Contacts of the helix formed by residues 522 - 535 (chain A) in PDB entry 3GEB
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 3.8 10.8 - - + +
424A TRP* 3.6 20.0 - - - -
520A ILE* 4.2 0.7 - - - +
521A SER* 1.3 84.5 - - - +
523A HIS* 1.3 67.3 - - - +
524A ALA* 3.1 19.7 - - + +
525A ASP* 3.2 38.0 + - - +
526A LEU* 3.7 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 4.4 5.6 - + - -
294A TYR* 4.3 22.9 - + - -
421A THR 2.9 26.9 + - - -
422A ASP* 3.5 25.2 + - + -
424A TRP* 3.4 40.1 - + - -
427A HIS* 4.0 24.6 - + + +
522A CYS* 1.3 74.0 - - - +
524A ALA* 1.3 56.9 + - - +
526A LEU* 3.2 13.2 + - - +
527A GLU* 2.9 33.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
522A CYS* 3.1 16.1 - - + +
523A HIS* 1.3 76.5 - - - +
525A ASP* 1.3 61.6 + - - +
527A GLU* 3.3 22.4 + - - +
528A ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TRP* 3.6 9.3 + - - +
519A ARG* 3.5 20.4 - - - +
520A ILE* 3.5 14.4 - - + +
521A SER* 2.6 37.4 + - - -
522A CYS* 3.2 20.2 + - - +
524A ALA* 1.3 75.2 - - - +
526A LEU* 1.3 66.4 + - - +
528A ALA* 3.4 7.4 + - - +
529A LEU* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TRP* 4.6 8.1 - - + -
278A THR 4.0 7.9 - - - +
424A TRP* 3.8 34.1 - - + +
427A HIS* 3.7 34.8 - - + +
428A SER* 3.9 20.0 - - - +
431A ALA* 4.9 5.0 - - + +
520A ILE* 3.3 35.0 - - + -
522A CYS 4.1 7.0 - - - +
523A HIS* 3.2 12.1 + - - +
525A ASP* 1.3 78.6 - - - +
527A GLU* 1.3 56.9 + - - +
529A LEU* 3.3 8.0 + - + +
530A ARG* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A HIS* 3.7 26.1 + - + -
523A HIS* 2.9 24.5 + - - +
524A ALA* 3.3 22.3 + - - +
525A ASP 3.3 0.2 - - - -
526A LEU* 1.3 76.1 - - - +
528A ALA* 1.3 57.1 + - - +
530A ARG* 2.9 34.0 + - - +
531A HIS* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TRP* 3.7 14.6 - - + +
524A ALA 2.9 16.1 + - - +
525A ASP* 3.6 8.7 - - - +
527A GLU* 1.3 73.2 - - - +
529A LEU* 1.3 65.1 + - - +
531A HIS* 3.3 8.8 + - - +
532A ALA* 3.1 21.7 + - - +
528D ALA* 5.8 1.4 - - - +
531D HIS* 4.8 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 4.5 3.1 - - + -
273A TRP* 3.8 21.5 - - + -
431A ALA* 4.4 3.8 - - + -
500A ILE* 3.5 40.2 - - + -
518A TRP* 3.4 39.2 - - + -
520A ILE* 4.5 6.1 - - + -
525A ASP 3.0 14.2 + - - +
526A LEU* 3.3 9.6 + - + +
528A ALA* 1.3 77.0 - - - +
530A ARG* 1.3 63.9 + - - +
532A ALA* 3.2 2.8 + - - +
533A LEU* 3.0 42.5 + - + +
537D TYR* 4.5 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A HIS 5.4 1.3 - - - +
430A LYS* 4.1 46.9 - - + +
431A ALA* 4.5 7.1 - - + +
434A LEU* 3.7 9.9 - - + +
526A LEU 3.0 17.0 + - - +
527A GLU* 2.9 45.5 + - - +
529A LEU* 1.3 75.3 - - - +
531A HIS* 1.3 82.8 + - - +
533A LEU* 3.2 15.8 + - - +
534A GLU* 3.2 46.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
527A GLU 3.0 13.5 + - - +
528A ALA* 3.4 11.4 - - - +
530A ARG* 1.3 87.2 + - - +
532A ALA* 1.3 61.7 + - - +
534A GLU* 2.9 40.8 + - - +
535A LEU* 3.1 18.3 - - + +
524D ALA* 3.8 30.5 - - + -
525D ASP* 2.9 28.2 + - - -
528D ALA* 3.8 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TRP* 4.0 18.4 - - + -
528A ALA 3.1 12.3 + - - +
529A LEU 3.5 7.6 - - - +
531A HIS* 1.3 75.4 - - - +
533A LEU* 1.3 62.5 + - - +
534A GLU 3.3 0.7 + - - -
535A LEU* 3.4 10.7 + - - -
536A GLU* 3.7 10.9 + - - +
518D TRP* 3.9 25.5 - - + -
528D ALA* 5.3 6.8 - - + +
532D ALA* 5.3 2.7 - - + -
537D TYR* 4.1 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.7 23.8 - - + -
431A ALA* 3.5 47.1 - - + +
434A LEU* 3.6 15.5 - - + +
435A ILE* 3.6 27.1 - - + -
438A ARG* 3.0 42.7 + - - +
529A LEU* 3.0 25.0 + - + +
530A ARG* 3.2 11.6 + - - +
532A ALA* 1.3 78.6 - - - +
534A GLU* 1.3 58.1 + - - +
535A LEU 3.8 0.2 + - - -
536A GLU 4.1 2.8 - - - +
537D TYR* 3.7 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 4.0 14.4 - - + +
530A ARG* 3.2 35.0 + - - +
531A HIS* 2.9 42.9 + - + +
533A LEU* 1.3 77.9 - - - +
535A LEU* 1.3 66.0 + - + +
536A GLU 3.5 2.2 - - - -
537A TYR* 4.0 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A HIS* 3.1 24.7 - - + +
532A ALA 3.4 1.4 + - - +
534A GLU* 1.3 87.0 - - + +
536A GLU* 1.3 58.8 + - - +
537A TYR* 3.3 9.7 - - - -
517D PHE 3.3 3.8 - - - +
518D TRP* 3.3 29.0 - - + -
519D ARG* 2.9 39.4 + - + +
520D ILE* 5.9 0.7 - - + -
525D ASP* 3.7 54.7 - - + +
528D ALA* 3.8 20.2 - - + -
----------------------------------------------------------
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