Contacts of the helix formed by residues 279 - 305 (chain A) in PDB entry 6FWF
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 ALA 279 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER 3.7 3.3 + - - +
277A GLN 3.2 0.2 - - - -
278A LYS* 1.3 75.7 - - + +
280A LEU* 1.3 63.5 + - - +
281A GLY 3.2 2.9 - - - -
282A LYS* 3.2 28.8 + - - +
283A TYR* 3.3 16.0 + - + -
368A ARG* 4.4 10.1 - - + -
371A VAL* 4.3 16.2 - - + -
372A ASN* 3.1 36.1 - - - +
375A TYR* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 4.1 12.3 - - - +
277A GLN* 3.3 32.3 + - + +
279A ALA* 1.3 75.6 - - - +
281A GLY* 1.3 62.3 + - - +
282A LYS 3.2 0.6 + - - -
283A TYR* 3.4 21.7 - - + +
284A VAL* 3.6 8.0 + - - +
349A THR* 3.3 52.0 + - - +
352A LEU* 3.8 29.6 - - + +
353A PHE* 4.0 20.6 - - + +
356A PRO* 6.1 0.2 - - + -
371A VAL* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLN* 3.6 10.9 + - - -
278A LYS 3.6 6.4 + - - -
279A ALA 3.2 1.0 - - - -
280A LEU* 1.3 77.7 - - - +
282A LYS* 1.3 58.5 + - - +
284A VAL* 3.1 25.2 - - - +
285A PHE* 3.7 7.1 + - - +
657A LEU* 5.9 5.6 - - - -
749A ARG* 4.6 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 4.4 11.1 - - - +
279A ALA* 3.2 28.8 + - - +
281A GLY* 1.3 74.9 - - - +
283A TYR* 1.3 57.7 + - - +
284A VAL 3.2 1.8 - - - -
285A PHE* 3.2 11.2 + - + +
286A LEU* 2.8 31.5 + - - +
372A ASN* 3.8 20.4 + - - +
375A TYR* 3.3 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA* 3.3 23.3 + - + -
280A LEU* 3.4 15.9 + - + +
282A LYS* 1.3 77.6 - - - +
284A VAL* 1.3 55.0 + - - +
286A LEU* 3.4 5.9 - - + +
287A THR* 2.8 32.3 + - - -
345A THR* 4.4 18.3 + - + -
348A LEU* 5.3 5.8 - - + -
349A THR* 2.9 42.4 - - - +
352A LEU* 4.5 6.4 - - + +
371A VAL* 2.7 46.9 + - + +
374A LEU* 4.0 17.9 - - + +
375A TYR* 3.3 47.8 + + + -
378A LEU* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU 3.6 4.7 + - - +
281A GLY* 3.1 26.9 - - - +
283A TYR* 1.3 74.1 - - - +
285A PHE* 1.3 56.1 + - + +
287A THR* 3.4 6.5 - - - -
288A VAL* 2.8 38.8 + - - +
349A THR* 3.7 29.8 - - + +
649A PHE 5.4 0.7 - - - +
650A VAL* 3.7 38.8 - - + +
654A ALA* 5.9 6.3 - - + +
742A ALA* 5.7 6.5 - - + +
749A ARG* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLY 4.1 8.3 - - - +
282A LYS* 3.2 13.6 + - + +
284A VAL* 1.3 77.4 - - - +
286A LEU* 1.3 60.4 + - - +
288A VAL* 3.4 10.5 + - + +
289A ALA* 2.8 48.6 + - + +
375A TYR* 5.6 2.5 - - - -
742A ALA* 5.5 3.4 - - - +
743A THR* 4.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LYS 2.8 16.5 + - - +
283A TYR* 3.4 8.1 - - + +
285A PHE* 1.3 76.2 - - - +
287A THR* 1.3 54.3 - - - +
289A ALA* 3.7 4.5 - - - +
290A LEU* 2.8 62.3 + - + +
345A THR* 3.5 33.7 - - + +
375A TYR* 4.1 34.8 - - + +
378A LEU* 5.4 3.6 - - + -
379A PHE* 4.7 25.4 - - + +
382A VAL* 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TYR 2.8 24.2 + - - -
284A VAL* 3.4 9.1 - - - -
286A LEU* 1.3 73.4 - - - +
288A VAL* 1.3 60.7 + - + +
291A PHE* 2.8 24.9 + - - +
342A TRP* 3.2 41.9 - - + +
345A THR* 2.8 27.1 + - - -
