Contacts of the helix formed by residues 416 - 432 (chain C) in PDB entry 2JIF
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 416 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C SER* 4.8 4.0 + - - +
411C THR 3.3 14.8 - - - +
412C ILE* 3.2 18.2 + - + +
415C GLY* 1.3 77.4 - - - +
417C SER* 1.3 67.1 + - - +
418C ASN 3.3 0.7 - - - -
419C ILE* 2.9 19.8 + - + +
420C GLN* 3.0 7.4 + - - +
1433C FAD 3.2 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU* 5.3 4.3 - - - -
371C LYS* 4.6 0.8 + - - +
372C TYR* 3.9 17.0 - - - +
375C SER* 4.3 2.9 + - - -
376C GLU* 2.7 30.2 + - - +
411C THR* 3.0 27.5 + - - +
416C ALA* 1.3 71.8 - - - +
418C ASN* 1.3 67.2 + - - +
420C GLN* 3.1 12.4 + - - +
421C LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 418 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 4.0 19.2 - - - +
335A GLN* 3.0 31.0 + - - +
388A TRP* 6.0 0.4 - - - -
416C ALA 3.3 0.6 - - - -
417C SER* 1.3 79.4 - - - +
419C ILE* 1.3 56.7 + - - +
421C LEU* 3.4 6.2 + - - +
422C ASN* 2.9 35.2 + - - +
1433C FAD 3.1 57.4 + - + +
334D HIS* 3.5 19.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 4.8 4.9 - - + -
183C SER* 3.8 27.1 - - - +
294C ARG* 4.2 8.1 - - - +
415C GLY* 4.2 1.6 - - - -
416C ALA* 2.9 24.7 + - + +
418C ASN* 1.3 74.6 - - - +
420C GLN* 1.3 64.6 + - - +
422C ASN* 3.3 11.0 + - + +
423C THR* 3.0 28.1 + - - +
426C LYS* 5.2 0.2 + - - -
1433C FAD 3.7 39.3 - - + +
1434C COS 3.4 45.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
294C ARG* 3.3 20.1 + - - +
368C SER* 3.3 31.6 + - - +
371C LYS* 3.7 22.1 - - + +
372C TYR* 3.9 22.9 - - + -
414C GLU 3.0 19.0 + - - -
415C GLY* 2.8 25.2 + - - +
416C ALA 3.0 12.2 + - - +
417C SER* 3.1 9.2 + - - +
419C ILE* 1.3 76.3 - - - +
421C LEU* 1.3 57.4 + - - +
423C THR* 3.2 6.0 + - - -
424C ILE* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN* 6.0 0.9 - - - +
372C TYR* 3.7 48.2 - - + +
417C SER* 3.0 17.0 + - - +
418C ASN* 3.7 11.0 - - - +
420C GLN* 1.3 75.5 - - - +
422C ASN* 1.3 57.9 + - - +
424C ILE* 3.4 4.8 + - + -
425C ALA* 2.9 27.4 + - - +
333D GLN 4.9 0.2 - - - +
334D HIS* 3.7 43.1 - - + +
337D ALA* 3.4 30.7 - - + +
338D HIS* 3.9 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ASN 2.9 20.3 + - - -
419C ILE* 3.5 17.0 - - + +
420C GLN 3.3 0.2 - - - -
421C LEU* 1.3 74.4 - - - +
423C THR* 1.3 58.3 + - - +
425C ALA* 3.4 2.9 + - - +
426C LYS* 3.0 46.7 + - - +
1433C FAD 3.4 33.1 + - - -
330D GLN* 3.4 12.1 + - - +
333D GLN* 4.1 14.0 - - - +
334D HIS* 2.8 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 4.2 10.9 + - - +
364C ILE* 4.0 22.4 - - + +
368C SER* 3.5 22.2 - - - +
419C ILE* 3.0 18.3 + - - +
420C GLN* 3.5 8.5 - - - -
422C ASN* 1.3 74.2 - - - +
424C ILE* 1.3 65.9 + - - +
426C LYS* 3.2 20.2 + - + +
