Contacts of the helix formed by residues 483 - 508 (chain A) in PDB entry 2AR0
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 483 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A PRO* 1.3 85.0 - - - +
484A PRO* 1.3 75.3 - - - +
485A ASP* 3.1 24.5 - - - +
486A VAL* 2.9 24.0 + - + +
487A LEU* 2.5 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU 3.9 13.5 - - - +
45A THR 3.7 13.2 - - - +
46A GLY* 5.0 3.4 - - - +
47A GLN* 5.7 0.4 - - - +
117A TRP* 5.4 2.3 - - + -
483A GLU* 1.3 99.8 - - + +
485A ASP* 1.3 56.4 + - - +
486A VAL 2.9 2.1 + - - -
487A LEU* 3.8 5.7 - - + +
488A ALA* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.2 21.6 + - + +
47A GLN* 3.2 35.9 + - - +
51A TYR* 5.5 1.8 - - - +
483A GLU* 3.1 23.2 - - - +
484A PRO* 1.3 77.0 - - - +
486A VAL* 1.3 66.0 + - - +
488A ALA* 4.3 0.5 - - - +
489A ALA* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A PRO* 5.5 2.0 - - + -
483A GLU* 2.9 30.5 + - + +
484A PRO 2.9 0.8 - - - -
485A ASP* 1.3 90.3 - - - +
487A LEU* 1.3 67.6 + - + +
488A ALA 3.3 0.2 - - - -
489A ALA* 3.4 4.6 + - - +
490A GLU* 3.2 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 3.8 32.3 + - + +
482A PRO* 3.7 30.3 - - + -
483A GLU 2.5 29.7 + - - +
484A PRO* 3.8 3.8 - - + +
486A VAL* 1.3 72.7 - - + +
488A ALA* 1.3 61.1 + - - +
490A GLU* 2.9 28.9 - - - +
491A ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MSE 4.3 13.3 - - + +
44A GLU* 4.0 9.6 - - + +
45A THR* 3.6 36.3 - - - +
117A TRP* 4.6 8.2 - - + -
484A PRO 2.8 15.6 + - - +
485A ASP 4.3 0.4 - - - +
487A LEU* 1.3 78.6 - - - +
489A ALA* 1.3 55.2 + - - +
491A ALA* 3.2 7.1 + - - +
492A MSE 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 5.0 1.3 + - - +
485A ASP 3.3 19.7 + - - +
486A VAL* 3.6 6.5 - - - +
487A LEU 3.2 0.4 - - - -
488A ALA* 1.3 76.8 - - - +
490A GLU* 1.3 66.3 + - - +
492A MSE 3.3 8.6 + - - +
493A GLY* 3.2 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 5.8 2.1 - - - -
486A VAL* 3.2 19.7 + - - +
487A LEU* 2.9 46.9 - - - +
489A ALA* 1.3 76.6 - - - +
491A ALA* 1.3 63.5 + - - +
493A GLY* 3.1 11.5 + - - -
494A GLU* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MSE 4.7 4.3 - - - -
117A TRP* 4.1 38.7 - - + +
487A LEU 2.8 19.3 + - - +
488A ALA* 3.3 9.0 - - - +
490A GLU* 1.3 78.8 - - + +
492A MSE 1.3 62.3 + - - +
494A GLU* 3.0 17.8 + - - +
495A LEU* 3.0 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA 5.8 0.4 - - - +
37A LEU* 5.5 2.7 - - - -
38A PHE* 3.2 47.6 - - + +
41A MSE 4.0 24.7 - - + -
488A ALA 2.8 19.8 + - - +
489A ALA* 3.3 8.3 + - - +
491A ALA* 1.3 70.1 - - - +
493A GLY* 1.3 67.4 + - - +
495A LEU* 3.7 13.5 - - - +
496A VAL* 2.9 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ALA 3.2 6.8 + - - -
490A GLU* 3.1 9.9 + - - -
492A MSE 1.3 79.9 - - - +
494A GLU* 1.3 56.4 + - - +
496A VAL* 3.4 7.3 + - - +
497A GLN* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.7 14.6 - - + +
117A TRP* 5.8 5.1 - - - +
490A GLU* 3.2 21.3 + - - +
491A ALA* 3.0 16.3 + - - +
493A GLY* 1.3 74.8 - - - +
495A LEU* 1.3 55.5 + - - +
497A GLN* 2.9 9.9 + - - +
498A ALA* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.0 21.8 - - + -
12A LEU* 5.1 7.2 - - + -
37A LEU* 4.7 26.5 - - + -
41A MSE 3.8 43.1 - - + -
115A LEU* 5.2 8.7 - - + -
117A TRP* 3.7 22.7 - - + +
491A ALA* 3.0 17.1 + - + +
492A MSE 3.3 13.0 + - - +
494A GLU* 1.3 75.0 - - + +
496A VAL* 1.3 53.9 + - - +
498A ALA* 3.2 2.0 + - - +
