Contacts of the helix formed by residues 392 - 414 (chain B) in PDB entry 4WGK
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 ASP 392 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLY 3.9 0.6 - - - -
391B GLN* 1.3 80.4 - - - +
393B MET* 1.3 62.2 + - + +
394B PHE* 3.6 20.0 - - + +
395B ASP* 2.8 36.6 + - - +
396B SER* 2.9 32.4 + - - -
718B ARG* 5.0 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B SER 3.7 14.1 - - - +
307B MET* 3.5 18.2 - - + -
308B ASN* 3.2 56.1 - - - +
310B SER* 5.0 4.5 - - - -
311B ASN* 3.4 31.4 - - + -
392B ASP* 1.3 74.1 - - + +
394B PHE* 1.3 79.0 + - + +
396B SER* 3.7 5.9 - - - -
397B THR* 2.7 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.8 20.9 - - + -
307B MET* 3.6 30.1 - - + -
311B ASN* 4.9 2.9 - - - -
313B LEU* 4.2 12.3 - - + -
392B ASP* 3.3 16.8 + - + +
393B MET* 1.3 93.3 - - + +
395B ASP* 1.3 62.7 + - - +
397B THR* 3.4 4.3 + - - -
398B GLN* 3.1 32.6 + - - +
715B TRP* 5.7 0.8 - - - -
718B ARG* 3.3 51.8 - - - +
720B TYR* 4.1 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLY* 3.3 7.8 - - - -
391B GLN* 3.0 32.2 + - + +
392B ASP* 2.8 25.4 + - - +
394B PHE* 1.3 72.4 - - - +
396B SER* 1.3 59.6 + - - +
398B GLN* 3.3 13.8 + - - +
399B ILE* 2.9 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B SER* 4.4 11.4 - - - -
388B GLY* 3.2 19.8 + - - -
389B PRO* 3.7 12.8 - - - -
390B GLY* 2.9 27.6 + - - +
392B ASP 2.9 19.0 + - - -
393B MET* 3.7 9.1 - - - -
395B ASP* 1.3 77.0 - - - +
397B THR* 1.3 62.1 + - - +
399B ILE* 3.3 2.5 + - - +
400B ILE* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B SER* 3.2 21.3 - - - -
307B MET* 3.2 19.2 - - + +
317B ASP* 3.6 11.7 - - - -
318B ASN* 3.6 28.9 - - - +
321B TYR* 4.2 1.8 - - + -
393B MET 2.7 22.4 + - - -
394B PHE* 3.5 6.3 - - - -
395B ASP 3.3 0.2 - - - -
396B SER* 1.3 77.7 - - - +
398B GLN* 1.3 55.9 + - - +
401B GLY* 2.9 26.5 + - - -
715B TRP* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 3.3 37.5 + - + +
394B PHE* 3.1 20.5 + - - +
395B ASP* 3.3 14.0 + - - +
397B THR* 1.3 75.8 - - - +
399B ILE* 1.3 57.3 + - - +
402B ARG* 2.8 37.4 + - - +
715B TRP* 4.1 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ILE* 6.2 0.2 - - + -
389B PRO* 4.0 24.5 - - + +
390B GLY* 3.7 28.9 - - - +
395B ASP* 2.9 34.9 + - - +
396B SER* 3.3 4.0 + - - +
398B GLN* 1.3 77.4 - - + +
400B ILE* 1.3 65.5 + - + +
402B ARG* 4.0 3.6 - - - +
403B ALA* 3.2 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLY 4.6 2.5 - - - +
253B VAL* 4.0 27.4 - - + -
302B ILE* 3.7 29.4 - - + -
306B SER* 4.0 6.7 - - - +
318B ASN* 3.9 18.6 - - + +
355B PRO* 3.6 25.8 - - + +
357B ILE* 4.5 2.5 - - + -
389B PRO* 4.0 20.6 - - + -
396B SER 3.1 17.4 + - - +
397B THR 4.1 2.7 - - - +
399B ILE* 1.3 77.0 - - + +
401B GLY* 1.3 63.8 + - - +
403B ALA* 3.4 5.7 + - - +
404B MET* 3.2 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ASN* 3.4 25.3 - - - +
321B TYR* 3.8 11.7 - - - -
322B ALA* 3.2 12.6 - - - +
397B THR 2.9 17.3 + - - -
398B GLN 3.8 0.9 - - - -
400B ILE* 1.3 77.4 - - - +
402B ARG* 1.3 55.8 + - - +
404B MET* 3.5 5.0 + - - -
405B TYR* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 3.8 10.2 + - + -
325B LEU* 3.8 40.9 - - + +
398B GLN 2.8 22.8 + - - +
399B ILE* 4.0 3.6 - - - +
401B GLY* 1.3 71.3 - - - +
403B ALA* 1.3 61.9 + - - +
405B TYR* 3.2 21.3 + - + +
406B GLN* 2.8 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 4.5 4.0 - - + +
251B ASP 5.4 1.8 - - - +
253B VAL* 3.6 26.9 - - + -
399B ILE* 3.2 16.8 + - + +
400B ILE 3.7 1.1 - - - +
