Contacts of the helix formed by residues 463 - 485 (chain A) in PDB entry 2I6W
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 THR 463 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLY 3.0 1.2 - - - -
462A SER* 1.3 79.0 + - - +
464A GLY* 1.3 53.1 + - - +
465A ALA 2.6 6.1 - - - -
466A ILE* 2.5 32.4 + - + +
467A TYR* 3.0 37.1 + - + -
563A PHE* 3.8 18.0 - - + -
867A ARG* 3.4 19.9 + - - -
868A LEU* 3.1 39.0 - - + +
872A GLN* 4.9 0.9 - - - -
925A VAL* 4.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PHE 4.6 0.7 - - - -
459A PHE* 3.2 37.6 + - - -
460A GLY 4.0 4.1 + - - -
461A GLY 3.1 5.9 + - - -
463A THR* 1.3 77.6 - - - +
465A ALA* 1.3 51.8 + - - +
466A ILE 2.8 1.1 - - - -
467A TYR* 3.7 13.8 - - - -
468A ARG* 2.7 41.2 + - - +
872A GLN* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.4 10.4 - - - +
37A THR 4.2 3.4 - - - +
38A ILE* 3.5 30.7 - - + +
459A PHE* 4.4 0.4 + - - -
461A GLY 3.8 4.2 + - - +
462A SER* 3.0 24.9 - - - +
464A GLY* 1.3 77.0 - - - +
466A ILE* 1.3 59.3 + - + +
468A ARG* 4.5 8.6 - - - +
469A GLN* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 5.4 1.6 - - + -
38A ILE* 4.9 1.3 - - + -
393A LEU* 3.2 45.5 - - + -
462A SER 3.8 1.1 - - - +
463A THR* 2.5 28.4 + - + +
465A ALA* 1.3 89.6 - - + +
467A TYR* 1.3 55.1 + - - +
468A ARG 2.9 1.6 - - - -
469A GLN* 2.7 7.5 + - - +
470A PHE* 2.6 36.0 + - + +
563A PHE* 3.5 34.5 - - + -
564A LEU* 5.0 7.2 - - + -
671A ILE* 5.5 2.0 - - + -
674A LEU* 4.6 5.4 - - + -
925A VAL* 4.0 23.8 - - + -
926A TYR* 6.2 2.2 - - + -
929A VAL* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A MET* 3.8 43.1 - - + +
458A PHE 5.2 0.4 - - - +
463A THR* 3.0 43.9 + - + -
464A GLY* 4.1 7.2 - - - -
466A ILE* 1.3 76.4 - - - +
468A ARG* 1.3 56.9 + - - +
470A PHE* 3.4 20.2 - + - -
471A SER* 2.5 37.9 + - - -
868A LEU* 3.8 15.5 - - + +
872A GLN* 4.0 24.0 - - - -
873A ALA* 5.8 2.1 - - + +
925A VAL* 3.8 20.9 - - + -
928A GLN* 3.1 44.8 + - + +
929A VAL* 4.8 1.8 - - + -
932A LEU* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 5.9 1.4 + - - -
388A PHE* 3.4 34.8 - - + -
457A ALA* 4.7 13.6 - - + +
459A PHE* 3.0 59.2 - - + +
464A GLY* 2.7 23.2 + - - +
465A ALA* 4.6 6.8 - - - +
467A TYR* 1.3 75.8 - - - +
469A GLN* 1.3 57.2 + - - +
470A PHE 2.4 16.5 + - - -
472A ILE* 2.7 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.6 31.0 - - + +
388A PHE* 3.4 40.8 - - - +
389A SER 4.2 2.4 - - - +
391A ASN* 3.7 13.6 + - - +
393A LEU* 3.6 17.9 - - + +
394A THR* 3.5 39.9 + - - +
465A ALA 3.2 20.2 - - - +
466A ILE* 2.7 12.8 + - - +
468A ARG* 1.3 77.5 - - + +
470A PHE* 1.3 51.2 + - - +
472A ILE* 3.7 4.0 - - - -
473A THR* 2.6 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 5.3 4.0 - - + -
