Contacts of the helix formed by residues 425 - 435 (chain C) in PDB entry 2JGN
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 425 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C VAL* 3.8 10.5 - - + -
422C GLU* 3.0 29.5 + - - +
424C SER* 1.3 84.9 + - - +
426C LYS* 1.3 58.8 + - - +
427C ARG 3.2 3.0 + - - -
428C SER* 3.3 11.1 + - - +
429C PHE* 2.8 35.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
421C VAL* 3.6 19.1 - - + -
422C GLU 3.4 11.6 + - - +
423C GLU* 2.9 45.3 + - - +
425C ASP* 1.3 78.9 - - - +
427C ARG* 1.3 58.8 + - + +
429C PHE* 3.4 1.8 - - - +
430C LEU* 2.8 30.1 + - - +
515C PHE* 2.9 55.6 + - + +
516C ASP* 3.1 15.8 + - - +
517C LEU 5.1 0.2 - - - +
543C PHE* 3.8 22.5 + - + -
545C ASN* 3.6 16.4 - - - +
547C ARG* 6.2 0.2 - - - +
548C ASN* 5.0 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLU 4.9 2.1 + - - +
424C SER 5.2 2.2 + - - +
425C ASP 3.2 0.8 - - - -
426C LYS* 1.3 78.6 - - + +
428C SER* 1.3 61.8 + - - +
430C LEU* 3.3 4.3 + - - +
431C LEU* 3.2 25.8 + - - +
452C GLY 5.3 0.6 + - - -
455C SER* 2.6 44.1 + - - -
456C LEU* 3.9 10.4 - - + +
459C PHE* 3.9 54.2 - - + +
515C PHE* 4.0 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C SER 5.6 1.3 + - - -
425C ASP* 3.3 13.1 + - - -
427C ARG* 1.3 74.0 - - - +
429C PHE* 1.3 66.3 + - - +
431C LEU* 3.3 14.0 + - - +
432C ASP* 3.0 33.7 + - - +
459C PHE* 5.0 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASN* 4.6 11.9 - - - -
534A VAL* 3.4 38.3 - - + +
535A GLY* 3.7 19.1 - - - -
419C VAL* 3.7 27.6 - - + -
420C TRP 4.6 1.1 - - - -
421C VAL* 3.8 27.4 - - + -
425C ASP* 2.8 24.3 + - + +
426C LYS* 3.4 9.0 - - - +
428C SER* 1.3 73.5 - - - +
430C LEU* 1.3 62.2 + - - +
432C ASP* 3.1 4.7 + - - -
433C LEU* 3.0 24.7 + - + +
543C PHE* 3.5 23.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C LYS 2.8 21.0 + - - +
427C ARG 3.4 6.3 - - - +
428C SER 3.3 0.2 - - - -
429C PHE* 1.3 73.0 - - - +
431C LEU* 1.3 54.1 + - - +
433C LEU* 3.2 4.9 + - + +
434C LEU* 2.8 53.7 + - + +
445C VAL* 4.5 8.3 - - + -
456C LEU* 3.8 35.0 - - + -
459C PHE* 5.4 0.7 - - + -
460C LEU* 4.0 19.5 - - + -
513C ILE* 3.7 40.2 - - + -
515C PHE* 3.8 15.0 - - + -
543C PHE* 4.1 6.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ARG 3.2 13.9 + - - +
428C SER* 3.5 14.6 - - - +
429C PHE 3.2 0.4 - - - -
430C LEU* 1.3 75.5 - - - +
432C ASP* 1.3 66.0 + - - +
434C LEU* 3.8 3.9 - - - +
435C ASN* 2.8 43.1 + - - +
459C PHE* 3.5 33.4 - - + -
460C LEU* 4.1 9.9 - - + -
463C GLU* 3.9 28.7 - - + +
465C TYR* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 4.1 25.6 - - + +
428C SER* 3.0 27.0 + - - +
429C PHE* 3.1 4.6 + - - +
431C LEU* 1.3 79.8 - - - +
433C LEU* 1.3 63.4 + - - +
435C ASN* 3.2 27.7 + - - +
437C THR 4.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.9 13.1 - - + +
535A GLY* 3.9 25.6 - - - -
429C PHE* 3.0 11.4 + - + +
430C LEU* 3.3 8.5 - - - +
432C ASP* 1.3 75.2 - - - +
434C LEU* 1.3 59.1 + - - +
437C THR* 2.7 52.3 + - - +
511C HIS* 4.0 12.3 - - + -
513C ILE* 4.0 18.8 - - + -
541C THR* 3.9 16.8 - - + +
543C PHE* 3.7 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 2.8 41.4 + - + +
431C LEU* 3.9 2.9 - - - +
433C LEU* 1.3 70.3 - - - +
435C ASN* 1.3 65.7 + - - +
437C THR* 5.0 1.8 - - - -
438C GLY* 3.6 16.8 + - - -
443C THR* 4.2 26.7 - - + +
460C LEU* 3.7 30.3 - - + -
465C TYR* 3.6 30.5 + - + +
493C ILE* 3.8 30.7 - - + -
511C HIS* 6.1 0.2 - - - +
513C ILE* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 2.8 34.5 + - - +
432C ASP* 3.2 22.9 + - - +
434C LEU* 1.3 82.2 - - - +
437C THR 3.8 5.8 + - - -
438C GLY* 3.7 21.6 + - - -
465C TYR* 2.2 29.9 + - - -
----------------------------------------------------------
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