Contacts of the helix formed by residues 247 - 267 (chain E) in PDB entry 6O81
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E TYR* 4.9 0.2 + - - -
242E THR* 5.3 3.1 - - - +
243E PRO* 5.8 0.2 - - - +
246E GLU* 1.3 77.6 - - - +
248E LEU* 1.3 65.8 + - - +
249E SER* 4.2 15.0 - - - +
250E ARG* 4.3 2.4 + - - +
251E ASP* 3.3 26.7 + - - +
289E SER* 2.9 31.6 + - - +
74L ARG* 3.6 23.0 - - - -
79L LYS* 5.8 5.7 - - + +
81L TYR* 3.5 42.0 - - + -
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Residues in contact with LEU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR* 3.7 37.5 - - + -
242E THR* 4.5 14.6 - - + +
247E GLU* 1.3 73.5 - - - +
249E SER* 1.3 61.9 + - - +
250E ARG 3.1 2.6 + - - -
252E LEU* 2.9 56.1 + - + +
284E ILE* 5.0 1.8 - - + -
287E VAL* 4.6 20.4 - - + -
293E GLU* 4.9 9.0 - - + +
296E ALA* 4.9 11.4 - - + -
297E LYS* 4.9 13.5 - - + -
300E LEU* 4.2 17.3 - - + -
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Residues in contact with SER 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E GLU* 3.4 12.4 + - - +
248E LEU* 1.3 75.5 + - - +
250E ARG* 1.3 56.2 + - - +
252E LEU* 5.3 0.7 - - - -
253E VAL* 3.3 20.0 - - - +
284E ILE* 3.3 24.2 + - - +
285E THR* 4.0 13.0 - - - -
287E VAL* 2.9 34.0 + - - +
288E GLY 5.1 0.7 + - - -
289E SER* 5.5 1.9 + - - -
29L MET* 4.7 8.5 - - - +
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Residues in contact with ARG 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E GLU* 5.6 2.0 - - - +
247E GLU* 3.9 2.6 + - - +
248E LEU 3.1 0.2 - - - -
249E SER* 1.3 79.2 - - - +
251E ASP* 1.3 60.6 + - - +
252E LEU 3.3 1.8 - - - -
253E VAL* 3.3 6.5 + - + +
254E ASN* 2.9 47.0 + - - +
29L MET* 6.0 4.2 - - + +
32L TYR* 4.4 23.7 - - + -
42L GLU* 5.9 1.4 + - - +
43L GLY* 5.8 2.2 - - - -
44L MET* 3.6 43.2 - - + +
46L LEU* 5.6 2.6 - - - +
80L GLY 4.8 3.6 + - - -
81L TYR* 3.5 61.8 - - + +
82L ILE 4.9 7.5 + - - +
83L ASP* 5.9 1.4 - - - +
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Residues in contact with ASP 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR* 3.5 13.3 + - - +
243E PRO* 3.3 32.6 - - + +
246E GLU* 4.8 14.0 + - + +
247E GLU 3.3 20.1 + - - +
250E ARG* 1.3 75.6 - - - +
252E LEU* 1.3 60.7 + - - +
254E ASN* 3.7 10.1 - - - +
255E LYS* 2.9 38.4 + - - +
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E VAL* 5.3 7.0 - - + -
237E ILE* 4.9 14.4 - - + -
240E TYR* 3.7 36.9 + - + +
248E LEU* 2.9 38.8 + - + +
251E ASP* 1.3 76.5 - - - +
253E VAL* 1.3 57.0 + - - +
255E LYS* 4.6 7.0 - - - -
256E LEU* 2.9 52.4 + - + +
284E ILE* 3.8 38.4 - - + -
300E LEU* 4.4 6.7 - - + -
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Residues in contact with VAL 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E SER 3.3 23.8 - - - +
250E ARG* 3.3 6.7 + - + +
251E ASP 3.3 0.4 - - - -
252E LEU* 1.3 77.7 - - - +
254E ASN* 1.3 63.5 + - - +
255E LYS 3.4 0.5 + - - -
256E LEU* 4.3 1.5 - - - +
257E LYS* 3.3 44.6 + - + +
281E ASN* 4.3 18.1 - - + +
284E ILE* 3.7 26.7 - - + -
285E THR* 4.6 9.4 - - - +
27L ALA* 5.7 3.4 - - + -
28L GLU* 5.5 8.7 - - - +
29L MET* 5.3 9.6 - - + +