402B ARG* 1.3 80.8 - - - +
404B MET* 1.3 60.9 + - - +
406B GLN* 3.3 15.4 + - - +
407B ARG* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 4.6 9.2 - - + -
253B VAL* 4.7 5.2 - - + -
281B MET* 3.5 12.0 - - + +
300B PHE* 3.6 36.8 - - + -
302B ILE* 3.7 17.0 - - - -
318B ASN* 3.6 43.5 - - + +
319B VAL* 3.7 15.0 - - + +
322B ALA* 4.2 1.6 - - + -
345B PHE* 3.9 17.9 - - + -
400B ILE* 3.2 21.6 + - + +
401B GLY* 3.8 2.7 - - - +
403B ALA* 1.3 74.6 - - - +
405B TYR* 1.3 60.5 + - - +
407B ARG 3.4 0.7 + - - -
408B ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA* 3.9 17.6 - - - +
325B LEU* 3.5 48.9 - - + -
326B LEU* 3.5 27.1 - - + -
329B GLU* 3.4 31.9 + - - +
345B PHE* 4.6 0.4 - - - -
401B GLY 3.0 15.4 + - - +
402B ARG* 3.4 33.2 - - + +
404B MET* 1.3 77.6 - - - +
406B GLN* 1.3 72.8 + - - +
408B ALA* 3.3 5.5 + - - +
409B LYS* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ARG* 2.8 21.9 + - + +
403B ALA* 3.5 9.6 - - - +
404B MET 3.2 0.2 - - - -
405B TYR* 1.3 95.1 - - + +
407B ARG* 1.3 58.1 + - + +
409B LYS* 3.4 19.1 + - - +
410B GLU* 2.8 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY* 3.4 31.3 - - - -
249B ASN 2.8 21.6 + - - +
250B VAL* 3.8 33.4 - - + -
251B ASP 5.5 0.4 - - - +
281B MET* 4.2 3.8 - - - -
403B ALA 3.3 11.3 + - - +
404B MET 4.0 4.5 - - - +
406B GLN* 1.3 78.8 - - + +
408B ALA* 1.3 60.8 + - - +
410B GLU* 2.7 46.5 + - - +
411B LEU* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B MET* 3.6 19.4 - - - -
283B VAL* 4.0 12.0 - - + +
296B LEU* 5.0 2.1 - - + +
298B SER* 4.4 3.6 - - - +
326B LEU* 3.9 17.3 - - + -
345B PHE* 3.8 16.2 - - + -
404B MET 3.0 18.7 + - - +
405B TYR 3.6 4.7 - - - +
407B ARG* 1.3 76.7 - - - +
409B LYS* 1.3 57.1 + - - +
411B LEU 3.7 0.2 + - - -
412B TYR* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 4.0 13.6 - - + +
329B GLU* 3.1 39.5 + - - +
330B LYS* 5.3 6.5 - - - +
405B TYR* 2.8 33.5 + - + +
406B GLN* 3.6 20.4 + - - +
407B ARG 3.2 0.2 - - - -
408B ALA* 1.3 75.3 - - - +
410B GLU* 1.3 65.8 + - - +
412B TYR* 3.3 6.6 + - - +
413B ALA* 3.0 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLN* 2.8 53.1 + - - +
407B ARG* 2.7 46.4 + - - +
409B LYS* 1.3 78.2 - - + +
411B LEU* 1.3 63.0 + - - +
413B ALA* 3.4 6.5 + - - +
414B SER* 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASN* 2.9 41.9 + - + +
247B LYS* 3.4 26.5 - - - +
248B GLY* 3.7 20.0 - - - +
281B MET* 3.9 24.2 - - + +
283B VAL* 3.8 23.8 - - + -
407B ARG* 2.9 43.1 + - + +
410B GLU* 1.3 73.5 - - - +
412B TYR* 1.3 65.2 + - - +
414B SER* 4.0 1.3 - - - +
415B ALA* 3.1 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 4.3 10.0 - - + +
285B LYS* 3.3 64.0 + - + +
286B MET 4.0 7.3 + - - -
293B ASP* 2.8 42.7 + - - +
295B GLY 3.7 5.4 - - - -
296B LEU* 3.5 42.0 - - + -
330B LYS* 3.7 24.7 - - - +
341B PHE* 3.4 10.7 - + - -
408B ALA 3.0 19.7 + - - +
409B LYS* 3.5 8.3 - - - +
411B LEU* 1.3 77.9 - - - +
413B ALA* 1.3 66.9 + - + +
415B ALA* 3.4 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS* 4.3 9.3 + - - +
409B LYS* 3.0 19.3 + - + +
410B GLU* 3.8 7.0 - - - +
411B LEU 3.4 0.2 - - - -
412B TYR* 1.3 84.1 - - + +
414B SER* 1.3 58.7 + - - +
415B ALA 3.4 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASN* 3.1 19.9 + - - -
410B GLU 3.1 15.1 + - - -
411B LEU* 4.0 2.9 - - - +
413B ALA* 1.3 77.9 - - - +
415B ALA* 1.3 64.4 + - - +
416B SER* 3.4 9.5 + - - -
----------------------------------------------------------
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