Contacts of the helix formed by residues 519 - 532 (chain A) in PDB entry 2DFS
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 SER 519 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLU* 3.9 2.3 - - - +
517A LYS 5.1 1.3 - - - -
518A GLY* 1.3 75.1 - - - -
520A ASP* 1.4 57.2 + - - +
521A ASP* 2.6 30.4 + - - +
522A THR* 3.1 23.1 + - - +
523A TRP* 3.1 28.6 + - - +
565A LEU* 3.7 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A SER* 1.4 73.4 - - - +
521A ASP* 1.3 56.7 + - - +
523A TRP* 3.6 6.5 + - - +
524A ALA* 2.9 29.3 + - - +
546A LYS* 4.0 17.9 - - - +
561A CYS* 3.3 23.6 - - + +
562A GLU* 3.5 6.2 - - - +
563A GLY* 2.8 25.9 + - - -
564A PHE* 3.9 1.4 - - - +
565A LEU* 2.9 42.3 + - - +
566A GLU 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A SER* 2.6 26.8 + - - +
520A ASP* 1.3 72.0 + - - +
522A THR* 1.4 64.8 + - + +
524A ALA* 3.4 8.0 + - - +
525A GLN* 3.1 23.0 + - - +
545A ASN 5.3 0.8 - - - +
546A LYS* 2.6 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLU* 2.7 25.6 + - - +
517A LYS 5.0 6.5 - - - +
518A GLY* 3.9 1.8 - - - -
519A SER* 3.1 34.1 + - - +
521A ASP* 1.4 74.3 - - + +
523A TRP* 1.4 58.5 + - - +
525A GLN* 3.4 7.6 + - - +
526A LYS* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL* 3.6 29.3 + - + -
508A LEU* 3.6 13.9 - - + -
509A LEU* 3.2 53.6 - - + +
512A GLU* 3.8 11.7 - - + -
519A SER 3.1 18.0 + - - +
520A ASP* 3.6 12.3 - - - +
522A THR* 1.4 76.8 + - - +
524A ALA* 1.4 54.8 + - - +
526A LYS* 3.1 7.8 + - + +
527A LEU* 2.9 46.1 + - + +
548A PHE* 3.7 17.9 - + - -
561A CYS* 3.8 26.0 - - + -
564A PHE* 3.4 45.3 - + + -
565A LEU* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ASP 2.9 18.8 + - - +
521A ASP* 3.4 8.7 + - - +
523A TRP* 1.4 75.3 - - - +
525A GLN* 1.3 56.1 + - - +
527A LEU* 3.3 16.0 + - - +
528A TYR* 3.1 38.4 + - - +
545A ASN 3.6 22.7 - - - +
546A LYS* 4.7 1.1 - - - -
561A CYS* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASP 3.1 14.2 + - - +
522A THR* 3.8 9.0 - - - +
524A ALA* 1.3 75.1 - - - +
526A LYS* 1.3 57.6 + - - +
528A TYR* 3.2 26.2 + - + +
529A ASN* 2.8 68.2 + - - +
545A ASN* 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU* 4.2 38.6 - - + +
511A GLU* 5.5 5.0 - - + +
512A GLU* 2.7 44.2 + - - +
515A MET* 5.0 8.7 - - - +
522A THR* 3.0 13.0 + - - +
523A TRP* 3.1 12.3 + - + +
525A GLN* 1.3 72.8 - - - +
527A LEU* 1.4 56.0 + - - +
529A ASN* 3.8 8.1 - - - +
530A THR* 2.9 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL* 4.1 19.3 - - + -
508A LEU* 4.1 6.1 - - + -
523A TRP* 2.9 60.2 + - + +
524A ALA* 3.4 13.5 - - - +
526A LYS* 1.4 75.5 - - - +
528A TYR* 1.4 57.3 + - + +
531A HIS* 2.8 65.1 + - + +
532A LEU 3.7 0.2 + - - -
538A PHE* 3.8 12.0 - - + -
548A PHE* 3.9 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ALA* 3.1 29.0 + - + +
525A GLN* 3.2 31.8 + - + +
527A LEU* 1.4 75.8 - - + +
529A ASN* 1.3 58.1 + - - +
532A LEU* 3.0 27.8 + - + +
534A LYS* 3.0 21.5 + - - -
538A PHE* 4.1 21.3 - + - -
540A LYS* 3.6 46.4 - - + -
545A ASN* 2.7 36.4 + - + -
547A ALA 3.0 26.4 + - - -
548A PHE* 4.7 2.9 - - + -
561A CYS* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLN* 2.8 55.2 + - - +
526A LYS* 3.8 7.7 - - - +
528A TYR* 1.3 70.7 - - - +
530A THR* 1.3 59.0 + - - +
534A LYS* 2.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A MET* 3.7 32.4 - - + +
508A LEU* 3.8 13.2 - - + +
526A LYS* 2.9 22.1 + - - +
529A ASN* 1.3 76.2 - - - +
531A HIS* 1.4 78.0 + - - +
534A LYS* 3.1 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 4.1 18.2 - - + +
503A MET 3.1 25.7 + - - -
504A GLY* 4.2 9.4 - - - -
505A VAL* 4.1 6.8 - - + +
508A LEU* 3.4 13.6 - - + +
527A LEU* 2.8 54.7 + - - +
530A THR* 1.4 83.5 - - + +
532A LEU* 1.4 58.7 + - - +
533A ASN 3.1 1.0 + - - -
534A LYS* 2.9 24.8 + - - -
535A CYS* 3.3 16.6 + - + +
538A PHE* 3.7 36.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A LEU 3.7 1.6 + - - -
528A TYR* 3.0 30.6 + - + +
531A HIS* 1.4 72.9 - - - +
533A ASN* 1.3 81.5 + - - +
534A LYS* 2.7 23.1 + - - +
538A PHE* 3.9 27.1 - - + +
539A GLU* 3.9 1.3 - - - -
540A LYS* 3.7 55.6 - - + +
----------------------------------------------------------
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