346A GLY* 3.1 20.8 + - - -
349A THR* 4.6 0.3 - - - +
650A VAL* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL 2.8 26.7 + - - +
285A PHE* 3.5 16.8 - - + +
287A THR* 1.3 75.9 - - + +
289A ALA* 1.3 62.5 + - - +
291A PHE* 3.3 11.4 + - + +
292A VAL* 2.8 34.1 + - - +
647A LEU* 4.6 18.6 - - + -
650A VAL* 4.4 18.2 - - + -
738A VAL* 5.1 2.7 - - + +
739A ALA* 4.5 24.9 - - + +
742A ALA* 4.4 21.1 - - + -
743A THR* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 2.8 38.4 + - + +
286A LEU* 3.7 4.9 - - - +
288A VAL* 1.3 72.9 - - - +
290A LEU* 1.3 54.9 + - + +
292A VAL* 3.2 8.0 + - - +
293A VAL* 2.8 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 2.8 47.9 + - + +
289A ALA* 1.3 72.0 - - + +
291A PHE* 1.3 59.0 + - - +
293A VAL* 3.4 17.3 - - + +
294A GLN* 2.8 31.2 + - - +
338A SER* 3.8 9.2 - - - +
341A PHE* 3.7 32.1 - - + +
342A TRP* 3.5 19.7 - - + +
345A THR* 4.9 0.7 - - + +
382A VAL* 4.0 14.4 - - + -
386A TYR* 4.2 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR 2.8 18.2 + - - +
288A VAL* 3.3 17.0 + - + +
290A LEU* 1.3 73.0 - - - +
292A VAL* 1.3 61.8 + - + +
294A GLN* 3.3 2.6 - - - +
295A VAL* 3.1 27.9 + - + +
342A TRP* 3.4 42.1 - + + +
639A PHE* 3.3 39.5 - + - -
647A LEU* 4.7 13.5 - - + -
675A LEU* 4.0 5.4 - - + -
731A PHE* 4.0 1.6 - + - -
735A ALA* 3.3 40.4 - - + -
738A VAL* 4.4 11.4 - - + -
1002A HEM 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL 2.8 22.7 + - - +
289A ALA* 3.6 7.4 - - - +
291A PHE* 1.3 74.8 - - + +
293A VAL* 1.3 61.1 + - + +
295A VAL* 2.9 16.9 - - + +
296A LEU* 2.8 36.1 + - + +
732A ILE* 5.9 1.3 - - + -
735A ALA* 4.0 18.2 - - + +
736A ILE* 4.5 16.2 - - + +
739A ALA* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA* 2.8 25.2 + - + +
290A LEU* 3.4 27.6 - - + +
292A VAL* 1.3 75.5 - - + +
294A GLN* 1.3 55.0 + - - +
296A LEU* 3.2 20.3 + - + +
297A LEU* 2.8 44.4 + - + +
338A SER* 4.0 11.7 - - - +
386A TYR* 5.6 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU 2.8 23.7 + - - +
291A PHE 3.3 7.1 - - - +
293A VAL* 1.3 74.2 - - - +
295A VAL* 1.3 63.1 + - - +
297A LEU* 3.5 5.1 + - - +
298A GLY* 2.8 23.7 + - - -
335A HIS* 3.4 14.6 - - - +
338A SER* 3.3 11.9 - - - -
339A ALA* 3.1 42.5 - - - +
342A TRP* 3.9 7.9 - - + -
1002A HEM 3.0 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 3.1 29.7 + - + +
292A VAL* 2.9 31.8 + - + +
294A GLN* 1.3 87.7 - - - +
296A LEU* 1.3 59.9 + - - +
298A GLY 3.8 1.1 - - - +
299A GLY 2.8 22.0 + - - -
731A PHE* 3.8 8.7 - - + -
732A ILE* 3.3 30.9 - - + +
735A ALA* 4.2 11.7 - - + -
1002A HEM 3.3 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL* 2.8 27.0 + - + +
293A VAL* 3.2 24.7 + - + +
295A VAL* 1.3 73.6 - - - +
297A LEU* 1.3 57.5 + - + +
299A GLY* 3.5 0.9 + - - -
300A LEU* 2.8 34.1 + - - +
732A ILE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 2.8 30.8 + - + +
294A GLN 3.9 0.2 - - - +
296A LEU* 1.3 75.5 - - + +
298A GLY* 1.3 56.8 + - - +
300A LEU* 4.3 9.4 - - + +
301A THR* 2.8 37.8 + - - -
