Contacts of the helix formed by residues 498 - 512 (chain A) in PDB entry 2DB3
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 498 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A VAL* 3.5 2.3 - - - +
497A GLU* 1.3 93.2 - - + +
499A LYS* 1.3 65.0 + - - +
500A ARG* 3.6 10.6 + - - +
501A GLY* 2.8 23.3 + - - -
502A ALA 3.0 18.2 + - - -
546A THR* 3.5 11.4 - - - +
565A ASP* 4.8 0.2 + - - -
316B LEU* 4.9 2.9 - - - +
2E U 3.9 16.4 - - - +
3E U 3.4 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A THR* 1.3 71.1 - - - +
500A ARG* 1.3 64.1 + - + +
502A ALA* 3.1 12.3 + - - +
503A ASP* 3.1 14.4 + - - +
520A HIS* 3.5 23.7 + - + -
521A GLY* 3.7 3.7 - - - -
522A ASP* 3.3 49.4 + - - +
546A THR* 3.6 9.4 - - + +
3E U 2.8 32.9 + - - +
4E U 3.4 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A THR* 3.3 9.0 + - - +
499A LYS* 1.3 79.7 - - + +
501A GLY* 1.3 57.7 + - - +
503A ASP* 3.4 0.8 + - - -
504A PHE* 2.9 31.0 + - - +
522A ASP* 4.8 9.9 - - - +
316B LEU* 3.8 34.8 + - + +
317B GLY* 4.2 3.2 - - - -
362B ASN* 4.2 13.8 + - - +
365B ILE* 6.0 1.4 - - - +
366B THR* 3.5 34.3 + - + +
386B THR 4.2 5.7 + - - -
387B PHE* 3.4 67.6 + - - +
3E U 4.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A VAL* 4.1 9.7 - - - +
498A THR* 2.8 21.2 + - - -
500A ARG* 1.3 77.6 - - - +
502A ALA* 1.3 61.0 + - - +
504A PHE* 3.8 3.1 - - - +
505A LEU* 3.0 26.7 + - - +
316B LEU* 4.0 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A VAL* 3.4 23.5 - - + +
498A THR 3.0 8.8 + - - +
499A LYS 3.1 7.6 + - - +
501A GLY* 1.3 75.4 - - - +
503A ASP* 1.3 58.2 + - - +
506A ALA* 2.9 31.8 + - - +
518A SER* 4.8 2.7 - - - -
520A HIS* 4.0 14.8 - - - +
544A ILE* 3.6 22.4 - - + +
545A ALA* 4.6 6.1 - - - -
546A THR* 4.3 8.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
499A LYS 3.1 11.8 + - - +
500A ARG* 3.9 1.3 - - - +
502A ALA* 1.3 78.0 - - - +
504A PHE* 1.3 61.4 + - - +
506A ALA* 3.8 5.9 - - - +
507A SER* 3.1 25.3 + - - -
518A SER* 3.9 7.5 + - - -
520A HIS* 2.8 29.6 + - + +
523A ARG* 4.3 6.6 + - - +
363B GLU* 5.3 2.1 - - - +
366B THR* 3.8 20.8 - - + +
367B ARG* 4.6 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ARG* 3.7 26.9 - - - -
500A ARG 2.9 17.4 + - - +
501A GLY* 3.8 5.8 - - - +
503A ASP* 1.3 77.2 - - - +
505A LEU* 1.3 69.4 + - + +
507A SER* 3.6 5.1 - - - -
508A PHE* 3.0 32.0 + + + +
314B LEU* 3.3 30.1 - - + -
315B GLU 3.8 3.1 - - - -
316B LEU* 3.6 42.2 - - + -
348B LYS* 5.8 0.7 - - - -
366B THR 3.4 25.7 + - - +
367B ARG 4.1 8.4 - - - +
368B GLY* 4.1 15.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
478A ARG* 4.5 11.9 - - + +
481A LEU* 3.7 33.2 - - + -
494A VAL* 4.1 7.6 - - + -
496A VAL* 3.8 25.6 - - + -
501A GLY 3.0 17.4 + - - +
502A ALA 4.0 2.5 - - - +
504A PHE* 1.3 80.2 - - + +
506A ALA* 1.3 61.6 + - - +
508A PHE* 3.3 12.0 + - + +
509A LEU* 2.9 52.1 + - + +
544A ILE* 4.2 8.3 - - + -
564A TYR* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA 2.9 18.7 + - - +
503A ASP* 3.8 4.7 - - - +
505A LEU* 1.3 76.7 - - - +
507A SER* 1.3 63.9 + - - +
509A LEU* 3.8 1.2 - - - +
510A SER* 3.0 26.8 + - - -
516A THR* 4.0 14.6 - - + +
517A THR* 4.3 4.9 - - - +
518A SER* 3.9 23.6 - - - +
544A ILE* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ASP* 3.1 18.1 + - - -
504A PHE 3.6 4.5 - - - -
506A ALA* 1.3 78.0 - - - +
508A PHE* 1.3 62.8 + - - +
510A SER* 3.1 18.8 + - - -
511A GLU* 3.1 18.3 + - - +
348B LYS* 4.2 7.7 + - - +
367B ARG* 3.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ARG* 3.1 41.3 - - + -
482A ILE* 3.4 24.7 - - + -
504A PHE* 3.0 25.8 + + + +
505A LEU* 3.5 11.7 - - + +
507A SER* 1.3 76.4 - - - +
509A LEU* 1.3 78.6 + - + +
511A GLU* 3.0 19.0 + - + +
512A LYS* 3.3 49.7 + - + +
313B GLU* 3.6 21.3 - - - -
314B LEU* 5.7 1.6 - - + -
348B LYS* 5.7 4.3 - - - +
367B ARG 5.6 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 4.2 4.7 - - + -
482A ILE* 3.9 23.8 - - + -
485A LEU* 3.8 30.7 - - + -
505A LEU* 2.9 34.5 + - + +
506A ALA 3.8 2.2 - - - +
508A PHE* 1.3 86.8 - - + +
510A SER* 1.3 58.4 + - - +
512A LYS* 2.8 27.9 + - - +
514A PHE* 3.5 18.0 + - + +
516A THR* 3.6 12.6 - - + +
542A VAL* 4.2 6.5 - - + -
544A ILE* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ALA 3.0 14.0 + - - -
507A SER* 3.1 16.6 + - - -
509A LEU* 1.3 76.5 - - - +
511A GLU* 1.3 61.0 + - - +
512A LYS 2.9 0.9 + - - -
513A GLU* 3.2 11.6 + - - -
514A PHE 3.3 18.5 + - - +
515A PRO* 5.6 0.2 - - - -
516A THR* 4.1 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A SER* 3.1 16.8 + - - +
508A PHE* 3.0 14.4 + - + +
510A SER* 1.3 77.8 + - - +
512A LYS* 1.3 63.1 + - + +
513A GLU* 3.4 3.9 + - - +
346B TYR* 3.7 35.1 - - - +
348B LYS* 3.3 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ILE* 4.6 13.7 - - + -
508A PHE* 3.3 49.5 + - + +
509A LEU* 2.8 13.2 + - - +
511A GLU* 1.3 82.9 - - + +
513A GLU* 1.3 73.0 + - - +
514A PHE* 3.4 19.0 - - + -
313B GLU* 3.8 14.1 + - - -
----------------------------------------------------------
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