Contacts of the helix formed by residues 309 - 336 (chain B) in PDB entry 4WLU
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 SER 309 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 4.1 11.0 + - - -
223B LEU* 5.9 1.0 - - - +
308B VAL* 1.3 75.8 - - - +
310B SER* 1.3 58.9 + - - +
311B PHE* 3.4 11.1 + - - +
312B GLU* 2.9 39.9 + - - +
313B GLU* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B SER* 1.3 74.2 - - - +
311B PHE* 1.3 63.3 + - - +
313B GLU* 3.2 8.8 + - - +
314B LYS* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLN* 3.5 29.2 - - - +
223B LEU* 3.9 27.8 - - + -
224B THR* 4.5 18.2 - - + -
227B THR* 3.6 24.0 - - + -
309B SER* 3.4 10.2 + - - +
310B SER* 1.3 80.8 - - - +
312B GLU* 1.3 64.3 + - + +
314B LYS* 3.4 6.1 + - + +
315B MET* 3.3 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.4 1.3 - - + +
207B PRO 4.3 4.7 - - - +
208B LEU* 3.9 23.0 - - + +
209B ILE* 3.1 9.9 + - - +
210B SER* 2.6 48.2 + - - -
223B LEU* 6.1 1.4 - - - +
308B VAL* 3.4 16.6 - - + +
309B SER* 2.9 29.7 + - - +
311B PHE* 1.3 77.5 - - + +
313B GLU* 1.3 65.1 + - - +
315B MET* 3.3 21.9 + - + +
316B ILE* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B VAL* 4.1 15.9 - - + +
309B SER 2.8 17.0 + - - +
310B SER* 3.2 10.1 + - - +
312B GLU* 1.3 77.3 - - - +
314B LYS* 1.3 60.7 + - - +
316B ILE* 3.3 17.7 + - - +
317B SER* 3.1 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER 3.0 12.4 + - - +
311B PHE* 3.7 10.8 - - + +
312B GLU 3.3 0.2 - - - -
313B GLU* 1.3 78.0 - - - +
315B MET* 1.3 59.0 + - + +
317B SER* 3.1 8.9 + - - -
318B ASP* 2.9 49.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS 4.6 3.0 - - - +
206B ILE* 3.7 25.4 - - + +
207B PRO* 4.7 5.8 - - + +
227B THR* 3.7 27.6 - - + +
231B GLN* 4.1 12.8 - - - +
311B PHE* 3.3 55.0 + - + +
312B GLU* 3.3 21.5 + - + +
314B LYS* 1.3 78.1 - - + +
316B ILE* 1.3 62.9 + - - +
318B ASP* 3.4 7.9 + - - +
319B ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 3.9 23.6 - - + -
206B ILE* 3.6 21.5 - - + -
283B THR* 5.1 2.9 - - + -
288B PHE* 4.7 15.8 - - + -
305B ILE* 4.0 23.8 - - + -
308B VAL* 4.4 11.2 - - + -
312B GLU* 3.1 22.8 + - + +
313B GLU* 3.5 20.4 - - - +
314B LYS 3.2 0.2 - - - -
315B MET* 1.3 78.1 - - - +
317B SER* 1.3 62.4 + - - +
319B ALA* 3.4 2.1 + - - +
320B ILE* 3.3 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLU* 3.1 18.3 + - - -
314B LYS* 3.1 14.2 + - - -
316B ILE* 1.3 79.4 - - - +
318B ASP* 1.3 65.7 + - - +
319B ALA 3.3 0.2 + - - -
320B ILE* 3.5 11.5 + - - +
321B PRO* 3.3 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 5.7 9.4 - - + +
314B LYS* 2.9 42.6 + - - +
315B MET* 3.9 7.5 - - - +
317B SER* 1.3 81.5 + - - +
319B ALA* 1.3 60.4 + - - +
320B ILE 3.5 0.2 - - - -
321B PRO* 3.5 13.7 - - - +
322B GLU* 4.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 3.7 24.5 - - - +
204B THR* 3.8 18.2 - - + -
206B ILE* 4.1 9.2 - - + -
288B PHE* 6.3 0.2 - - + -
315B MET 3.0 17.7 + - - +
316B ILE 3.9 3.4 - - - +
317B SER 3.2 0.2 - - - -
318B ASP* 1.3 77.3 - - - +
320B ILE* 1.3 65.7 + - - +
321B PRO 3.3 0.2 - - - -
322B GLU* 3.1 10.3 + - - +
323B LEU* 3.1 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B THR* 5.0 7.4 - - - +
284B GLU* 3.8 31.6 - - + +
285B CYS* 3.8 20.4 - - - -
288B PHE* 5.2 4.5 - - + -
316B ILE* 3.3 33.2 + - + +
317B SER* 3.8 9.2 - - - +
319B ALA* 1.3 77.5 - - - +
321B PRO* 1.3 72.5 - - + +
323B LEU* 3.3 6.1 + - + +
324B LYS* 3.0 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER 3.3 16.4 - - - +
318B ASP* 3.5 13.9 - - - +
319B ALA 3.5 0.2 - - - -
320B ILE* 1.3 95.3 - - + +
322B GLU* 1.3 62.4 + - - +
324B LYS* 3.5 7.5 + - + +
325B ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN* 4.9 0.7 + - - -
201B ALA* 3.9 20.9 - - - +
202B GLY* 5.5 0.6 - - - -
203B LYS* 4.7 15.6 + - - +
204B THR* 3.7 22.1 - - + +
318B ASP 4.8 2.1 + - - +
319B ALA* 3.1 12.0 + - - +
321B PRO* 1.3 75.7 - - - +
323B LEU* 1.3 61.8 + - - +
