Contacts of the helix formed by residues 404 - 423 (chain C) in PDB entry 4P0S
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 404 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C GLU* 3.9 11.7 - - - +
370C GLU* 5.0 1.8 - - + +
402C THR* 3.3 1.8 - - - +
403C ALA* 1.3 83.5 - - - +
405C ILE* 1.3 60.1 + - + +
406C LYS* 3.1 20.5 + - - +
407C GLU* 3.3 14.9 + - - +
408C SER* 2.7 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C PRO* 5.1 15.5 - - + +
286C GLU 5.6 0.7 - - - -
287C LEU* 4.6 26.7 - - + +
290C GLU* 5.9 4.0 - - + -
334C ARG* 4.1 16.8 - - - +
336C ARG* 5.3 3.6 - - - +
369C GLU* 2.9 31.9 - - - +
404C ASP* 1.3 77.3 - - + +
406C LYS* 1.3 52.4 + - - +
408C SER* 3.0 10.3 - - - -
409C ALA* 2.6 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLU* 3.6 28.4 + - + +
293C ARG* 2.9 39.7 - - - +
294C LEU* 4.9 2.5 - - + +
404C ASP* 3.1 14.3 + - - +
405C ILE* 1.3 76.0 - - - +
407C GLU* 1.3 61.7 + - + +
409C ALA* 3.3 6.2 + - - +
410C ALA* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LYS* 6.1 1.0 - - - -
401C ARG 5.5 0.5 - - - +
402C THR* 3.8 17.9 + - + +
403C ALA* 4.0 18.2 + - - +
404C ASP* 3.3 11.3 + - - +
406C LYS* 1.3 78.9 - - + +
408C SER* 1.3 54.7 + - - +
410C ALA* 3.4 6.5 - - - +
411C TYR* 2.5 38.9 + - + +
370D PHE* 3.6 24.7 - - - -
405D ARG* 2.7 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 5.6 0.7 - - - -
334C ARG* 5.9 4.3 - - - -
367C LEU* 4.5 18.5 - - - +
369C GLU* 4.0 13.5 + - - +
402C THR* 3.1 16.7 - - - +
404C ASP 2.7 19.6 + - - -
405C ILE* 3.0 20.3 - - - -
407C GLU* 1.3 76.4 - - - +
409C ALA* 1.3 63.7 + - - -
411C TYR* 3.1 4.9 + - - +
412C LEU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 3.8 19.9 - - + +
290C GLU* 3.6 31.2 - - + -
291C LEU* 4.0 16.9 - - + +
294C LEU* 4.2 6.3 - - + -
405C ILE* 2.6 17.4 + - + +
406C LYS 3.3 3.8 + - - +
408C SER* 1.3 71.9 - - - +
410C ALA* 1.3 59.3 + - - +
412C LEU* 3.3 5.8 + - - +
413C ALA* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 4.0 15.8 - - + +
406C LYS* 3.0 20.2 + - + +
407C GLU* 3.5 7.2 - - - +
409C ALA* 1.3 76.7 - - - +
411C TYR* 1.3 58.6 + - - +
413C ALA* 3.0 9.2 + - - +
414C LEU* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C VAL* 5.7 0.4 - - + -
365C VAL* 4.5 8.9 - - + +
367C LEU* 3.8 29.4 - - + -
398C PHE* 3.7 13.4 - + - -
400C LYS* 3.5 49.2 - - + +
402C THR* 4.9 4.7 - - - +
407C GLU* 2.5 28.3 + - + +
408C SER* 3.8 4.3 - - - +
410C ALA* 1.3 68.9 - - - +
412C LEU* 1.3 68.6 + - + +
414C LEU* 3.3 4.5 + - + +
415C LEU* 2.9 55.9 + - + +
409D GLU* 4.5 8.3 - - + +
412D LEU* 6.2 2.5 - - + -
413D VAL* 4.6 14.4 - - + -
416D GLN* 3.4 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 4.1 28.7 - - + -
287C LEU* 4.6 7.4 - - + -
291C LEU* 4.4 12.3 - - + -
308C PHE* 3.7 53.6 - - + -
310C TRP* 4.0 4.5 - - + -
332C VAL* 4.7 12.3 - - + -
367C LEU* 4.6 15.7 - - + -
408C SER* 2.9 20.1 + - - +
409C ALA* 3.6 4.9 - - - +
411C TYR* 1.3 78.2 - - - +
413C ALA* 1.3 53.6 + - - +
415C LEU* 3.8 9.1 - - + +
416C THR* 2.4 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 5.4 0.4 - - - +
294C LEU* 4.4 12.3 - - + +
296C VAL* 3.8 27.4 - - + -
409C ALA 2.8 14.3 + - - +
410C ALA* 3.0 15.2 + - - +
412C LEU* 1.3 77.6 - - - +
414C LEU* 1.3 57.9 + - + +
416C THR* 3.0 9.3 + - - -
417C ARG* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C ALA* 2.8 27.9 + - + +
411C TYR* 4.1 4.9 - - + +
413C ALA* 1.3 76.3 - - + +