397A GLY* 5.0 4.0 - - - -
400A LEU* 5.1 1.1 - - + -
453A PHE* 3.3 38.8 - + - -
456A MET* 4.9 2.5 - - + -
466A ILE* 2.6 18.2 + - + +
467A TYR* 3.2 26.9 - + - +
468A ARG 2.4 8.1 + - - -
469A GLN* 1.3 70.3 - - - +
471A SER* 1.3 66.8 - - - +
472A ILE* 2.2 23.4 + - - +
473A THR* 2.7 20.6 + - - -
474A ILE* 3.4 20.9 - - + +
929A VAL* 3.1 44.9 - - + -
932A LEU* 3.5 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 2.2 36.1 + - - +
454A VAL* 3.1 3.5 + - - -
456A MET* 3.8 7.6 - - - -
457A ALA* 2.9 31.1 + - - -
467A TYR 2.5 17.5 + - - -
468A ARG 4.6 0.2 - - - -
470A PHE* 1.3 84.7 - - - +
472A ILE* 1.3 57.4 + - - +
474A ILE* 4.5 2.2 - - - -
475A VAL* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 4.6 3.1 - - + -
386A PHE* 4.7 16.2 - - + -
388A PHE* 3.3 46.4 - - + -
394A THR* 5.1 0.2 - - + -
457A ALA* 4.7 13.7 - - + -
468A ARG* 2.7 26.2 - - + +
469A GLN* 3.5 6.3 - - - +
470A PHE 2.2 13.9 + - - -
471A SER* 1.3 67.0 - - - +
473A THR* 1.3 84.7 + - - +
474A ILE 2.4 19.6 + - - -
475A VAL* 2.6 19.0 + - + +
476A SER* 2.9 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 3.7 3.0 - - + +
383A LEU* 4.7 13.6 - - + +
394A THR* 3.5 33.1 + - + +
397A GLY* 4.9 1.9 - - - +
398A MET* 4.2 26.2 - - - +
469A GLN 2.6 27.9 + - - -
470A PHE* 2.7 5.9 + - - -
472A ILE* 1.3 85.3 - - - +
474A ILE* 1.3 63.8 + - - +
476A SER* 2.8 19.2 + - - -
477A ALA* 3.0 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLY* 3.6 32.5 - - - +
400A LEU* 5.6 2.5 - - + -
401A ALA* 3.9 10.4 - - + +
404A LEU* 4.2 11.4 - - + -
449A LEU* 4.5 3.4 - - + -
453A PHE* 3.2 54.7 - - + -
470A PHE* 3.4 32.3 - - + +
471A SER 4.6 1.1 - - - +
472A ILE 2.4 8.5 + - - -
473A THR* 1.3 82.1 - - - +
475A VAL* 1.3 55.8 + - - +
476A SER 3.1 1.6 - - - -
477A ALA* 3.2 5.3 + - - +
478A MET* 2.5 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A SER* 3.9 4.0 - - - -
453A PHE* 3.5 18.4 - - + -
454A VAL* 3.3 38.6 - - + -
471A SER 2.8 27.8 - - - +
472A ILE* 2.6 12.4 + - + +
474A ILE* 1.3 73.0 - - - +
476A SER* 1.3 51.9 + - - +
478A MET* 3.2 31.3 - - + +
479A ALA* 2.8 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 3.3 9.4 + - - +
382A VAL* 4.0 31.6 - - - -
383A LEU* 5.6 2.3 - - - +
472A ILE* 2.9 11.1 + - - -
473A THR* 2.8 22.5 + - - -
475A VAL* 1.3 73.1 - - - +
477A ALA* 1.3 68.4 + - - -
478A MET 2.6 14.7 + - - -
479A ALA* 2.7 19.2 + - - +
480A LEU* 2.9 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.2 12.2 - - + +
376A LEU* 5.9 2.2 - - + -
379A THR* 3.4 13.7 - - + +
397A GLY 5.5 0.4 - - - +
398A MET* 5.7 3.6 - - - +
401A ALA* 4.5 14.6 - - + -
405A LEU* 3.2 16.6 - - + +
473A THR 3.0 19.5 - - - +
474A ILE* 3.2 6.7 + - - +
476A SER* 1.3 79.2 + - - +
478A MET* 1.3 56.2 + - - +
