Contacts of the helix formed by residues 469 - 488 (chain A) in PDB entry 5E3H
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 ASP 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ILE 3.3 7.1 + - - +
468A SER* 1.3 71.5 + - - +
470A LYS* 1.3 54.8 + - - +
471A PHE 3.4 2.0 - - - -
472A LYS* 3.7 21.0 - - - +
473A TYR* 2.8 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER* 3.3 16.5 + - - +
469A ASP* 1.3 79.1 - - - +
471A PHE* 1.3 62.2 + - - +
473A TYR* 3.5 13.4 - - - +
474A ILE* 3.8 7.1 + - - +
560A MET* 5.2 0.4 - - + -
597A LEU* 5.3 0.7 - - - +
600A VAL* 4.1 25.2 - - + +
606A ASN* 4.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER 4.9 0.8 + - - +
469A ASP 3.4 0.4 - - - -
470A LYS* 1.3 76.9 - - - +
472A LYS* 1.3 67.5 + - - +
473A TYR 3.1 5.3 + - - -
474A ILE* 3.4 4.9 + - - +
475A ILE* 3.4 43.6 - - + +
551A ALA* 4.4 7.4 - - + -
552A LEU* 5.4 2.5 - - + -
555A SER* 4.2 18.2 - - - -
560A MET* 3.6 65.9 - - + +
563A ALA* 4.1 20.0 - - + -
564A LEU* 4.1 20.2 - - + -
567A LEU* 5.6 3.1 - - + -
597A LEU* 4.3 24.8 - - + +
600A VAL* 4.2 12.5 - - + +
601A SER* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER 5.5 1.5 + - - +
469A ASP* 3.5 19.1 + - - +
471A PHE* 1.3 81.5 - - + +
473A TYR* 1.3 56.7 + - - +
475A ILE* 4.0 0.8 - - - +
476A ALA* 2.9 32.6 + - - +
552A LEU* 4.1 27.1 - - + +
555A SER* 5.6 3.4 - - - +
556A GLU* 5.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ASP* 2.8 29.0 + - + +
470A LYS* 3.5 8.5 - - - +
471A PHE 3.1 0.6 - - - -
472A LYS* 1.3 77.6 - - - +
474A ILE* 1.3 63.8 + - - +
476A ALA* 3.3 8.0 + - - +
477A GLN* 3.2 18.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
470A LYS 3.8 4.6 + - - +
471A PHE 3.4 2.9 + - - +
473A TYR* 1.3 79.7 - - - +
475A ILE* 1.3 60.1 + - + +
477A GLN* 3.1 11.5 + - - +
478A LEU* 3.1 28.8 + - - +
593A LYS* 5.0 10.3 - - + -
596A GLU* 5.3 10.1 - - - +
597A LEU* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 3.4 38.7 + - + +
472A LYS 4.2 2.2 - - - +
473A TYR 3.3 0.4 - - - -
474A ILE* 1.3 72.3 - - - +
476A ALA* 1.3 61.1 + - - +
477A GLN 3.0 2.0 - - - -
478A LEU* 3.5 11.6 - - + +
479A MET* 2.8 46.9 + - + +
548A TYR* 4.3 26.5 - - + +
551A ALA* 5.7 2.5 - - + -
552A LEU* 3.8 24.2 - - + -
567A LEU* 4.9 8.7 - - + -
597A LEU* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LYS 2.9 21.2 + - - +
473A TYR* 3.5 8.7 - - - +
475A ILE* 1.3 77.5 - - - +
477A GLN* 1.3 55.8 + - - +
479A MET* 4.1 9.1 - - - +
480A ARG* 3.0 27.0 + - - +
552A LEU* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR 3.2 10.4 + - - +
474A ILE* 3.1 14.5 + - - +
475A ILE 3.0 0.6 - - - -
476A ALA* 1.3 74.8 - - - +
478A LEU* 1.3 56.7 + - + +
480A ARG* 3.0 7.7 + - - +
481A ASP* 2.8 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE 3.1 20.0 + - - +
475A ILE* 3.1 19.9 + - + +
477A GLN* 1.3 79.1 - - + +
479A MET* 1.3 57.5 + - - +
481A ASP* 3.2 14.2 + - - +
482A THR* 2.9 32.5 + - - -
548A TYR* 3.5 40.8 - - + +
589A ARG* 4.3 21.3 - - + +