415C LEU* 1.3 60.8 + - - +
417C ARG* 3.8 9.2 - - + +
418C GLY* 3.0 21.3 + - - -
406D VAL* 4.0 26.7 - - + +
409D GLU* 4.2 11.9 - - + -
410D GLU* 3.9 37.7 - - + +
413D VAL* 3.5 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C TRP* 3.6 27.8 - - + -
330C HIS* 5.1 6.7 - - + -
332C VAL* 4.4 14.8 - - + -
365C VAL* 5.0 4.5 - - + -
411C TYR* 2.9 51.7 + - + +
412C LEU* 3.8 7.4 - - + +
414C LEU* 1.3 77.9 - - - +
416C THR* 1.3 61.9 + - - +
418C GLY* 3.2 3.5 + - - -
419C LEU* 3.1 27.1 + - + +
413D VAL* 4.0 19.0 - - + +
416D GLN* 3.3 32.5 - - - +
417D LEU* 4.9 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 4.8 3.3 - - + +
271C LEU* 3.9 18.7 - - + +
296C VAL* 4.9 7.1 - - + +
297C THR* 4.4 15.7 - - - +
310C TRP* 3.0 33.8 + - + +
412C LEU 2.4 23.9 + - - -
413C ALA* 3.2 11.6 - - - -
415C LEU* 1.3 77.5 - - - +
417C ARG* 1.3 55.9 + - - +
419C LEU* 3.1 6.1 + - - +
420C GLN* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA 2.8 17.8 + - - +
414C LEU* 4.0 12.1 - - + +
415C LEU 3.4 0.2 - - - -
416C THR* 1.3 71.2 - - - +
418C GLY* 1.3 63.8 + - - +
420C GLN* 2.7 57.3 + - - +
421C ARG* 3.1 38.1 + - + +
424C GLN* 4.1 17.4 - - - +
410D GLU* 6.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU 3.0 15.9 + - - -
415C LEU 3.2 5.4 + - - -
416C THR 3.2 0.4 - - - -
417C ARG* 1.3 77.6 - - - +
419C LEU* 1.3 50.3 + - - +
421C ARG* 3.1 10.1 + - - +
422C LEU* 2.6 35.5 + - - +
410D GLU* 6.4 1.6 - - - -
413D VAL* 4.3 12.3 - - - -
414D ASP* 4.6 9.7 - - - +
417D LEU* 4.3 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 4.2 9.0 - - + +
310C TRP* 3.4 48.2 - - + -
328C LEU* 3.6 27.8 - - + -
330C HIS* 4.4 11.7 - - + +
415C LEU* 3.1 13.8 + - + +
416C THR* 3.1 7.4 + - - +
418C GLY* 1.3 73.6 - - - +
420C GLN* 1.3 66.7 + - - +
422C LEU* 3.2 25.9 + - + +
423C TYR* 3.2 22.3 + - + +
417D LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 420 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ARG* 6.1 1.2 - - - +
269C VAL* 3.3 41.7 + - + +
297C THR* 3.4 31.9 + - - +
416C THR* 3.0 18.4 + - + +
417C ARG* 2.7 59.0 + - - +
419C LEU* 1.3 77.8 - - - +
421C ARG* 1.3 58.8 + - - +
423C TYR 4.5 0.3 - - - -
424C GLN* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ARG* 3.1 36.4 + - + +
418C GLY* 3.6 8.5 - - - +
419C LEU 3.1 0.4 - - - -
420C GLN* 1.3 76.4 - - - +
422C LEU* 1.3 66.3 + - - +
423C TYR 3.3 0.8 + - - -
424C GLN* 3.8 18.2 + - - +
329D LYS* 3.5 10.4 - - - +
410D GLU* 3.8 15.2 + - - +
414D ASP* 2.6 45.5 + - - -
418D HIS* 5.4 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C HIS* 5.4 0.2 - - + -
418C GLY 2.6 19.6 + - - +
419C LEU* 3.2 24.2 + - + +
421C ARG* 1.3 77.9 - - - +
423C TYR* 1.3 70.4 + - + +
424C GLN 4.7 0.2 - - - +
426C HIS* 3.6 20.8 + - + -
448C ASN* 4.0 16.6 - - + +
449C PRO* 3.8 25.3 - - + +
417D LEU* 3.6 32.5 - - + +
418D HIS* 3.9 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C TYR* 2.4 40.1 + - + +
269C VAL* 5.7 4.9 - - + -
328C LEU* 3.9 32.5 - - + +
329C ASP* 4.6 5.5 + - - +
419C LEU* 3.2 21.4 + - + +
420C GLN 4.5 1.1 - - - +
422C LEU* 1.3 99.1 - - + +
424C GLN* 1.3 61.3 + - - +
426C HIS* 3.2 21.1 + - + +
428C LEU* 3.4 32.5 - - + -
448C ASN* 5.3 2.1 + - - -
449C PRO* 4.6 6.2 - - + +
450C LEU* 2.4 45.4 + - - +
451C CYS* 4.6 3.4 - - - -
453C LEU* 4.0 14.0 - - + +
----------------------------------------------------------
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