Contacts of the helix formed by residues 541 - 552 (chain D) in PDB entry 5JA4
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 GLN 541 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D ALA* 3.0 9.8 + - - +
539D GLU* 4.3 28.6 + - + +
540D GLY* 1.3 75.8 - - - +
542D LEU* 1.3 59.0 + - - +
543D ARG 3.5 0.7 - - - +
544D ARG* 3.5 43.2 - - + +
545D VAL* 2.9 32.7 + - - +
577D ILE* 3.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D GLY 3.6 2.9 + - - +
541D GLN* 1.3 68.6 - - - +
543D ARG* 1.3 64.3 + - + +
544D ARG 3.1 1.8 - - - -
545D VAL* 4.3 5.2 - - + -
546D GLN* 2.9 58.1 + - + +
576D GLU* 3.2 55.0 - - + +
577D ILE* 3.5 22.6 - - + +
580D PHE* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D GLN* 3.5 0.6 - - + +
542D LEU* 1.3 79.2 - - + +
544D ARG* 1.3 60.2 + - + +
546D GLN* 3.8 12.8 - - - +
547D ASP* 3.3 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D ALA* 4.3 9.9 - - + -
541D GLN* 3.5 44.2 + - + +
542D LEU 3.1 0.6 - - - -
543D ARG* 1.3 77.3 - - + +
545D VAL* 1.3 67.9 + - - +
546D GLN 3.2 0.9 - - - -
547D ASP* 3.2 4.9 + - - -
548D LEU* 2.8 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D LEU* 5.0 4.7 - - + +
536D ALA* 3.5 33.1 - - + +
537D CYS* 3.7 7.9 - - + +
541D GLN 2.9 26.5 + - - +
542D LEU* 3.9 9.0 - - + +
544D ARG* 1.3 71.9 - - - +
546D GLN* 1.3 54.9 + - - +
548D LEU* 3.9 2.2 - - - +
549D VAL* 2.8 37.9 + - + +
577D ILE* 3.8 20.9 - - + -
580D PHE* 3.6 15.7 - - + -
581D LEU* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D LEU* 2.9 42.1 + - + +
543D ARG* 3.8 16.5 - - - +
545D VAL* 1.3 79.8 - - - +
547D ASP* 1.3 69.0 + - - +
548D LEU 3.2 0.3 + - - -
549D VAL* 3.2 9.0 + - - +
550D ARG* 3.2 17.4 + - - +
580D PHE* 3.5 44.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ARG* 3.3 19.2 + - - +
544D ARG* 3.2 6.4 + - - +
546D GLN* 1.3 80.8 - - - +
548D LEU* 1.3 64.7 + - + +
550D ARG* 3.2 58.4 + - - +
551D GLN* 4.4 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D TRP* 5.5 6.9 - - + -
532D LEU* 3.9 33.4 - - + +
533D LEU* 5.1 3.1 - - + -
536D ALA* 4.0 17.0 - - + -
544D ARG* 2.8 37.6 + - + +
545D VAL* 3.9 2.9 - - - +
547D ASP* 1.3 71.7 - - + +
549D VAL* 1.3 64.0 + - - +
550D ARG 2.8 5.3 + - - -
551D GLN* 3.3 4.3 + - - +
552D GLY* 2.8 24.1 + - - -
553D HIS* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D LEU* 4.0 24.7 - - + -
545D VAL 2.8 24.1 + - - +
546D GLN 3.7 0.2 - - - +
548D LEU* 1.3 71.9 - - - +
550D ARG* 1.3 67.5 + - - +
551D GLN 4.0 0.2 - - - -
552D GLY* 3.1 10.9 + - - +
553D HIS* 4.8 5.1 + - - +
555D LEU* 6.1 2.7 - - + -
580D PHE* 3.3 32.5 - - + -
581D LEU* 4.4 11.0 - - + -
584D HIS* 3.6 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D GLN* 3.2 11.9 + - - +
547D ASP* 3.2 53.1 + - - +
548D LEU 2.8 1.4 + - - -
549D VAL* 1.3 79.8 - - - +
551D GLN* 1.3 60.0 + - + +
580D PHE* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D TRP* 3.7 34.6 + - + +
547D ASP 4.4 0.9 + - - +
548D LEU 3.3 2.7 + - - +
550D ARG* 1.3 80.6 - - + +
552D GLY* 1.3 63.0 + - - +
553D HIS 3.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D TRP* 2.9 39.8 + - - -
548D LEU 2.8 20.2 + - - -
549D VAL 3.1 9.5 + - - -
551D GLN* 1.3 79.8 - - - +
553D HIS* 1.3 74.1 + - - +
----------------------------------------------------------
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