427C HIS* 3.1 34.7 + - + -
1434C COS 4.0 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LYS* 4.1 11.7 - - + +
368C SER* 3.8 18.2 - - - +
369C MET* 3.7 46.0 - - + +
372C TYR* 4.7 3.4 - - + -
420C GLN 2.9 25.9 + - - +
421C LEU* 3.7 15.5 - - + +
423C THR* 1.3 76.9 - - - +
425C ALA* 1.3 57.1 + - - +
427C HIS* 3.2 5.0 + - - +
428C ILE* 2.9 40.3 + - + +
337D ALA* 3.6 18.8 - - + +
341D THR* 3.7 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU 2.9 17.8 + - - +
422C ASN 3.7 4.0 - - - +
424C ILE* 1.3 73.7 - - - +
426C LYS* 1.3 61.3 + - - +
428C ILE* 3.2 11.7 + - + -
429C ASP* 2.9 25.8 + - - +
327D PHE* 3.3 14.9 - - + -
333D GLN* 3.6 47.3 - - + +
336D VAL* 5.7 0.4 - - + -
337D ALA* 4.1 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ASN* 3.0 35.2 + - - +
423C THR* 3.2 27.3 + - + +
425C ALA* 1.3 75.6 - - + +
427C HIS* 1.3 67.0 + - + +
429C ASP* 3.4 8.5 + - - +
430C ALA* 3.2 21.1 + - - +
1434C COS 4.0 45.5 + - + +
327D PHE* 5.5 0.4 - - - -
333D GLN* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C PRO* 6.6 0.2 - - + -
364C ILE* 3.5 38.6 - - + +
365C LYS* 3.8 30.5 - - + +
423C THR* 3.1 36.6 + - + +
424C ILE 3.2 7.4 + - - +
426C LYS* 1.3 77.5 - - + +
428C ILE* 1.3 64.3 + - - +
430C ALA* 3.1 17.3 + - - +
431C GLU* 3.1 22.3 + - - +
1434C COS 5.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LYS* 4.8 8.7 - - + +
424C ILE* 2.9 31.6 + - + +
425C ALA* 3.2 8.5 + - - +
427C HIS* 1.3 74.7 - - - +
429C ASP* 1.3 62.1 + - - +
431C GLU* 3.1 18.5 + - - +
432C TYR* 3.1 34.5 + - + +
309D PHE* 4.3 5.4 - - + -
313D ILE* 4.1 16.4 - - + -
327D PHE* 4.2 3.8 - - + -
336D VAL* 3.9 28.5 - - + -
337D ALA* 4.0 4.7 - - - -
340D ALA* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ALA 2.9 13.8 + - - +
426C LYS* 3.4 12.6 - - - +
428C ILE* 1.3 75.9 - - - +
430C ALA* 1.3 59.9 + - - +
431C GLU 3.4 0.2 + - - -
432C TYR 3.4 3.3 + - - +
317D LYS* 2.6 49.7 + - - +
325D ARG* 2.9 45.2 + - - -
327D PHE* 3.6 17.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C LYS 3.2 9.5 + - - +
427C HIS* 3.1 13.0 + - - +
429C ASP* 1.3 78.7 - - - +
431C GLU* 1.3 59.7 + - + +
432C TYR 3.5 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LYS* 2.9 39.5 + - - +
427C HIS* 3.3 15.5 - - - +
428C ILE* 3.1 14.3 + - - +
430C ALA* 1.3 79.4 - - + +
432C TYR* 1.3 81.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ILE* 3.1 36.2 + - + +
429C ASP 3.4 1.8 + - - +
430C ALA 4.6 2.4 - - - +
431C GLU* 1.3 101.7 + - + +
306D GLN* 3.7 5.4 + - - -
309D PHE* 3.6 21.0 - + - -
310D ASP* 2.5 56.1 + - + -
313D ILE* 3.7 25.6 - - + -
314D PRO* 4.1 21.9 - - + +
317D LYS* 2.7 35.2 + - + +
----------------------------------------------------------
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