Contacts of the helix formed by residues 414 - 433 (chain C) in PDB entry 1C7G
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 TYR 414 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR* 3.2 24.6 - - + +
4C PRO* 2.7 38.4 + - - +
5C ALA* 4.7 0.4 - - - -
6C GLU* 4.2 5.1 + - - -
317C HIS* 3.6 17.8 - + - -
321C GLN* 3.9 24.3 + - + -
324C TYR* 3.6 53.8 - + + +
413C THR* 1.3 75.3 - - - +
415C ALA* 1.3 57.9 + - - +
417C MET* 3.2 7.6 + - - +
418C ASP* 2.8 32.7 + - - +
415D ALA* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C THR* 3.1 2.8 + - - +
414C TYR* 1.3 78.0 - - - +
416C HIS* 1.3 63.8 + - - +
418C ASP* 3.3 12.7 + - - +
419C VAL* 3.1 25.5 + - - +
3D TYR 6.1 0.2 - - - +
5D ALA* 3.7 17.8 - - + +
6D GLU* 3.5 22.2 - - - +
414D TYR* 4.2 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 3.5 26.8 + + - -
45C ILE* 3.6 17.2 - - + +
411C VAL 4.7 0.7 - - - -
412C TYR* 3.5 30.1 - + + -
413C THR* 3.1 34.4 + - + +
415C ALA* 1.3 76.8 - - - +
417C MET* 1.3 63.2 + - + +
419C VAL* 3.1 12.7 + - - +
420C VAL* 3.0 20.9 - - - +
5D ALA* 4.3 2.7 - - + -
6D GLU* 3.0 39.1 + - + +
8D PHE* 3.3 21.7 + + - -
9D ARG* 4.7 3.1 - - - +
10D ILE* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 5.2 1.6 - - + -
47C LEU* 4.7 5.6 - - + -
321C GLN* 4.1 30.1 - - + +
324C TYR* 3.8 18.2 - - + -
325C LEU* 3.8 27.3 - - + +
407C ILE* 4.2 31.9 - - + -
412C TYR* 3.9 30.3 - - + -
413C THR 3.2 11.8 + - - +
414C TYR* 3.3 11.4 - - - +
416C HIS* 1.3 79.1 - - + +
418C ASP* 1.3 59.7 + - - +
420C VAL* 3.4 10.4 + - + +
421C ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 418 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C TYR* 2.5 31.3 + - - -
328C LYS* 3.2 22.6 + - - +
414C TYR* 2.8 14.1 + - - +
415C ALA* 3.5 15.4 - - - +
416C HIS 3.2 0.2 - - - -
417C MET* 1.3 76.7 - - - +
419C VAL* 1.3 58.5 + - - +
421C ALA* 4.3 3.6 - - - -
422C ASP* 2.8 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 419 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 4.5 13.0 - - + -
45C ILE* 3.9 16.4 - - + -
374C THR* 3.8 30.2 - - + +
376C VAL* 4.6 0.4 - - + -
415C ALA 3.1 15.4 + - - +
416C HIS* 3.1 11.2 + - - +
418C ASP* 1.3 77.0 - - - +
420C VAL* 1.3 63.5 + - - +
422C ASP* 4.2 2.4 - - - +
423C GLY 3.1 17.3 + - - -
5D ALA* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 420 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 4.6 4.7 - - + -
47C LEU* 4.3 15.9 - - + -
325C LEU* 3.9 24.9 - - + -
370C ILE* 6.1 0.2 - - - -
374C THR* 4.8 2.8 - - - +
376C VAL* 4.2 28.9 - - + -
405C LEU* 4.5 9.2 - - + -
416C HIS 3.0 18.4 - - - +
417C MET* 3.6 15.5 - - + +
419C VAL* 1.3 75.2 - - - +
421C ALA* 1.3 58.7 + - - +
423C GLY* 3.4 0.7 + - - -
424C ILE* 3.0 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C TYR* 6.1 0.2 - - + -
325C LEU* 3.8 15.0 - - + -
328C LYS* 3.8 32.8 - - + -
329C LEU* 4.0 11.4 - - + +
417C MET 2.9 18.4 + - - +
418C ASP 3.9 0.9 - - - +
420C VAL* 1.3 77.8 - - - +
422C ASP* 1.3 61.5 + - - +
424C ILE* 3.3 1.9 + - - +
425C ILE* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LYS* 3.3 22.2 + - - -
418C ASP* 2.8 33.2 + - - +
419C VAL* 4.2 3.3 - - - +
421C ALA* 1.3 72.4 - - - +
423C GLY* 1.3 63.3 + - - +
425C ILE* 3.5 10.6 + - - +