499A LEU* 2.6 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A MSE 2.9 46.2 + - + +
493A GLY* 3.5 7.0 - - - +
495A LEU* 1.3 76.1 - - + +
497A GLN* 1.3 63.0 + - - +
499A LEU* 3.4 12.8 + - + +
500A SER* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLY 3.1 13.1 + - - +
494A GLU* 2.9 13.6 + - - +
496A VAL* 1.3 77.6 - - - +
498A ALA* 1.3 62.3 - - - +
500A SER* 3.3 10.8 + - - -
501A GLU* 3.0 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.4 35.0 - - + -
9A VAL* 4.1 20.0 - - + +
12A LEU* 3.6 17.0 - - + -
494A GLU 2.7 8.5 + - - -
495A LEU 3.5 5.4 - - - +
497A GLN* 1.3 74.6 - - - +
499A LEU* 1.3 56.7 + - - +
501A GLU* 3.3 7.5 + - - +
502A LEU* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 17.3 - - + -
30A VAL* 3.8 25.3 - - + +
33A LEU* 4.2 29.6 - - + -
34A ALA* 4.2 20.4 - - + -
37A LEU* 3.9 21.5 - - + -
492A MSE 6.4 1.1 - - - -
495A LEU* 2.6 32.2 + - + +
496A VAL* 3.6 12.6 - - + +
497A GLN 3.3 0.2 - - - -
498A ALA* 1.3 75.1 - - - +
500A SER* 1.3 57.0 + - - +
502A LEU* 3.4 8.3 + - + +
503A ASP* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A VAL* 3.0 20.1 + - - +
497A GLN* 3.5 14.1 - - - -
498A ALA 3.2 0.2 - - - -
499A LEU* 1.3 73.0 - - - +
501A GLU* 1.3 67.1 + - - +
503A ASP* 2.9 18.6 + - - +
504A ALA* 3.0 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN 4.7 3.6 + - - -
9A VAL* 3.7 22.3 - - + +
497A GLN* 3.0 49.8 + - - +
498A ALA* 3.6 5.6 - - - +
500A SER* 1.3 78.7 - - - +
502A LEU* 1.3 63.7 + - - +
504A ALA* 3.1 23.5 + - - +
505A LEU* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.1 14.3 - - + +
12A LEU* 3.7 33.2 - - + -
13A TRP* 4.1 21.5 - - + -
16A CYS* 4.4 5.6 - - - -
30A VAL* 4.5 8.7 - - + -
33A LEU* 4.0 20.2 - - + -
498A ALA 2.8 18.4 + - - +
499A LEU* 3.5 10.1 - - + +
501A GLU* 1.3 76.6 - - - +
503A ASP* 1.3 64.5 + - - +
505A LEU* 3.4 35.0 + - + +
506A MSE 3.7 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 5.3 4.8 - - - +
30A VAL* 3.5 36.0 - - + +
31A ASN* 4.6 5.9 + - - -
499A LEU 2.9 9.0 + - - +
500A SER* 2.9 13.3 + - - +
502A LEU* 1.3 74.1 - - - +
504A ALA* 1.3 53.8 + - - +
506A MSE 2.5 31.5 + - - +
507A ARG* 2.6 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A SER 3.0 10.1 + - - +
501A GLU* 3.2 13.9 - - - +
503A ASP* 1.3 75.5 - - - +
505A LEU* 1.3 58.0 + - + +
507A ARG* 4.1 15.7 - - - +
508A GLU* 2.6 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.2 9.6 - - + -
13A TRP* 3.2 41.7 - - + -
501A GLU 3.3 6.5 + - - +
502A LEU* 3.4 27.8 - - + +
503A ASP 3.2 0.8 + - - -
504A ALA* 1.3 76.1 - - + +
506A MSE 1.3 68.1 + - - +
508A GLU* 4.2 1.3 - - - -
509A LEU* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 4.7 20.4 - - + +
16A CYS* 4.9 2.2 - - - -
26A TYR* 2.9 44.0 - - + +
27A GLN* 5.1 4.3 - - - +
29A TYR* 3.2 35.4 - - + -
30A VAL* 5.9 2.0 - - + -
502A LEU* 3.8 29.8 - - + +
503A ASP* 2.5 21.5 + - - +
505A LEU* 1.3 84.1 - - - +
507A ARG* 1.3 60.1 + - - +
508A GLU 3.0 1.3 - - - -
509A LEU* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ASP* 2.6 30.9 + - - +
504A ALA* 3.9 11.7 - - - +
506A MSE 1.3 73.4 - - - +
508A GLU* 1.3 59.8 + - - +
509A LEU 3.3 2.5 + - - -
510A GLY* 5.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ALA* 2.6 31.0 + - + +
505A LEU* 4.2 2.7 - - - -
507A ARG* 1.3 77.9 - - + +
509A LEU* 1.3 54.6 + - - +
510A GLY 3.1 10.9 + - - -
----------------------------------------------------------
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