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Residues in contact with ASN 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ARG* 2.9 39.2 + - - +
251E ASP* 3.9 11.5 - - - +
252E LEU 3.3 0.4 - - - -
253E VAL* 1.3 80.0 - - - +
255E LYS* 1.3 57.6 + - - +
257E LYS* 4.5 12.1 - - - +
258E PRO* 3.4 19.2 - - - +
32L TYR* 4.8 16.1 - - - -
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Residues in contact with LYS 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E HIS* 5.9 3.4 - - - -
236E VAL* 5.5 4.0 + - - +
239E ASP 5.5 1.4 + - - -
240E TYR* 3.3 40.4 - - + +
241E THR* 5.2 4.2 + - - +
251E ASP* 2.9 26.8 + - - +
252E LEU* 4.1 7.2 - - + +
253E VAL 3.3 0.2 - - - -
254E ASN* 1.3 76.9 - - - +
256E LEU* 1.3 62.6 + - - +
257E LYS 3.3 2.2 - - - -
258E PRO* 3.4 12.9 - - + +
259E TYR* 3.4 48.6 + - + +
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Residues in contact with LEU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E LEU* 3.8 24.5 - - + -
236E VAL* 4.4 12.1 - - + -
237E ILE* 6.3 2.0 - - + -
252E LEU* 2.9 34.1 + - + +
253E VAL* 3.7 3.8 + - - +
255E LYS* 1.3 76.2 - - - +
257E LYS* 1.3 60.5 + - + +
259E TYR* 3.2 25.1 + - + +
260E MET* 2.9 41.3 + - + +
280E LEU* 3.8 26.2 - - + -
281E ASN* 4.8 7.9 - - - +
284E ILE* 4.0 19.5 - - + -
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Residues in contact with LYS 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E VAL* 3.3 39.1 + - + +
254E ASN* 4.5 11.2 - - - +
256E LEU* 1.3 76.0 - - + +
258E PRO* 1.4 65.8 - - + +
260E MET* 3.8 6.7 - - + +
261E SER* 2.9 29.1 + - - -
281E ASN* 4.9 11.9 - - - +
27L ALA* 5.3 11.7 - - - +
28L GLU 5.4 5.7 - - - +
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Residues in contact with PRO 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E VAL* 6.5 0.2 - - + -
202E VAL* 5.4 7.2 - - + +
203E ILE* 4.5 9.9 - - + +
254E ASN 3.4 17.5 - - - +
255E LYS* 3.4 16.2 - - + +
257E LYS* 1.4 90.9 - - + +
259E TYR* 1.3 62.4 + - + +
261E SER* 3.7 6.9 - - - -
262E PHE* 2.9 29.8 + - - +
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Residues in contact with TYR 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E SER 5.0 2.9 + - - -
202E VAL 3.4 25.3 + - - -
203E ILE* 4.0 15.8 - - + -
204E HIS* 3.4 31.3 + - + +
207E MET* 3.7 24.7 - - + +
236E VAL* 4.3 15.0 - - + -
255E LYS* 3.4 53.1 + - + +
256E LEU* 3.2 24.6 + - + +
258E PRO* 1.3 80.2 - - + +
260E MET* 1.3 69.0 + - + +
262E PHE* 3.3 6.1 + - - +
263E LEU* 2.9 31.1 + - - +
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Residues in contact with MET 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E MET* 4.0 10.1 - - + -
229E LEU* 4.5 4.5 - - + -
233E LEU* 3.9 29.4 - - + -
256E LEU* 2.9 32.9 + - + +
257E LYS* 4.0 6.3 - - + +
259E TYR* 1.3 85.4 - - + +
261E SER* 1.3 56.3 + - - +
263E LEU* 3.6 20.9 - - + +
264E THR* 2.6 38.9 + - - +
269E LEU* 4.3 2.3 - - + +
277E ILE* 3.7 46.4 - - + -
280E LEU* 6.1 0.4 - - + -
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Residues in contact with SER 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E LYS 2.9 18.6 + - - -
258E PRO* 3.7 7.6 - - - -
260E MET* 1.3 75.8 - - - +
262E PHE* 1.3 59.8 + - - +
264E THR* 3.4 7.8 + - - -
265E GLN* 2.9 33.1 + - - +
