Contacts of the helix formed by residues 284 - 315 (chain B) in PDB entry 5J0Z
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 GLN 284 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.2 24.3 + - + +
282B GLU* 3.3 31.2 - - - +
283B SER* 1.3 78.0 - - - +
285B PRO* 1.4 52.1 - - - +
286B ALA* 2.6 20.3 + - + -
287B ARG* 2.6 46.1 + - + +
288B ALA* 3.1 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU 4.6 2.4 - - - +
280B LYS* 3.8 33.3 + - + +
283B SER* 3.3 14.4 - - - +
284B GLN* 1.4 86.3 - - - +
286B ALA* 1.3 61.6 + - - +
288B ALA* 3.9 6.7 - - + +
289B ALA* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLN* 2.6 6.6 + - - +
285B PRO* 1.3 76.2 - - - +
287B ARG* 1.3 51.2 + - - +
289B ALA* 3.4 1.4 - - - +
290B SER* 2.8 40.7 + - - +
293B ARG* 4.8 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.9 12.9 - - + +
284B GLN* 2.6 41.8 + - + +
286B ALA* 1.3 72.8 - - - +
288B ALA* 1.3 66.0 + - - +
290B SER* 3.3 19.4 + - - -
291B ILE* 3.3 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLN* 3.7 26.3 - - + +
279B LEU* 3.5 33.1 - - + +
280B LYS* 4.2 9.2 - - + +
284B GLN 3.1 6.7 + - - +
285B PRO* 3.9 14.4 - - + +
287B ARG* 1.3 81.2 - - - +
289B ALA* 1.3 58.7 + - - +
290B SER 3.2 0.2 + - - -
291B ILE* 3.2 7.0 + - - +
292B THR* 3.1 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 5.3 6.1 - - + -
276B GLN* 5.4 0.9 - - - +
280B LYS* 4.4 13.7 - - - +
285B PRO 3.1 15.6 + - - +
286B ALA* 3.4 3.1 - - - -
288B ALA* 1.3 75.4 - - - +
290B SER* 1.3 60.4 + - - +
292B THR* 3.7 21.8 - - + -
293B ARG* 3.0 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA* 2.8 25.5 + - - +
287B ARG* 3.4 16.3 - - - -
288B ALA 3.1 0.4 - - - -
289B ALA* 1.3 75.9 - - - +
291B ILE* 1.3 57.7 + - - +
293B ARG* 3.1 18.0 + - - +
294B ALA* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLU* 4.0 25.6 - - + +
275B VAL* 3.9 30.1 - - + -
276B GLN* 5.7 1.6 - - + +
279B LEU* 3.9 13.7 - - + -
287B ARG* 3.4 27.8 - - + +
288B ALA 3.2 6.3 + - - +
290B SER* 1.3 77.9 - - - +
292B THR* 1.3 64.7 + - - +
294B ALA* 2.8 20.3 + - - +
295B SER* 2.8 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.5 26.5 + - - +
218B SER 5.1 0.2 - - - +
219B THR* 5.2 2.7 - - + -
272B GLU* 2.6 26.7 + - - -
276B GLN* 2.8 29.8 + - - +
288B ALA 3.1 9.7 + - - -
289B ALA* 3.7 22.0 - - + +
290B SER 3.3 0.2 - - - -
291B ILE* 1.3 79.6 - - - +
293B ARG* 1.3 64.0 + - + +
295B SER* 3.5 5.5 - - - -
296B ARG* 3.4 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA* 4.8 4.4 + - - +
289B ALA* 3.0 34.1 + - + +
290B SER* 3.1 15.0 + - - +
292B THR* 1.3 78.4 - - + +
294B ALA* 1.3 67.5 + - - +
296B ARG* 3.2 54.0 - - - +
297B ILE* 4.1 6.4 + - - +
278C TYR* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B SER 2.8 16.1 + - - +
291B ILE* 2.8 13.9 + - + +
293B ARG* 1.3 70.2 - - - +