325B ALA* 3.2 7.9 + - + +
326B SER* 2.9 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN* 3.6 32.0 - - + +
198B GLY* 4.3 6.7 - - - -
199B GLY* 3.9 9.0 - - - -
204B THR* 3.8 13.9 - - + -
277B PHE* 4.1 13.2 - - + -
285B CYS* 3.8 15.5 - - + -
287B TYR 5.1 0.4 - - - +
288B PHE* 4.0 32.3 - - + -
319B ALA* 3.1 30.9 + - + +
320B ILE* 3.3 7.2 + - + +
322B GLU* 1.3 74.8 - - - +
324B LYS* 1.3 52.2 + - - +
326B SER* 3.2 5.4 + - - -
327B ILE* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 2.6 54.8 + - - +
285B CYS* 4.1 12.8 - - - -
320B ILE* 3.0 29.5 + - + +
321B PRO* 3.8 6.5 - - + +
323B LEU* 1.3 75.1 - - - +
325B ALA* 1.3 57.4 + - - +
327B ILE* 3.3 9.1 + - + +
328B LYS* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PRO 3.1 12.8 + - - +
322B GLU* 3.4 11.2 - - + +
324B LYS* 1.3 77.2 - - - +
326B SER* 1.3 58.4 + - - +
328B LYS* 3.5 6.8 + - - +
329B LYS* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 5.6 2.6 + - - -
145B ASN* 3.6 28.5 + - - +
146B SER* 2.7 32.3 + - - -
322B GLU* 2.9 28.0 + - - +
323B LEU* 3.6 4.5 - - - -
325B ALA* 1.3 74.1 - - - +
327B ILE* 1.3 65.5 + - - +
329B LYS* 3.4 4.7 + - - +
330B GLY 3.2 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN 4.1 9.9 - - - +
149B PRO* 3.7 10.7 - - + +
277B PHE* 4.6 3.4 - - + -
285B CYS* 3.9 12.1 - - + -
286B THR* 4.0 10.8 - - - +
287B TYR* 3.6 59.0 - - + +
323B LEU* 2.8 32.4 + - + +
324B LYS* 3.6 7.9 - - + +
326B SER* 1.3 73.6 - - - +
328B LYS* 1.3 62.5 + - - +
330B GLY 3.3 2.1 + - - -
331B GLU* 3.1 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LYS 2.8 21.9 + - - +
325B ALA* 3.8 6.5 - - - +
327B ILE* 1.3 73.5 - - - +
329B LYS* 1.3 53.5 + - - +
331B GLU* 3.3 13.4 + - - +
332B ASP* 2.7 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 2.9 38.3 + - - +
114B PHE* 3.7 41.2 - - + +
115B ASN* 5.8 0.4 - - - -
146B SER* 4.3 3.6 - - - +
325B ALA 3.0 18.4 + - - +
326B SER* 3.5 9.0 - - - +
328B LYS* 1.3 76.8 - - - +
330B GLY* 1.3 57.2 + - - +
332B ASP* 3.4 8.9 + - - +
333B PHE* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 4.2 6.0 - - - -
146B SER* 3.7 12.1 - - - -
149B PRO* 4.4 3.1 - - - -
150B ILE* 3.3 36.5 - - - +
326B SER 3.2 7.7 + - - -
327B ILE 3.3 3.3 + - - -
329B LYS* 1.3 79.0 - - - +
331B GLU* 1.3 62.1 + - - +
333B PHE* 3.4 1.7 + - - +
334B VAL* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PRO* 4.3 8.7 - - + +
153B GLU* 4.2 35.6 - - + +
286B THR* 4.6 8.0 + - - +
287B TYR* 3.8 12.4 + - + -
327B ILE* 3.1 31.0 + - - +
328B LYS* 3.6 19.1 - - + +
330B GLY* 1.3 73.9 - - - +
332B ASP* 1.3 67.7 + - - +
334B VAL* 3.3 13.2 + - - +
335B LYS* 3.4 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 2.7 61.4 + - - +
329B LYS* 3.6 7.5 - - - +
331B GLU* 1.3 73.7 - - - +
333B PHE* 1.3 63.6 + - - +
335B LYS* 3.0 38.4 + - + +
336B THR* 3.6 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.7 19.5 - + + -
115B ASN* 5.8 1.8 - - - -
118B ALA* 3.6 29.8 - - + -
119B THR* 3.5 34.1 - - - -
122B ALA* 3.8 14.8 - - + -
150B ILE* 3.9 17.5 - - + -
329B LYS 3.0 17.8 + - - +
330B GLY 3.6 4.3 - - - +
332B ASP* 1.3 76.1 - - - +
334B VAL* 1.3 65.0 + - + +
336B THR* 2.6 34.6 + - - -
337B LEU* 3.9 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE* 3.8 39.3 - - + +
153B GLU* 3.7 28.0 - - + +
154B VAL* 4.4 7.6 - - + +
157B LYS* 4.2 27.0 + - + +
330B GLY 3.3 13.4 + - - +
331B GLU 3.3 8.2 + - - +
332B ASP 3.2 0.4 - - - -
333B PHE* 1.3 78.3 - - + +
335B LYS* 1.3 63.4 + - - +
336B THR 3.3 0.2 + - - -
337B LEU* 3.4 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU 3.6 8.7 - - - +
332B ASP* 3.0 34.8 + - + +
334B VAL* 1.3 79.0 - - - +
336B THR* 1.3 61.7 + - + +
337B LEU 3.4 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP 3.7 13.7 - - - +
333B PHE* 2.6 27.8 + - - +
335B LYS* 1.3 77.1 - - + +
337B LEU* 1.3 66.3 + - - +
----------------------------------------------------------
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