480A LEU* 3.1 15.0 - - - +
481A SER 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ALA* 5.9 0.2 - - - +
404A LEU* 5.6 8.7 - - + +
405A LEU* 4.9 1.1 - - - -
408A ASP* 6.0 0.4 - - - +
445A ILE* 5.9 1.1 - - + -
446A ALA* 3.2 37.9 - - + +
449A LEU* 2.9 37.7 - - + -
450A SER* 4.0 5.2 - - - -
474A ILE* 2.5 21.1 + - + +
475A VAL* 3.2 40.8 - - + +
476A SER 2.6 3.2 + - - -
477A ALA* 1.3 68.5 - - - +
479A ALA* 1.3 67.7 + - + +
480A LEU 3.0 1.6 - - - -
481A SER* 2.3 30.7 + - - +
482A VAL* 2.5 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A VAL* 2.8 16.1 + - + +
476A SER* 2.7 10.0 + - - +
478A MET* 1.3 83.7 - - + +
480A LEU* 1.3 53.6 + - + +
482A VAL* 2.9 8.7 + - - +
483A LEU* 2.6 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.1 11.2 - - + -
375A VAL* 3.4 12.8 - - + +
378A GLY* 3.2 29.8 - - - +
379A THR* 3.3 30.5 - - + +
382A VAL* 3.7 16.6 - - + -
476A SER 2.9 9.1 + - - +
477A ALA* 3.1 33.0 - - - +
479A ALA* 1.3 78.6 - - + +
481A SER* 1.3 52.6 + - - +
483A LEU* 3.4 5.0 - - - +
484A VAL* 2.5 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.3 9.8 - - - +
404A LEU 3.9 9.4 + - - -
405A LEU* 3.2 40.4 - - - +
408A ASP* 3.9 7.9 + - - -
477A ALA 3.0 1.4 + - - -
478A MET* 2.3 33.2 + - - +
480A LEU* 1.3 77.3 - - - +
482A VAL* 1.3 48.9 + - - +
484A VAL* 3.7 6.2 - - - +
485A ALA* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP* 4.9 6.1 - - - +
442A LEU* 4.0 17.0 - - + +
443A VAL* 4.9 6.7 - - + -
445A ILE* 4.7 5.6 - - + -
446A ALA* 3.1 37.0 - - + -
478A MET* 2.5 29.9 + - + +
479A ALA* 3.4 9.9 - - - +
481A SER* 1.3 73.3 + - - +
483A LEU* 1.3 61.6 + - - +
485A ALA* 3.5 5.9 + - - +
486A LEU* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.6 14.1 - - + -
15A ILE* 5.6 6.3 - - + -
479A ALA 2.6 15.8 + - - +
480A LEU* 3.4 8.3 - - - +
482A VAL* 1.3 69.1 - - - +
484A VAL* 1.3 63.0 + - - +
486A LEU* 2.6 44.3 + - + +
487A ILE* 3.0 35.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.4 11.2 - - + -
371A ALA* 4.4 10.5 - - + +
374A VAL* 4.4 9.2 - - + -
375A VAL* 3.5 34.3 - - + -
480A LEU* 2.5 39.6 + - + +
481A SER 3.7 3.6 - - - +
483A LEU* 1.3 74.5 - - + +
485A ALA* 1.3 56.5 + - - +
486A LEU 2.8 2.1 + - - -
487A ILE* 2.2 34.5 - - - +
488A LEU* 4.3 21.5 - - + -
489A THR* 3.7 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP* 3.9 33.0 - - + +
409A ALA* 5.2 0.9 - - - +
412A VAL* 4.4 9.4 - - + +
435A MET* 5.5 0.2 - - - +
442A LEU* 5.1 9.0 - - + +
481A SER 2.6 24.8 + - - +
482A VAL* 3.5 6.7 - - - +
484A VAL* 1.3 72.8 - - - +
486A LEU* 1.3 56.1 + - - +
489A THR* 3.7 17.0 - - + +
490A PRO* 3.0 21.4 - - - +
----------------------------------------------------------
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