295B SER* 1.3 55.2 + - - +
297B ILE* 2.7 31.2 + - - +
298B ALA* 3.0 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.7 28.9 - - - -
272B GLU* 3.5 18.4 - - - +
291B ILE* 2.8 19.1 + - - +
292B THR 3.5 9.0 - - - -
294B ALA* 1.3 71.7 - - - +
296B ARG* 1.3 53.9 + - - +
297B ILE 2.6 13.0 + - - -
298B ALA* 3.0 20.7 + - - +
299B PHE* 3.1 28.3 + - - +
300B PRO* 3.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.1 32.7 + - + -
217B TRP* 3.4 71.2 - - + +
219B THR* 6.0 2.6 - - - +
292B THR* 3.4 20.3 + - - +
293B ARG* 3.2 45.6 - - - +
294B ALA 3.0 0.2 + - - -
295B SER* 1.3 76.7 - - - +
297B ILE* 1.3 67.1 + - + +
300B PRO* 3.5 16.4 - - - +
278C TYR* 3.8 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG 4.4 6.3 - - - +
294B ALA 2.7 10.5 + - - +
295B SER 2.6 2.4 + - - -
296B ARG* 1.3 87.6 - - + +
298B ALA* 1.3 65.5 + - - +
299B PHE 3.1 2.5 + - - -
300B PRO* 3.3 4.8 - - - +
301B VAL* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 3.0 10.4 + - + +
295B SER* 3.8 18.4 - - - +
297B ILE* 1.3 77.9 - - - +
299B PHE* 1.3 61.0 + - + +
301B VAL* 3.7 4.4 - - - +
302B VAL* 2.8 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 3.5 28.0 - + + -
216B PHE* 3.4 37.2 - + + -
265B PHE* 4.0 16.8 - + - -
268B VAL* 3.4 30.5 - - + -
269B ALA* 3.8 26.0 - - + -
272B GLU* 4.5 5.4 - - + -
295B SER* 3.1 32.0 + - - +
298B ALA* 1.3 83.8 - - + +
300B PRO* 1.4 72.5 - - + +
301B VAL 3.1 0.3 + - - -
302B VAL* 3.8 2.2 - - - -
303B PHE* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 3.9 31.6 - - + -
216B PHE* 5.6 0.9 - - + -
217B TRP* 6.3 0.4 - - + -
295B SER 3.8 1.3 - - - +
296B ARG* 3.5 22.4 - - - +
297B ILE* 3.3 8.5 - - - +
299B PHE* 1.4 95.0 - - + +
301B VAL* 1.3 55.5 + - + +
303B PHE* 3.7 0.9 - - - +
304B LEU* 3.1 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 3.0 38.7 + - + +
298B ALA* 3.7 4.9 - - - +
300B PRO* 1.3 72.1 - - + +
302B VAL* 1.3 74.7 + - + +
303B PHE 3.0 1.3 - - - -
304B LEU* 2.8 18.3 + - - +
305B LEU* 2.9 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B PHE* 3.9 18.8 - - + -
298B ALA* 2.8 32.4 + - + +
299B PHE* 4.0 2.7 - - - +
301B VAL* 1.3 79.5 - - + +
303B PHE* 1.3 56.4 + - - +
305B LEU* 3.7 12.6 - - + +
306B ALA* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 3.6 28.5 - - + -
209B LEU* 3.6 23.6 - - + -
210B PHE* 4.8 4.9 - + - -
213B TRP* 4.0 17.0 - + + -
258B ILE* 5.8 1.3 - - + -
261B MET* 3.3 28.5 - - + -
262B ILE* 4.2 15.5 - - + -
265B PHE* 3.3 27.9 - + + -
299B PHE 2.9 17.1 + - - +
300B PRO 3.7 4.3 - - - +
301B VAL 2.9 0.8 + - - -
302B VAL* 1.3 74.1 - - - +
304B LEU* 1.3 70.1 + - + +
306B ALA* 3.2 0.8 + - - -
307B ASN* 2.8 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO* 3.1 21.3 + - + +
301B VAL* 2.8 9.4 + - - +
303B PHE* 1.3 80.8 - - + +
305B LEU* 1.3 67.1 + - + +
