Contacts of the helix formed by residues 455 - 478 (chain A) in PDB entry 3JCK
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 GLU 455 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A SER* 1.3 96.0 + - - +
456A ASP* 1.3 55.7 + - - +
457A PRO* 3.2 3.4 - - - -
458A GLN* 2.6 61.4 + - - +
459A GLN* 3.4 8.7 + - + +
262E GLN* 5.6 2.6 + - - -
266E THR* 4.4 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 6.0 0.2 - - - +
451A ILE* 3.7 32.5 - - + +
454A SER* 3.4 8.2 + - - -
455A GLU* 1.3 76.7 - - - +
457A PRO* 1.3 70.5 - - + +
458A GLN 3.0 0.5 + - - -
459A GLN* 3.1 22.4 + - - +
460A VAL* 3.0 30.0 + - + +
400D TYR* 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.9 14.4 - - + +
452A TYR* 3.6 11.0 - - + +
454A SER 3.3 8.7 - - - +
456A ASP* 1.3 92.3 - - + +
458A GLN* 1.3 60.2 + - - +
460A VAL* 4.4 0.2 - - + -
461A PHE* 2.9 36.5 + - + -
400D TYR* 3.2 39.7 - - + +
270E ASN* 3.2 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLU* 2.6 48.9 + - - +
457A PRO* 1.3 72.8 - - - +
459A GLN* 1.3 62.4 + - - +
461A PHE* 3.8 1.4 - - - +
462A ASP* 2.9 24.1 + - - +
266E THR* 4.8 7.9 + - - +
269E THR* 3.2 31.2 - - + +
270E ASN* 3.1 18.5 + - - +
273E LEU* 3.6 25.1 - - + +
259H ILE* 4.8 13.7 - - + +
262H LYS* 3.9 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLU* 3.4 6.9 + - + +
456A ASP* 3.1 26.4 + - - +
458A GLN* 1.3 75.3 - - - +
460A VAL* 1.3 66.6 + - + +
462A ASP* 3.0 6.5 + - - +
463A GLU* 3.0 30.7 + - + +
262H LYS* 3.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ASP* 3.0 21.2 + - + +
457A PRO 4.0 0.2 - - - +
459A GLN* 1.3 78.6 - - + +
461A PHE* 1.3 66.1 + - + +
462A ASP 3.0 1.0 + - - -
463A GLU* 3.1 12.3 + - - +
464A ARG* 3.0 54.8 + - + +
400D TYR* 3.7 21.5 - - - +
404D VAL* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A PRO* 2.9 34.4 + - + +
458A GLN 3.9 2.0 - - - +
460A VAL* 1.3 77.8 - - + +
462A ASP* 1.3 57.2 + - - +
464A ARG* 3.3 6.5 + - + +
465A ILE* 2.8 37.2 + - + +
409C TYR* 4.5 6.3 - - - -
400D TYR* 3.4 36.1 - + - -
403D LEU* 4.6 11.0 - - + -
404D VAL* 4.9 9.2 - - + -
270E ASN* 4.5 11.7 - - - -
273E LEU* 4.3 25.8 - - + +
274E MET* 4.0 23.6 - - + -
277E TYR* 3.6 41.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLN 2.9 14.9 + - - +
459A GLN* 3.0 13.0 + - - +
461A PHE* 1.3 77.5 - - - +
463A GLU* 1.3 67.8 + - - +
465A ILE* 2.9 4.5 + - - +
466A LYS* 2.9 52.7 + - - +
273E LEU* 5.5 0.9 - - + +
257H THR* 5.8 1.0 - - - +
262H LYS* 3.8 25.4 - - + +
266H TYR* 2.2 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLN* 3.0 20.9 + - + +
460A VAL* 3.6 10.0 - - - +
462A ASP* 1.3 80.7 - - - +
464A ARG* 1.3 82.7 + - - +
466A LYS* 3.3 7.1 + - - +
467A PHE* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A VAL* 3.0 31.7 + - + +
461A PHE* 3.6 8.3 - - + +
463A GLU* 1.3 100.9 + - - +
465A ILE* 1.3 62.8 + - - +
467A PHE* 3.5 9.7 + - - +
468A ALA* 2.9 21.3 + - - +
404D VAL* 3.7 20.4 - - + +
408D ASP* 2.7 43.8 + - - -
411D LEU* 4.5 11.4 - - + +
277E TYR* 3.4 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A PHE* 2.8 30.2 + - + +
462A ASP* 2.9 6.3 + - - +
464A ARG* 1.3 70.2 - - - +
466A LYS* 1.3 61.2 + - - +
468A ALA* 2.6 28.9 + - - +
469A ASN* 2.9 16.4 + - - +
273E LEU* 4.4 11.4 - - + +
276E ILE* 3.9 18.6 - - + -
277E TYR* 3.8 22.7 - - + -
280E ASN* 3.1 26.2 + - - +
266H TYR* 3.5 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ASP* 2.9 45.4 + - - +
463A GLU* 3.8 8.1 - - - +
465A ILE* 1.3 73.9 - - - +
467A PHE* 1.3 51.8 + - - +
469A ASN* 2.7 33.1 + - - +
470A GLN* 2.6 24.5 + - - +
257H THR* 5.5 8.5 - - - +
