Contacts of the helix formed by residues 356 - 378 (chain B) in PDB entry 4CQ8
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 356 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASP 3.2 17.6 + - - +
354B ASN 3.6 0.5 - - - +
355B GLN* 1.4 75.6 - - - +
357B ALA* 1.4 61.6 + - - +
358B GLY* 3.2 15.2 + - - -
359B LYS* 3.0 39.9 + - + +
360B LEU* 2.9 30.1 + - - +
438B GLN* 6.2 3.6 - - - +
441B GLU* 5.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLN 3.4 5.4 + - - -
356B GLU* 1.4 74.5 - - - +
358B GLY* 1.3 57.3 + - - +
360B LEU* 3.4 3.6 + - - +
361B LYS* 3.0 26.6 + - - +
441B GLU* 3.9 38.8 + - + +
442B ILE* 5.2 2.8 - - - +
445B VAL* 3.5 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLU* 3.2 15.5 + - - -
357B ALA* 1.3 78.0 - - - +
359B LYS* 1.3 60.9 + - - +
361B LYS* 3.6 7.1 + - - +
362B ASN* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASP* 3.8 31.2 + - - +
354B ASN* 4.0 27.2 + - - +
356B GLU* 3.0 22.5 + - + +
358B GLY* 1.3 72.6 - - - +
360B LEU* 1.3 66.2 + - - +
362B ASN* 3.4 8.5 + - - +
363B ILE* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ILE* 5.8 0.7 - - + -
343B VAL* 4.1 16.6 - - + -
354B ASN 3.4 18.5 + - - +
355B GLN* 4.3 4.5 - - - +
356B GLU 2.9 14.9 + - - +
357B ALA* 3.8 4.0 - - - +
359B LYS* 1.3 75.3 - - - +
361B LYS* 1.3 57.3 + - - +
363B ILE* 3.2 8.5 + - + +
364B ILE* 2.9 43.5 + - + +
428B VAL* 4.0 21.5 - - + -
430B LEU* 4.8 7.6 - - + -
442B ILE* 3.8 37.2 - - + -
445B VAL* 4.3 7.4 - - + -
446B LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ALA 3.0 17.0 + - - +
358B GLY* 3.8 7.6 - - - +
359B LYS 3.3 0.2 - - - -
360B LEU* 1.3 76.1 - - - +
362B ASN* 1.3 56.0 + - - +
364B ILE* 3.4 1.7 + - - +
365B LEU* 3.0 52.2 + - + +
445B VAL* 3.7 21.5 - - + +
448B GLU* 3.2 40.2 + - - +
449B THR* 3.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ASN* 5.5 1.2 + - - -
322B VAL* 3.8 22.0 - - - +
358B GLY 3.4 9.2 + - - +
359B LYS* 3.4 10.8 + - - +
361B LYS* 1.3 77.5 - - - +
363B ILE* 1.4 55.8 + - - +
365B LEU* 3.8 5.4 - - - +
366B SER* 2.8 44.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 3.8 13.5 - - + -
322B VAL* 3.9 24.0 - - + +
325B LEU* 3.7 21.8 - - + -
341B ILE* 3.7 23.1 - - + -
343B VAL* 4.2 7.6 - - + -
354B ASN* 3.6 44.0 - - + +
359B LYS* 3.0 20.8 + - + +
360B LEU* 3.5 11.9 - - + +
362B ASN* 1.4 76.3 - - - +
364B ILE* 1.4 58.1 + - - +
366B SER* 3.7 1.4 - - - -
367B VAL* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ILE* 4.3 14.6 - - + -
360B LEU* 2.9 39.2 + - + +
361B LYS 3.9 3.4 - - - +
363B ILE* 1.4 74.3 - - - +
365B LEU* 1.4 58.4 + - - +
367B VAL* 3.3 2.4 + - - +
368B LYS* 2.9 42.4 + - + +
428B VAL* 5.0 2.5 - - + -
445B VAL* 4.2 5.4 - - + -
446B LEU* 3.7 30.3 - - + -
449B THR* 3.5 30.5 - - - +
451B ILE* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LYS* 3.0 45.8 + - + +
362B ASN* 4.1 5.4 - - - +
364B ILE* 1.4 73.1 - - - +
366B SER* 1.4 56.7 + - - +
368B LYS* 3.8 9.9 - - + +
369B GLU* 2.9 39.1 + - - +
449B THR* 3.9 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.7 30.8 - - - +
326B LYS* 4.7 9.1 - - - +
362B ASN* 2.8 37.6 + - - -
363B ILE 3.7 3.6 - - - -
365B LEU* 1.4 71.3 - - - +
367B VAL* 1.4 61.6 + - - +
369B GLU* 3.5 10.9 + - - +
370B GLU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 4.8 1.3 - - + -
