Contacts of the helix formed by residues 452 - 467 (chain C) in PDB entry 2J2M
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 HIS 452 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 3.3 48.5 + - - +
388B TYR* 4.2 11.5 + - - -
161C ASP* 2.9 35.1 + - - -
450C VAL* 3.3 8.3 - - - +
451C ARG* 1.3 89.2 - - + +
453C GLU* 1.3 64.6 + - - +
454C ASN* 3.1 4.4 + - + +
455C THR* 3.2 12.4 + - - +
456C VAL* 3.3 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C VAL 5.8 0.2 - - - -
451C ARG 4.1 2.0 + - - -
452C HIS* 1.3 72.9 - - - +
454C ASN* 1.3 62.7 + - + +
456C VAL* 3.4 11.3 + - - +
457C LEU* 2.9 40.3 + - + +
480C VAL* 5.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C HIS* 3.1 3.0 - - + +
453C GLU* 1.3 83.3 - - + +
455C THR* 1.3 63.8 + - - +
457C LEU* 3.5 16.6 + - - +
458C LEU* 3.1 36.5 + - - +
485C PHE 6.3 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 2.6 33.7 + - - +
164C TRP* 3.5 46.4 - - + +
165C ASP* 3.6 9.0 + - - +
168C THR* 3.4 12.1 + - + +
450C VAL* 3.8 9.6 - - + -
452C HIS* 3.2 9.9 + - - +
454C ASN* 1.3 77.3 - - - +
456C VAL* 1.3 63.6 + - - +
458C LEU* 3.1 8.0 + - - +
459C ALA* 3.0 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C LEU* 4.0 17.0 - - + +
450C VAL* 3.7 29.6 - - + +
452C HIS 3.3 12.7 + - - +
453C GLU* 3.5 12.1 - - - +
455C THR* 1.3 76.9 - - - +
457C LEU* 1.3 62.7 + - - +
459C ALA* 3.3 7.6 + - - +
460C ILE* 3.1 30.0 + - + +
478C LEU* 4.1 30.3 - - + -
480C VAL* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C GLU* 2.9 28.9 + - + +
454C ASN* 3.7 20.0 - - - +
456C VAL* 1.3 76.7 - - - +
458C LEU* 1.3 58.2 + - + +
460C ILE* 3.3 6.9 + - + +
461C CYS* 3.0 38.4 + - - -
480C VAL* 4.0 29.6 - - + -
481C ASP 4.6 3.8 - - - +
482C ILE* 4.2 22.9 - - + -
485C PHE* 4.5 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C THR* 3.7 21.1 - - - +
169C LEU* 3.8 27.6 - - + -
454C ASN* 3.1 29.9 + - - +
455C THR* 3.1 10.1 + - - +
457C LEU* 1.3 73.9 - - + +
459C ALA* 1.3 67.5 + - - +
461C CYS* 3.3 10.3 + - + +
462C ASN* 2.9 40.5 + - - +
465C ARG* 6.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TRP* 3.8 18.2 - - + -
168C THR* 3.5 10.6 - - + +
447C LEU* 3.7 30.3 - - + -
455C THR 3.0 11.3 + - - +
456C VAL 3.5 8.5 - - - +
458C LEU* 1.3 76.2 - - - +
460C ILE* 1.3 58.0 + - - +
462C ASN* 3.1 5.3 + - - +
463C PHE* 2.9 40.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C LEU* 5.2 1.1 - - + -
456C VAL* 3.1 21.7 + - + +
457C LEU* 3.5 10.1 - - - +
458C LEU 3.2 0.2 - - - -
459C ALA* 1.3 80.3 - - + +
461C CYS* 1.3 56.2 + - - +
463C PHE* 3.5 7.2 + - - +
464C TYR* 2.9 27.9 + - + +
471C GLY* 4.1 19.9 - - - +
474C LEU* 4.3 11.9 - - + -
475C SER* 4.1 16.2 - - - -
478C LEU* 3.8 30.3 - - + -
480C VAL* 4.3 17.7 - - + +
482C ILE* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LEU* 3.0 23.6 + - - +
458C LEU* 3.3 16.4 + - + +
460C ILE* 1.3 73.6 - - - +
462C ASN* 1.3 63.4 + - - +
464C TYR* 3.2 7.6 + - - +
465C ARG* 2.8 48.4 + - - +
482C ILE* 5.0 13.0 - - - -
485C PHE* 5.6 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C MET 4.9 0.8 + - - -
168C THR* 3.6 30.1 + - - +
171C PRO* 4.2 9.7 - - - +
174C THR* 3.8 20.7 + - + +
421C PHE* 3.4 36.6 - - + -
458C LEU* 2.9 33.3 + - - +
459C ALA* 3.5 6.5 - - - +
461C CYS* 1.3 76.2 - - - +
463C PHE* 1.3 68.1 + - + +
465C ARG* 3.4 5.9 + - - -
466C ALA* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TRP* 3.7 31.2 - + - -
174C THR* 4.1 12.3 - - + -
177C LEU* 3.9 23.8 - - + -
178C MET* 3.7 29.3 - - + +
443C LEU* 3.5 31.9 - - + -
447C LEU* 4.8 2.2 - - + -
459C ALA* 2.9 31.8 + - + +
460C ILE 3.9 1.8 - - - +
462C ASN* 1.3 77.0 - - + +
464C TYR* 1.3 52.5 + - - +
466C ALA* 3.2 6.5 + - - +
467C ASP* 2.8 36.2 + - - +
470C LEU* 4.2 12.1 - - + +
471C GLY* 4.5 1.6 - - - -
474C LEU* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C ILE* 2.9 21.2 + - + +
461C CYS* 3.3 10.3 - - - +
462C ASN 3.1 0.2 - - - -
463C PHE* 1.3 73.6 - - - +
465C ARG* 1.3 71.4 + - + +
466C ALA 3.9 0.2 - - - -
467C ASP 3.2 21.6 - - - -
468C ALA* 3.2 42.7 + - + +
471C GLY* 3.9 11.4 - - - -
472C GLU* 4.1 16.1 + - - -
482C ILE* 3.8 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C PHE* 3.8 53.4 - - + +
422C GLY* 5.8 0.3 - - - -
458C LEU* 6.1 3.2 - - - +
461C CYS* 2.8 35.6 + - - +
462C ASN* 3.4 5.9 + - - +
464C TYR* 1.3 78.9 - - + +
466C ALA* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C THR* 4.4 1.6 - - + -
178C MET* 3.8 24.2 - - + -
421C PHE* 3.3 26.2 - - + +
422C GLY* 5.1 1.0 - - - +
424C ALA* 4.0 5.6 - - + -
425C GLY* 3.3 10.6 - - - +
429C ARG* 3.2 18.2 + - - -
462C ASN 3.2 11.8 + - - +
463C PHE* 3.2 9.1 + - - +
464C TYR 3.1 0.6 - - - -
465C ARG* 1.3 79.8 - - - +
467C ASP* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLY* 4.7 3.1 - - - -
428C TYR* 3.3 29.0 - - + -
429C ARG* 3.1 38.1 + - - +
463C PHE 2.8 14.9 + - - +
464C TYR 3.2 4.1 - - - +
466C ALA* 1.3 75.6 - - + +
468C ALA* 1.3 66.4 + - - +
469C SER* 2.7 32.4 + - - -
470C LEU* 2.9 18.1 + - + +
471C GLY 3.0 18.4 + - - -
----------------------------------------------------------
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