Contacts of the helix formed by residues 522 - 535 (chain B) in PDB entry 3HB0
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 CYS 522 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 3.8 5.6 - - - +
294B TYR* 3.1 19.1 - - + +
424B TRP* 4.1 8.0 - - - -
520B ILE* 3.6 5.0 - - - +
521B SER* 1.3 82.1 - - - +
523B HIS* 1.3 69.1 + - - +
524B ALA* 3.9 13.0 - - - -
525B ASP* 2.9 43.6 + - - +
526B LEU 3.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 6.4 0.7 - + - -
294B TYR* 3.0 24.9 + + + -
421B THR 3.5 16.6 - - - -
422B ASP* 3.0 25.7 + - + -
424B TRP* 3.5 41.6 - + + -
427B HIS* 2.9 37.2 - + + -
522B CYS* 1.3 71.9 - - - +
524B ALA* 1.3 64.3 + - - +
526B LEU* 2.8 21.0 + - + +
527B GLU* 3.0 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B TYR* 5.7 0.2 - - - -
522B CYS* 3.2 14.4 - - - +
523B HIS* 1.3 78.7 - - - +
525B ASP* 1.3 57.0 - - - +
527B GLU* 3.4 9.9 + - - +
528B ALA* 3.0 26.7 + - - +
531C HIS* 3.6 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ARG 3.7 2.8 - - - +
520B ILE* 3.8 19.1 - - + +
521B SER* 2.8 35.0 + - - -
522B CYS* 2.9 24.8 + - - +
524B ALA* 1.3 73.4 - - - +
526B LEU* 1.3 66.6 + - - +
528B ALA* 3.2 2.4 + - - +
529B LEU* 3.0 24.4 + - - +
531C HIS* 2.9 21.5 + - - -
534C GLU* 5.0 1.4 - - - +
535C LEU* 3.4 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TRP* 4.9 4.9 - - + -
278B THR 4.0 12.6 - - - +
424B TRP* 3.6 49.4 - - + +
427B HIS* 4.0 16.6 - - + +
428B SER* 4.0 20.9 - - - +
431B ALA* 5.1 3.1 - - + -
520B ILE* 4.0 18.5 - - + +
522B CYS 3.3 4.2 + - - +
523B HIS* 2.8 18.7 + - - +
525B ASP* 1.3 79.6 - - - +
527B GLU* 1.3 62.8 + - - +
529B LEU* 3.3 16.8 + - + +
530B ARG* 3.0 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B HIS* 2.9 57.6 + - + +
523B HIS* 3.0 15.3 + - + +
524B ALA* 3.6 11.7 - - - +
526B LEU* 1.3 81.5 - - - +
528B ALA* 1.3 56.2 + - - +
530B ARG* 3.4 20.6 + - - +
531B HIS* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TRP* 4.6 1.9 - - - -
524B ALA 3.0 14.5 + - - +
525B ASP 3.6 7.4 - - - +
527B GLU* 1.3 74.3 - - - +
529B LEU* 1.3 59.5 + - - +
531B HIS* 3.2 8.7 + - - +
532B ALA* 2.9 28.1 + - - +
518C TRP* 5.9 0.3 - - - -
528C ALA 5.5 1.8 - - - +
531C HIS* 4.1 21.8 - - + +
532C ALA* 5.1 8.5 - - + +
535C LEU* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TRP* 3.5 33.0 - - + -
431B ALA* 4.7 1.3 - - + -
500B ILE* 4.0 14.4 - - + -
518B TRP* 3.5 34.7 - - + -
520B ILE* 3.9 21.3 - - + -
525B ASP 3.0 12.7 + - - +
526B LEU* 3.6 12.8 - - + +
528B ALA* 1.3 75.8 - - - +
530B ARG* 1.3 64.7 + - - +
532B ALA* 3.0 5.5 + - - +
533B LEU* 2.9 29.6 + - + +
538B LEU* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 6.1 0.8 - - - +
519A ARG* 5.1 5.9 - - - +
426B THR* 5.7 1.2 - - - +
427B HIS* 3.6 32.2 + - - +
430B LYS* 3.5 38.7 - - - +
431B ALA* 4.0 31.0 - - + +
434B LEU* 4.7 2.0 - - + +
526B LEU 3.0 16.9 + - - +
527B GLU* 3.6 19.6 + - - +
529B LEU* 1.3 80.0 - - - +
531B HIS* 1.3 57.7 + - - +
533B LEU* 3.1 14.1 + - + +
534B GLU* 3.0 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU 3.0 14.7 + - - +
528B ALA* 3.2 12.2 + - - +
530B ARG* 1.3 74.6 - - - +
532B ALA* 1.3 66.7 + - - +
534B GLU* 3.0 25.6 + - + +
535B LEU* 3.1 46.7 + - + +
518C TRP* 3.7 28.5 - + - -
528C ALA* 4.7 11.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TRP* 3.7 26.0 - - + -
528B ALA 2.9 12.7 + - - +
529B LEU 3.2 9.6 - - - +
531B HIS* 1.3 79.3 + - - +
533B LEU* 1.3 59.0 + - - +
535B LEU* 3.4 0.9 + - - -
536B GLU 3.0 5.7 + - - -
537B TYR* 2.8 49.8 + - + +
538B LEU* 3.3 7.7 + - + -
518C TRP* 4.8 5.8 - - + -
532C ALA* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 4.1 14.4 - - + -
273B TRP* 4.8 0.2 - - + -
431B ALA* 3.8 41.3 - - + +
434B LEU* 3.8 17.1 - - + +
435B ILE* 4.0 25.4 - - + -
438B ARG* 3.0 20.5 + - - +
529B LEU* 2.9 29.3 + - + +
530B ARG* 3.3 9.2 - - - +
531B HIS 3.1 0.2 - - - -
532B ALA* 1.3 75.7 - - - +
534B GLU* 1.3 64.2 + - - +
536B GLU* 2.9 12.5 + - - +
538B LEU* 3.4 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A VAL* 5.9 1.9 - - - +
507A GLU* 4.9 0.7 - - - +
511A LYS* 5.6 3.3 + - - -
519A ARG* 3.1 34.8 + - - -
430B LYS* 5.5 3.3 - - - +
434B LEU* 3.9 20.7 - - - +
530B ARG* 3.0 46.6 + - - +
531B HIS* 3.2 19.5 - - + +
533B LEU* 1.3 77.8 - - - +
535B LEU* 1.3 66.6 + - + +
536B GLU* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B HIS* 3.1 46.7 + - + +
532B ALA 3.4 3.8 + - - +
534B GLU* 1.3 82.0 - - + +
536B GLU* 1.3 72.2 + - - +
537B TYR* 3.1 10.6 + - + +
516C PRO* 3.4 15.6 - - - +
517C PHE 4.1 20.8 + - - +
518C TRP* 3.6 33.9 - - + -
519C ARG 5.2 1.6 - - - +
----------------------------------------------------------
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