MET* 6.2 0.2 - - - -
277F ILE* 3.7 46.7 - - + -
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Residues in contact with SER 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F LYS 2.9 16.6 + - - -
258F PRO* 3.6 9.9 - - - -
260F MET* 1.3 74.8 - - - +
262F PHE* 1.3 58.8 + - - +
264F THR* 3.3 6.8 + - - -
265F GLN* 2.9 45.9 + - - +
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Residues in contact with PHE 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F VAL* 3.7 26.2 - - + -
192F LEU* 3.7 23.6 - - + -
193F THR* 4.0 10.5 - - + -
196F MET* 3.8 19.3 - - + -
203F ILE* 3.8 25.4 - - + -
207F MET* 4.2 8.7 - - + -
208F VAL* 3.7 42.2 - - + -
211F GLY* 4.5 2.0 - - - -
212F LEU* 5.4 0.7 - - + -
258F PRO 2.9 17.4 + - - +
259F TYR* 3.6 5.2 - - - +
261F SER* 1.3 75.8 - - - +
263F LEU* 1.3 61.2 + - + +
265F GLN* 3.3 8.2 + - - +
266F CYS* 3.0 51.8 + - - -
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Residues in contact with LEU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F MET* 3.7 40.2 - - + +
210F LEU* 3.7 28.9 - - + -
211F GLY* 3.7 20.0 - - - +
214F TYR* 4.1 12.7 - - + -
229F LEU* 3.8 10.5 - - + -
259F TYR 3.0 14.0 + - - +
260F MET* 3.8 27.1 - - + +
261F SER 3.3 0.2 - - - -
262F PHE* 1.3 78.4 - - + +
264F THR* 1.3 59.3 + - - +
266F CYS* 3.5 5.0 + - - +
267F ARG* 2.9 25.6 + - - +
269F LEU* 4.1 14.3 - - + +
273F MET* 5.1 0.9 - - + -
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Residues in contact with THR 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F TYR* 5.3 2.8 - - - -
260F MET* 2.6 23.0 + - - +
261F SER* 3.6 7.7 - - - -
262F PHE 3.3 0.2 - - - -
263F LEU* 1.3 77.5 - - - +
265F GLN* 1.3 63.2 + - + +
267F ARG 3.2 21.9 + - - +
268F PRO* 3.8 10.8 - - + +
269F LEU* 3.4 26.3 - - + +
274F HIS* 6.3 0.9 - - + -
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Residues in contact with GLN 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F VAL* 3.4 19.5 + - - +
168F PRO 3.0 23.3 + - - +
169F THR* 3.9 26.1 - - - +
170F ARG* 3.4 25.3 + - + +
186F TYR* 4.0 21.3 - - + +
192F LEU* 3.7 8.7 - - + +
261F SER* 2.9 32.2 + - - +
262F PHE* 3.3 4.6 + - - +
264F THR* 1.3 75.2 - - + +
266F CYS* 1.3 65.1 + - - +
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Residues in contact with CYS 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ARG* 3.1 25.5 + - - +
186F TYR* 4.9 4.1 - - - +
192F LEU* 5.2 6.5 - - - -
211F GLY* 3.7 39.9 - - - +
212F LEU* 6.0 0.9 - - - -
214F TYR* 4.9 2.0 - - + -
215F SER* 4.2 12.7 - - - +
262F PHE* 3.0 47.9 + - - +
263F LEU* 3.6 6.1 - - - +
264F THR 3.2 0.2 - - - -
265F GLN* 1.3 79.8 - - - +
267F ARG* 1.3 62.9 + - + +
268F PRO* 4.9 0.2 - - - +
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Residues in contact with ARG 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F ARG* 4.9 15.9 - - - +
214F TYR* 3.3 41.1 + - + +
215F SER* 4.9 1.6 - - - +
217F GLY* 5.8 1.2 - - - -
219F VAL 4.8 7.6 + - - -
220F SER* 5.1 13.6 + - - +
225F ARG* 3.0 47.7 + - - +
263F LEU 2.9 16.8 + - - +
264F THR* 3.2 7.6 + - - +
266F CYS* 1.3 82.0 - - - +
268F PRO* 1.3 74.6 - - + +
269F LEU* 3.5 5.0 + - - +
366F TRP* 5.5 3.2 - - - +
417F ARG* 4.7 15.0 - - - +
456F GLU* 3.1 37.8 + - - +
458F ASP* 5.3 4.2 + - - -
488F VAL* 5.1 1.6 - - - +
489F TYR* 5.3 2.0 + - - -
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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