262H LYS* 5.9 1.9 - - - +
265H ASP* 4.8 17.2 + - - -
266H TYR* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLU 3.0 18.4 + - - +
464A ARG* 3.8 3.8 - - - +
466A LYS* 1.3 75.2 - - - +
468A ALA* 1.3 59.3 + - - +
470A GLN* 3.0 33.6 + - - +
471A LEU* 3.3 28.1 - - + +
411D LEU* 3.6 45.5 - - + -
412D THR* 5.3 0.7 - - - -
415D GLN* 3.0 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ARG 2.9 11.6 + - - +
465A ILE* 2.6 20.6 + - - +
467A PHE* 1.3 71.7 - - - +
469A ASN* 1.3 67.1 + - - +
471A LEU* 3.2 9.7 + - - +
472A HIS* 3.0 11.8 + - - +
411D LEU* 5.1 2.7 - - + -
277E TYR* 5.5 0.9 - - + +
280E ASN* 4.1 23.3 - - + -
281E LEU* 4.6 14.1 - - + -
284E SER* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ILE* 2.9 18.0 + - - +
466A LYS* 2.7 25.0 + - - +
468A ALA* 1.3 70.4 - - - +
470A GLN* 1.3 56.4 + - - +
472A HIS* 2.3 36.1 + - - +
473A ASP* 2.9 17.6 + - - +
280E ASN* 4.8 8.8 - - - +
283E ARG* 4.2 16.3 + - - +
265H ASP 5.8 0.2 - - - -
266H TYR* 4.8 6.5 - - - +
269H SER* 3.2 38.2 + - - +
270H ILE* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LYS* 2.6 30.0 - - - +
467A PHE* 3.0 43.6 + - - +
469A ASN* 1.3 75.5 - - - +
471A LEU* 1.3 61.0 + - + +
473A ASP* 3.8 18.6 - - + +
474A GLU* 2.9 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PHE* 3.3 40.2 - - + +
468A ALA* 3.2 10.7 + - - +
469A ASN 2.7 3.2 + - - -
470A GLN* 1.3 77.5 - - + +
472A HIS* 1.3 66.3 + - - +
474A GLU* 4.6 4.3 - - + -
475A TYR* 2.9 60.0 + - + +
411D LEU* 4.4 10.5 - - + +
414D LEU* 4.2 24.0 - - + -
415D GLN* 4.4 22.9 - - + +
284E SER* 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA 3.0 9.7 + - - +
469A ASN* 2.3 24.5 + - - +
471A LEU* 1.3 69.8 - - - +
473A ASP* 1.3 75.3 + - - +
475A TYR* 3.2 3.6 + - - +
476A LEU* 3.0 51.4 + - + +
283E ARG* 2.9 53.6 + - + +
284E SER* 4.2 10.4 + - - +
287E ALA* 3.2 25.5 - - + +
269H SER 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ASN* 2.9 13.9 + - - +
470A GLN* 3.6 25.6 + - + +
472A HIS* 1.3 81.0 - - - +
474A GLU* 1.3 60.9 + - - +
476A LEU* 2.5 30.4 + - - +
477A VAL* 2.9 19.5 + - + +
269H SER* 5.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLN* 2.9 34.2 + - + +
471A LEU* 3.8 7.2 - - + +
473A ASP* 1.3 74.7 - - - +
475A TYR* 1.3 66.5 + - + +
477A VAL* 2.7 31.5 + - - +
478A SER* 3.1 16.3 + - - -
422D ARG* 3.1 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A LEU* 2.9 53.9 + - + +
472A HIS 3.6 3.6 - - - +
474A GLU* 1.3 81.7 - - + +
476A LEU* 1.3 59.1 + - - +
479A MET* 3.0 26.3 - - - +
414D LEU* 3.5 19.7 + - + +
415D GLN* 4.0 1.9 + - - -
418D GLY* 3.4 28.3 - - - -
422D ARG* 4.3 13.2 - - + -
284E SER 4.0 7.9 - - - -
287E ALA* 4.0 13.9 - - + -
288E PHE* 3.7 36.6 - + + -
291E LEU* 3.3 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A HIS* 3.0 47.6 + - + +
473A ASP* 2.5 19.1 + - - +
475A TYR* 1.3 77.1 - - - +
477A VAL* 1.3 63.4 + - + +
478A SER 3.5 0.2 - - - -
479A MET* 3.3 28.2 + - + +
480A ARG* 4.1 4.0 + - - +
287E ALA* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASP* 2.9 19.6 + - + +
474A GLU* 2.7 29.7 + - - +
476A LEU* 1.3 71.1 - - + +
478A SER* 1.3 62.3 + - - +
479A MET 3.0 5.3 + - - -
480A ARG* 3.6 24.0 + - - +
422D ARG* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLU 3.1 5.9 + - - -
477A VAL* 1.3 75.1 - - - +
479A MET* 1.3 58.2 + - - +
480A ARG 3.2 0.9 - - - -
481A TYR* 3.1 35.5 + - - -
422D ARG* 2.5 46.8 + - - -
291E LEU* 3.9 20.4 - - - +
294E ASN* 4.5 0.9 + - - +
295E LYS* 4.2 12.1 + - - -
----------------------------------------------------------
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