325B LEU* 3.9 26.9 - - + -
326B LYS* 5.9 0.7 - - + -
329B ILE* 3.7 27.8 - - + +
339B ILE* 4.6 5.2 - - + -
341B ILE* 3.8 21.1 - - + -
363B ILE 2.9 20.1 + - - +
364B ILE 3.3 3.6 + - - +
366B SER* 1.4 74.0 - - - +
368B LYS* 1.4 60.8 + - - +
370B GLU* 3.2 3.8 + - - +
371B ILE* 3.0 38.6 + - + +
426B VAL* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE* 2.9 32.7 + - + +
365B LEU* 3.8 12.1 - - + +
367B VAL* 1.4 76.1 - - - +
369B GLU* 1.3 55.9 + - - +
371B ILE* 3.4 5.7 + - - +
372B ASP* 2.9 49.4 + - - +
423B LYS* 5.4 5.7 - - - +
426B VAL* 4.1 21.9 - - + +
449B THR 3.5 26.2 - - - +
450B ASN* 3.6 19.1 - - - +
451B ILE* 4.9 3.1 - - - +
452B ASP* 5.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 2.9 26.9 + - - +
366B SER* 3.5 10.9 + - - +
368B LYS* 1.3 73.4 - - - +
370B GLU* 1.4 58.7 + - - +
372B ASP* 3.3 9.3 + - - +
373B ASN* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LYS* 3.3 36.0 - - + +
329B ILE* 3.8 19.7 - - + -
330B ASN* 2.7 39.6 + - - +
366B SER 2.9 17.2 + - - +
367B VAL 3.2 4.7 + - - +
369B GLU* 1.4 75.5 - - - +
371B ILE* 1.3 64.0 + - - +
373B ASN* 3.4 24.7 + - - +
374B LEU* 3.4 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 3.7 20.9 - - + -
339B ILE* 4.2 20.9 - - + -
367B VAL* 3.0 27.6 + - + +
368B LYS* 3.8 4.5 - - - +
370B GLU* 1.3 71.1 - - - +
372B ASP* 1.4 68.1 + - - +
374B LEU* 3.1 23.9 + - + +
375B GLU* 4.0 2.3 + - - +
416B TRP* 4.2 6.1 - - + -
423B LYS* 4.0 20.0 - - + +
424B PRO* 3.9 36.6 - - + +
426B VAL* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LYS* 2.9 37.5 + - - +
369B GLU* 3.6 8.1 + - - +
371B ILE* 1.4 75.5 - - - +
373B ASN* 1.4 60.0 + - - +
375B GLU* 3.5 11.9 + - - +
376B LYS* 3.4 45.1 + - - +
423B LYS* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ASN* 6.1 0.4 - - - +
369B GLU* 2.9 32.6 + - - +
370B GLU* 3.7 21.3 + - - +
371B ILE 3.2 0.8 - - - -
372B ASP* 1.4 72.9 - - - +
374B LEU* 1.4 57.8 + - - +
375B GLU 3.2 0.9 - - - -
376B LYS* 3.4 26.2 - - - +
377B ASN* 2.8 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 4.0 24.9 - - + +
330B ASN* 3.6 39.5 - - - +
333B GLY* 4.3 9.6 - - - -
334B ARG* 4.4 9.2 - - + +
370B GLU 3.4 7.5 + - - +
371B ILE* 3.1 20.6 + - + +
373B ASN* 1.4 75.5 - - - +
375B GLU* 1.3 56.1 + - - +
377B ASN* 5.0 0.9 - - - -
378B ASN* 3.3 41.0 + - - +
415B LEU* 3.8 8.5 - - + +
416B TRP* 4.0 28.3 - - + -
424B PRO* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE 4.0 1.2 + - - +
372B ASP* 3.5 12.7 + - - +
374B LEU* 1.3 76.0 - - - +
376B LYS* 1.4 66.0 + - + +
378B ASN 3.2 21.3 - - - -
415B LEU* 3.7 13.4 - - + +
416B TRP* 3.4 35.6 + - + +
423B LYS* 4.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ASP* 3.4 37.0 + - - +
373B ASN* 3.4 30.2 + - + +
375B GLU* 1.4 81.2 + - + +
377B ASN* 1.3 59.8 + - - +
378B ASN* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ASN* 2.8 35.5 + - - +
374B LEU* 4.5 1.3 - - - +
376B LYS* 1.3 74.2 - - - +
378B ASN* 1.4 75.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ARG* 5.8 3.6 - - - +
374B LEU* 3.3 27.3 + - - +
375B GLU* 3.2 19.9 + - - +
376B LYS 4.9 0.8 - - - +
377B ASN* 1.4 91.5 - - - +
414B PHE* 6.6 0.2 - - + -
415B LEU* 3.7 27.8 - - + +
----------------------------------------------------------
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