Contacts of the helix formed by residues 456 - 476 (chain A) in PDB entry 4E1O
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 456 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 4.3 5.3 + - - +
380A HIS* 4.6 2.7 - - + +
384A MET* 3.7 8.3 - - - -
454A PHE 3.5 15.5 - - - +
455A THR* 1.3 75.6 - - - +
457A ARG* 1.3 64.1 + - - +
458A ASP* 3.2 22.6 + - - +
459A ASP* 3.0 29.5 + - - +
460A ILE* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLU* 4.9 14.5 + - - +
384A MET* 3.6 31.6 - - + +
387A TYR* 3.4 57.9 - - + +
456A THR* 1.3 73.4 - - - +
458A ASP* 1.3 65.4 + - - +
460A ILE* 3.3 1.0 + - - -
461A LEU* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A THR* 3.2 11.7 + - - +
457A ARG* 1.3 81.1 - - - +
459A ASP* 1.3 58.6 + - - +
461A LEU* 3.5 5.5 + - - +
462A ARG* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.8 50.4 + - - -
75A PRO* 3.7 10.1 - - + +
76A HIS* 3.9 17.7 - - + +
455A THR* 3.5 13.7 - - + -
456A THR* 3.0 29.2 + - - +
458A ASP* 1.3 80.1 - - - +
460A ILE* 1.3 62.3 + - - +
462A ARG* 3.4 3.0 + - - +
463A ASP* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 4.7 3.8 - - + -
384A MET* 3.9 23.3 - - + +
387A TYR* 3.6 25.4 - - + -
388A PHE* 3.7 32.2 - - + +
391A LEU* 4.2 3.1 - - + -
448A PHE* 3.9 25.1 - - + -
450A VAL* 4.1 9.2 - - + -
455A THR* 3.8 20.0 - - + -
456A THR 3.1 13.9 + - - +
457A ARG 3.3 6.0 + - - +
459A ASP* 1.3 77.9 - - - +
461A LEU* 1.3 56.5 + - - +
463A ASP* 3.3 5.2 + - - +
464A TRP* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR* 3.7 20.6 - - - +
391A LEU* 4.0 24.2 - - + -
457A ARG 3.0 16.7 + - - +
458A ASP* 4.0 4.9 - - - +
460A ILE* 1.3 73.5 - - - +
462A ARG* 1.3 59.4 + - - +
464A TRP* 4.3 10.3 - - + -
465A ASN* 2.8 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG 4.6 6.9 + - - -
28A ARG 5.8 1.0 + - - -
76A HIS* 3.2 31.4 + - + -
432A ARG* 2.9 57.0 + - - +
458A ASP 3.0 18.9 + - - +
459A ASP* 3.6 7.0 - - - +
461A LEU* 1.3 78.3 - - - +
463A ASP* 1.3 83.0 + - - +
465A ASN* 3.4 7.5 + - - +
466A LEU* 3.1 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO 3.9 1.2 - - - +
76A HIS* 2.9 21.2 + - - -
78A HIS* 2.7 36.0 + - - +
433A LEU* 3.7 19.7 - - + +
448A PHE* 4.2 7.4 - - + -
459A ASP 3.0 16.0 + - - +
460A ILE 3.8 3.1 - - - +
462A ARG* 1.3 104.0 + - - +
464A TRP* 1.3 64.2 + - - +
466A LEU* 3.3 6.3 + - - +
467A ILE* 3.1 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.9 23.4 - + + -
391A LEU* 3.8 53.4 + - + +
392A VAL* 3.5 26.5 - - + -
395A ASP* 3.6 20.8 + - + -
398A PHE* 3.6 33.4 - + - -
411A PHE* 4.6 1.3 - + - -
460A ILE 2.9 17.5 + - - +
461A LEU* 3.7 9.2 - - + +
463A ASP* 1.3 74.2 - - - +
465A ASN* 1.3 70.9 + - - +
467A ILE* 3.1 26.9 + - + +
468A ARG* 2.8 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 2.8 43.7 + - - +
462A ARG* 3.7 7.4 - - - +
463A ASP 3.3 0.2 - - - -
464A TRP* 1.3 86.7 + - - +
466A LEU* 1.3 57.8 + - - +
468A ARG* 3.8 6.8 - - - +
469A ASP* 2.9 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 4.6 4.5 - - + +
432A ARG* 3.9 36.1 - - + +
433A LEU* 3.7 24.2 - - + -