331A THR* 3.8 18.9 - - + +
334A TRP* 3.3 57.2 - - + +
335A HIS* 3.8 19.7 - - - +
338A SER* 4.1 8.1 - - - +
386A TYR* 6.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN 2.8 18.0 + - - -
295A VAL 3.6 0.9 + - - -
296A LEU 3.5 0.2 - - - -
297A LEU* 1.3 72.6 - - - +
299A GLY* 1.3 49.3 - - - +
301A THR* 3.5 0.6 + - - -
302A ALA* 2.8 26.5 + - - +
335A HIS* 3.1 27.6 - - - -
1002A HEM 2.9 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL 2.8 20.8 + - - -
296A LEU* 3.8 1.3 - - - -
298A GLY* 1.3 70.8 - - - +
300A LEU* 1.3 58.7 + - - +
302A ALA* 3.2 6.5 - - - +
303A HIS* 2.8 26.3 + - - +
725A THR* 5.0 3.0 - - - +
728A ASP* 4.9 2.0 - - - -
732A ILE* 5.0 5.8 - - - -
1002A HEM 3.5 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU 2.8 20.8 + - - +
297A LEU* 4.2 9.4 - - + +
299A GLY* 1.3 69.6 - - - +
301A THR* 1.3 60.8 + - - +
302A ALA 3.2 0.2 - - - -
303A HIS* 4.2 5.2 - - + +
304A TYR* 2.8 36.1 + - + -
311A PHE* 3.4 39.5 - - + -
322A MET* 3.8 23.6 - - + -
326A PHE* 4.8 5.2 - - + +
331A THR* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 2.8 19.3 + - - -
298A GLY* 3.7 4.7 - - - -
300A LEU* 1.3 71.9 - - - +
302A ALA* 1.3 60.9 + - - +
304A TYR* 3.3 4.6 + - - +
305A THR* 3.1 24.4 + - - +
328A TYR* 3.8 12.6 - - + -
331A THR* 2.4 46.0 + - - -
332A ARG* 3.3 14.5 + - - +
335A HIS* 5.2 0.9 - - - -
1002A HEM 3.4 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLY 2.8 17.9 + - - +
299A GLY* 3.2 13.7 + - - +
301A THR* 1.3 73.1 - - - +
303A HIS* 1.3 56.7 + - - +
305A THR* 3.0 17.3 + - - -
306A VAL* 3.5 14.7 - - - +
721A ARG 4.8 2.1 - - - +
724A ARG* 4.6 5.6 - - - +
725A THR* 4.2 8.2 - - + +
728A ASP* 3.2 27.8 - - - +
1002A HEM 3.3 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLY 2.8 18.8 + - - +
300A LEU* 3.9 11.0 - - + +
301A THR 3.4 0.2 - - - -
302A ALA* 1.3 70.5 - - - +
304A TYR* 1.3 64.1 + - - +
306A VAL* 2.8 31.1 + - + +
307A GLU* 3.1 38.2 + - + +
310A GLY 4.1 5.4 - - - -
311A PHE* 3.2 40.4 - + + -
312A TYR* 3.3 37.9 + + - -
725A THR* 4.9 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.5 9.3 - - - +
162A ASP 5.5 1.4 - - - +
300A LEU* 2.8 35.8 + - + +
301A THR 3.3 1.8 + - - +
303A HIS* 1.3 74.9 + - - +
305A THR* 1.3 59.3 + - - +
306A VAL 3.3 1.3 + - - -
307A GLU 4.3 11.2 - - - -
308A GLY* 4.1 25.1 + - - -
310A GLY 5.8 1.8 - - - -
311A PHE* 5.4 8.1 - + - -
322A MET* 3.8 23.3 + - + +
323A SER* 4.3 8.2 - - - -
326A PHE 2.4 25.3 + - - -
327A PRO* 3.4 25.8 - - + +
328A TYR* 3.6 38.5 - - + -
331A THR* 3.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.1 25.1 - - + +
301A THR* 3.1 14.1 + - + +
302A ALA* 3.0 19.2 + - - -
303A HIS 3.2 0.2 - - - -
304A TYR* 1.3 75.1 - - - +
306A VAL* 1.3 58.8 + - - +
328A TYR* 3.9 15.9 - - + -
718A ASP* 5.5 2.9 - - - +
721A ARG* 3.6 52.3 + - - +
724A ARG* 5.4 1.7 - - - -
1002A HEM 4.0 10.3 - - + +
----------------------------------------------------------
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