590A PHE* 4.1 23.3 - - + +
593A LYS* 4.5 17.0 - - + -
597A LEU* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE* 2.8 29.8 + - + +
476A ALA* 4.1 7.2 - - - +
478A LEU* 1.3 71.0 - - - +
480A ARG* 1.3 59.5 + - - +
482A THR* 3.4 1.5 + - - -
483A GLU* 3.0 34.6 + - - +
504A PHE 4.3 9.6 - - - +
509A TYR* 3.3 44.2 - - + +
545A LEU* 3.6 25.0 - - + +
548A TYR* 3.7 28.0 - - + -
549A ASN* 4.4 5.2 - - + -
552A LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ALA 3.0 19.8 + - - +
477A GLN* 3.0 11.8 + - - +
479A MET* 1.3 77.1 - - - +
481A ASP* 1.3 62.9 + - - +
483A GLU* 3.5 10.7 - - - +
484A SER* 3.5 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLN* 2.8 27.9 + - - +
478A LEU* 3.5 17.0 - - - +
479A MET 3.2 0.2 - - - -
480A ARG* 1.3 76.5 - - - +
482A THR* 1.3 60.2 + - - +
483A GLU 3.1 1.8 - - - -
484A SER* 2.9 21.8 + - - -
485A LEU* 2.9 27.0 + - + +
589A ARG* 5.5 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LEU 2.9 17.7 + - - -
479A MET* 3.9 4.6 - - - -
481A ASP* 1.3 76.8 - - - +
483A GLU* 1.3 60.8 + - - +
485A LEU* 3.9 9.3 - - + +
486A ALA* 3.0 23.8 + - + +
541A TYR* 3.2 40.2 - - + +
544A HIS* 5.4 2.5 - - + +
545A LEU* 4.0 21.2 - - + +
548A TYR* 4.6 12.5 - - - -
586A LEU* 4.8 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A MET* 3.0 26.5 + - + +
480A ARG* 3.5 11.0 - - - +
482A THR* 1.3 78.1 - - - +
484A SER* 1.3 57.0 + - - +
486A ALA* 3.9 5.9 - - - +
487A LYS* 2.9 28.3 + - - +
493A LEU* 6.1 1.0 - - - +
509A TYR* 3.4 18.1 + - - +
512A TRP* 3.2 40.1 - - - -
513A ILE* 5.7 0.4 - - - +
545A LEU* 4.3 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ARG 3.5 8.8 + - - -
481A ASP* 2.9 11.3 + - - -
483A GLU* 1.3 77.2 - - - +
485A LEU* 1.3 59.1 + - - +
486A ALA 3.1 1.8 - - - -
487A LYS* 3.2 7.0 - - - +
488A ARG* 2.5 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ASP* 2.9 28.7 + - + +
482A THR* 3.5 9.6 + - + +
484A SER* 1.3 79.6 - - - +
486A ALA* 1.3 60.3 + - - +
488A ARG* 3.4 18.1 + - - +
489A ILE* 3.6 17.0 - - - +
541A TYR* 5.6 5.2 - - + -
585A ASP* 3.9 17.3 - - - +
586A LEU* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A THR* 3.0 18.2 + - + +
483A GLU* 3.9 7.6 - - - +
485A LEU* 1.3 72.9 - - - +
487A LYS* 1.3 60.0 + - - +
488A ARG 3.0 5.8 + - - -
489A ILE* 3.2 13.0 + - - +
490A CYS* 3.4 13.7 + - - +
538A LEU* 3.9 25.7 - - + +
541A TYR* 4.7 12.3 - - + +
542A THR* 5.5 8.3 - - + -
545A LEU* 6.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLU 2.9 21.0 + - - +
484A SER* 3.2 7.6 - - - +
486A ALA* 1.3 73.1 - - - +
488A ARG* 1.3 58.7 + - - +
489A ILE 3.1 3.8 - - - -
490A CYS* 5.7 0.2 - - - -
491A LYS* 3.3 33.9 - - - +
492A ASP 5.4 2.7 - - - +
493A LEU* 6.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER* 2.5 21.3 + - - +
485A LEU* 3.5 14.6 - - - +
486A ALA 3.0 0.6 - - - -
487A LYS* 1.3 73.2 - - - +
489A ILE* 1.3 62.0 + - + +
491A LYS* 5.8 0.4 - - - -
----------------------------------------------------------
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