462A ARG* 3.1 50.3 + - + +
463A ASP* 3.6 7.0 - - - +
464A TRP 3.2 0.2 - - - -
465A ASN* 1.3 73.7 - - + +
467A ILE* 1.3 64.1 + - - +
469A ASP* 3.4 14.6 + - + +
470A ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.9 31.6 - - + -
398A PHE* 4.4 7.0 - - + -
411A PHE* 3.9 30.5 - - + -
423A VAL* 4.5 7.1 - - + +
427A ILE* 4.0 26.5 - - + -
433A LEU* 4.0 17.9 - - + -
435A LEU* 4.1 7.0 - - + -
446A ILE* 5.5 0.4 - - + -
448A PHE* 4.2 4.9 - - + -
463A ASP 3.1 16.5 + - - +
464A TRP* 3.1 16.8 + - + +
466A LEU* 1.3 76.1 - - - +
468A ARG* 1.3 59.2 + - - +
470A ALA* 3.2 4.9 + - - +
471A ALA* 2.9 26.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
395A ASP* 2.8 35.8 + - - +
396A PRO* 5.7 0.4 - - - +
397A SER* 2.8 28.8 + - - -
398A PHE* 3.8 12.1 - - - -
464A TRP* 2.8 38.5 + - + +
465A ASN* 3.8 9.4 - - - +
467A ILE* 1.3 73.3 - - - +
469A ASP* 1.3 60.6 + - - +
471A ALA* 3.2 4.6 + - - +
472A THR* 2.8 61.3 + - - +
475A LEU* 4.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ASN* 2.9 30.7 + - - +
466A LEU* 3.6 18.0 - - + +
467A ILE 3.3 0.2 - - - -
468A ARG* 1.3 74.4 - - - +
470A ALA* 1.3 62.6 + - - +
472A THR* 3.4 8.0 + - - -
473A LEU* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A VAL* 4.1 12.3 - - + +
426A GLU* 3.7 28.0 - - + -
427A ILE* 3.8 19.7 - - + -
466A LEU 3.0 14.0 + - - +
467A ILE 3.2 8.3 + - - +
469A ASP* 1.3 76.3 - - - +
471A ALA* 1.3 57.6 + - - +
473A LEU* 3.3 3.5 + - - +
474A ILE* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PHE* 3.5 31.9 - - + -
413A LEU* 4.1 15.3 - - + -
423A VAL* 3.8 14.5 - - + +
467A ILE 2.9 10.1 + - - +
468A ARG* 3.2 17.0 + - - +
470A ALA* 1.3 76.8 - - - +
472A THR* 1.3 57.1 + - - +
474A ILE* 3.4 0.5 + - - +
475A LEU* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ARG* 2.8 43.5 + - - +
469A ASP* 3.6 8.2 - - - -
471A ALA* 1.3 76.7 - - - +
473A LEU* 1.3 63.1 + - - +
475A LEU* 3.6 4.1 + - - +
476A SER* 3.3 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLU* 3.4 38.4 - - + +
429A LYS* 5.9 0.2 - - - +
469A ASP 3.1 13.3 + - - +
470A ALA* 3.3 8.3 + - - +
472A THR* 1.3 76.4 - - - +
474A ILE* 1.3 65.3 + - + +
476A SER* 2.6 30.5 + - - +
477A GLN* 3.4 32.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
413A LEU* 4.4 3.6 - - + -
419A LEU* 3.7 44.6 - - + +
422A ASN* 3.7 43.3 - - + +
423A VAL* 3.8 8.7 - - + +
426A GLU* 3.9 15.9 - - + -
470A ALA 3.0 22.1 + - - +
471A ALA 3.9 2.5 - - - +
473A LEU* 1.3 87.1 - - + +
475A LEU* 1.3 63.1 + - - +
477A GLN* 3.1 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 3.9 28.5 - - - +
413A LEU* 4.2 19.5 - - + -
414A LYS 5.3 2.0 - - - +
419A LEU* 4.1 29.4 - - + -
468A ARG* 4.0 13.2 - - - +
471A ALA 2.9 21.5 + - - +
472A THR* 4.1 4.5 - - - +
474A ILE* 1.3 74.6 - - - +
476A SER* 1.3 59.6 + - - +
477A GLN* 3.3 4.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
472A THR* 3.3 12.4 + - - -
473A LEU* 2.6 29.9 + - - +
475A LEU* 1.3 76.7 - - - +
477A GLN* 1.3 62.5 - - - +
----------------------------------------------------------
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