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Residues in contact with PHE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E VAL* 4.3 14.4 - - + -
192E LEU* 3.6 30.7 - - + -
193E THR* 4.8 3.8 - - + -
196E MET* 3.9 18.2 - - + -
203E ILE* 3.7 30.3 - - + -
207E MET* 3.9 10.1 - - + -
208E VAL* 3.6 44.0 - - + -
211E GLY* 4.4 2.7 - - - -
212E LEU* 5.2 0.9 - - + -
258E PRO 2.9 17.4 + - - +
259E TYR 3.6 6.3 - - - +
261E SER* 1.3 73.6 - - - +
263E LEU* 1.3 64.2 + - + +
265E GLN* 3.3 7.2 + - - +
266E CYS* 2.9 48.5 + - - +
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Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E MET* 3.7 28.9 - - + +
210E LEU* 3.8 19.3 - - + -
211E GLY* 4.0 26.0 - - - +
214E TYR* 4.1 11.9 - - + -
229E LEU* 3.8 25.8 - - + -
259E TYR 2.9 15.8 + - - +
260E MET* 3.6 18.8 - - - +
261E SER 3.3 0.2 - - - -
262E PHE* 1.3 78.5 - - + +
264E THR* 1.3 57.5 + - - +
266E CYS* 3.2 4.3 + - - +
267E ARG* 2.8 28.6 + - - +
269E LEU* 3.6 14.0 - - + +
273E MET* 4.1 8.1 - - + -
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Residues in contact with THR 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E PRO* 6.0 0.9 - - - +
186E TYR* 4.6 4.7 + - - -
260E MET 2.6 24.4 + - - -
261E SER* 3.7 7.0 - - - -
262E PHE 3.3 0.2 - - - -
263E LEU* 1.3 76.7 - - - +
265E GLN* 1.3 62.6 + - - +
267E ARG* 3.2 21.0 - - - +
268E PRO* 3.8 11.5 - - + +
269E LEU* 3.4 25.6 - - + +
274E HIS* 5.9 3.1 - - + -
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Residues in contact with GLN 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E VAL* 3.7 12.3 - - - +
168E PRO 2.4 31.4 + - - +
169E THR* 3.4 5.5 - - - +
170E ARG* 3.1 43.0 - - + +
186E TYR* 3.4 23.2 - - - +
192E LEU* 3.4 25.1 - - + +
261E SER* 2.9 21.6 + - - +
262E PHE* 3.6 5.9 - - - +
263E LEU 3.3 0.2 - - - -
264E THR* 1.3 75.5 - - - +
266E CYS* 1.3 62.8 + - - +
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Residues in contact with CYS 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ARG* 3.3 22.4 + - - +
186E TYR* 4.6 3.2 - - - -
192E LEU* 4.7 9.6 - - - -
211E GLY* 3.6 36.1 - - - +
212E LEU* 5.5 3.1 - - - -
214E TYR* 5.2 1.8 - - + -
215E SER* 3.8 15.4 - - - +
262E PHE* 2.9 47.9 + - - +
263E LEU* 3.2 5.8 + - - +
265E GLN* 1.3 78.0 - - - +
267E ARG* 1.3 63.3 + - + +
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Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E TYR* 5.5 0.2 - - - -
188E ARG* 5.2 10.8 - - - +
214E TYR* 3.3 37.1 + - + +
215E SER* 4.9 1.6 - - - +
217E GLY* 5.8 2.0 - - - -
219E VAL 4.3 7.6 + - - -
220E SER* 4.8 8.8 + - - +
225E ARG* 3.1 48.8 - - - +
263E LEU 2.8 19.0 + - - +
264E THR* 3.2 9.5 - - - +
265E GLN 3.5 0.4 - - - -
266E CYS* 1.3 79.5 - - - +
268E PRO* 1.3 79.7 - - + +
269E LEU* 3.3 6.1 + - - +
366E TRP* 5.4 2.0 - - - +
417E ARG* 4.6 18.4 - - - +
456E GLU* 2.8 34.9 + - - +
458E ASP* 4.5 10.7 + - - -
488E VAL* 4.8 1.0 - - - +
489E TYR* 5.1 2.4 + - - -
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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
------------------------------------------------------------
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