307B ASN* 4.6 3.7 - - - +
308B ILE* 3.3 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 2.9 33.4 + - + +
302B VAL* 3.7 14.4 - - + +
304B LEU* 1.3 77.2 - - + +
306B ALA* 1.3 52.7 + - + +
308B ILE* 2.8 12.8 + - - +
309B ILE* 2.7 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B MET* 4.0 19.6 - - + +
265B PHE* 5.0 2.7 - - + -
302B VAL* 2.9 23.8 + - + +
303B PHE* 4.1 2.0 - - - +
305B LEU* 1.3 77.9 - - + +
307B ASN* 1.3 58.1 + - - +
309B ILE* 3.6 20.3 - - + +
310B LEU* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 6.1 0.8 - - - +
254B TYR* 5.2 4.8 + - - -
258B ILE* 4.0 31.3 - - - +
261B MET* 3.3 28.2 - - - +
303B PHE* 2.8 40.0 + - + +
304B LEU* 4.6 4.0 - - + +
306B ALA* 1.3 71.9 - - - +
308B ILE* 1.3 55.5 + - + +
310B LEU* 3.7 5.0 - - - +
311B ALA* 2.7 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.3 24.8 + - + +
305B LEU* 2.8 12.3 + - - +
307B ASN* 1.3 76.8 - - + +
309B ILE* 1.3 64.8 + - + +
310B LEU 3.3 0.2 - - - -
311B ALA* 4.0 8.5 - - + -
312B PHE* 3.2 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 2.7 26.2 + - + +
306B ALA* 3.6 30.1 - - + +
308B ILE* 1.3 72.2 - - + +
310B LEU* 1.3 61.8 + - + +
312B PHE* 3.5 3.1 + - - +
313B LEU* 3.0 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 4.6 6.3 - - + +
257B ALA* 3.8 26.9 - - + +
258B ILE* 4.0 23.8 - - + +
261B MET* 4.4 15.9 - - + -
306B ALA 3.1 18.1 + - - +
307B ASN* 3.7 4.9 - - - +
309B ILE* 1.3 77.1 - - + +
311B ALA* 1.3 69.6 + - - +
313B LEU* 2.9 25.1 + - + +
314B PHE* 2.9 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 4.3 19.4 - - - +
307B ASN 2.7 23.0 + - - +
308B ILE* 3.8 12.3 - - + +
310B LEU* 1.3 74.7 - - - +
312B PHE* 1.3 72.0 + - + +
314B PHE 3.2 0.5 + - - -
315B PHE* 3.2 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 3.2 33.7 + - + +
309B ILE* 4.2 2.7 - - - +
311B ALA* 1.3 82.9 - - + +
313B LEU* 1.3 53.5 + - - +
314B PHE 2.8 13.3 + - - -
315B PHE 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ILE* 3.0 35.9 + - + +
310B LEU* 2.9 28.0 + - + +
312B PHE* 1.3 74.7 - - - +
314B PHE* 1.3 63.6 + - + -
315B PHE 3.7 0.2 - - - -
404B HXA 4.6 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 3.6 25.4 - - + -
118B ARG* 3.4 25.0 + - + +
252B MET* 3.4 34.5 - - + -
253B THR 3.7 11.9 - - - -
254B TYR* 3.6 31.2 - + + -
257B ALA* 4.1 15.9 - - + -
310B LEU* 2.9 30.5 + - + +
312B PHE 2.8 1.8 + - - -
313B LEU* 1.3 77.8 - - + +
315B PHE* 1.3 83.4 + - + +
404B HXA 4.9 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.9 46.4 - - + +
121B PHE* 4.2 36.6 - + + -
254B TYR* 4.1 24.5 - + - -
311B ALA* 3.2 20.1 + - + +
312B PHE* 2.9 19.3 + - - +
313B LEU 3.7 0.2 - - - -
314B PHE* 1.3 110.0 - - + +
404B HXA 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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