426C LYS* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C GLU* 5.2 2.3 - - - +
374C THR* 3.5 30.5 - - - -
419C VAL 3.1 11.1 + - - -
421C ALA 3.2 0.2 - - - -
422C ASP* 1.3 77.6 - - - +
424C ILE* 1.3 55.7 + - - +
426C LYS* 3.4 10.2 + - - +
427C LEU* 3.0 33.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
329C LEU* 3.8 21.1 - - + -
334C VAL* 4.1 7.0 - - + -
347C LEU* 4.1 7.9 - - + -
352C PHE* 3.7 25.2 - - + -
370C ILE* 4.0 30.3 - - + -
374C THR* 6.1 0.2 - - + -
405C LEU* 4.0 25.4 - - + -
420C VAL* 3.0 43.7 + - + +
421C ALA 3.8 2.9 - - - +
423C GLY* 1.3 73.4 - - - +
425C ILE* 1.3 65.9 + - - +
427C LEU* 3.3 7.7 + - - +
428C TYR* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LYS* 3.8 28.0 - - + +
329C LEU* 4.4 3.6 - - + -
332C ALA* 3.5 27.1 - - + -
334C VAL* 4.1 10.3 - - + -
421C ALA* 2.9 32.0 + - + +
422C ASP* 3.8 12.8 - - - +
424C ILE* 1.3 75.4 - - - +
426C LYS* 1.3 63.9 + - - +
428C TYR* 3.2 10.2 + - + +
429C GLN* 3.0 45.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
373C GLU* 3.6 35.9 + - + +
422C ASP 3.0 19.1 + - - +
423C GLY* 3.5 7.9 - - - +
425C ILE* 1.3 79.3 - - - +
427C LEU* 1.3 73.9 + - - +
429C GLN* 3.3 14.7 + - - +
430C HIS* 3.2 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C PHE* 4.2 10.8 - - + -
366C LEU* 4.7 4.7 - - + -
369C SER* 3.8 44.2 - - - +
370C ILE* 3.9 21.1 - - + +
373C GLU* 4.2 27.1 - - + +
374C THR* 6.1 0.2 - - + -
423C GLY 3.0 21.0 + - - +
424C ILE* 3.7 8.1 - - - +
425C ILE 3.3 0.2 - - - -
426C LYS* 1.3 84.1 - - - +
428C TYR* 1.3 57.6 + - - +
430C HIS* 3.1 8.2 - - + +
431C LYS* 2.8 27.9 + - - -
434C ILE* 4.4 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ALA* 4.1 9.0 - - + -
333C GLY* 3.2 30.6 + - - -
334C VAL* 3.8 20.0 - - + -
335C PRO* 3.7 18.0 - - + +
351C ARG 4.5 4.1 + - - -
352C PHE* 3.6 30.5 - + + -
424C ILE 2.9 14.1 + - - +
425C ILE* 3.2 10.7 + - + +
427C LEU* 1.3 78.5 - - - +
429C GLN* 1.3 65.2 + - + +
430C HIS 3.1 1.5 + - - -
431C LYS* 3.4 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ALA* 5.7 2.2 + - - +
425C ILE* 3.0 35.3 + - - +
426C LYS* 3.6 17.3 - - - +
427C LEU 3.2 0.6 - - - -
428C TYR* 1.3 81.3 - - + +
430C HIS* 1.3 76.4 + - + +
431C LYS 3.6 0.2 - - - -
432C GLU* 3.5 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C LYS* 3.2 41.1 + - + +
427C LEU* 3.1 10.1 + - + +
428C TYR 3.1 0.2 - - - -
429C GLN* 1.3 93.7 + - + +
431C LYS* 1.3 58.5 + - - +
432C GLU* 3.1 14.1 - - - -
433C ASP* 2.8 45.0 + - + +
434C ILE* 4.1 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ARG 4.7 1.3 - - - +
352C PHE* 3.0 35.7 - - + +
354C PRO* 4.0 22.1 - - + +
355C HIS* 3.1 14.9 - - - -
427C LEU 2.8 10.6 + - - +
428C TYR* 3.4 45.1 - - + +
430C HIS* 1.3 77.7 - - - +
432C GLU* 1.3 72.8 + - + +
433C ASP 2.9 5.5 + - - -
434C ILE* 2.9 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C HIS* 3.7 29.5 - - + -
429C GLN 3.5 8.8 - - - +
430C HIS* 3.1 26.1 + - - +
431C LYS* 1.3 93.2 + - - +
433C ASP* 1.3 74.4 + - - +
434C ILE 3.3 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C HIS* 2.8 34.9 + - + +
432C GLU* 1.3 89.4 - - - +
434C ILE* 1.3 63.6 + - + +
435C ARG* 3.3 14.1 + - - +
----------------------------------------------------------
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