Contacts of the helix formed by residues 542 - 552 (chain B) in PDB entry 4RG7
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 MET 542 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B PHE* 5.4 1.8 - - + -
538B ARG 4.7 5.2 - - - +
539B VAL* 3.0 22.3 + - - +
540B GLU 4.8 0.7 - - - +
541B GLY* 1.3 76.6 - - - +
543B GLU* 1.3 68.1 + - - +
544B ILE 3.1 1.6 - - - -
545B TYR* 3.3 20.8 + - + +
546B SER* 3.1 20.8 + - - -
574B GLU* 5.0 2.5 - - + -
578B ALA* 5.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL 3.8 1.2 - - - +
541B GLY* 2.9 19.3 + - - -
542B MET* 1.3 85.9 + - - +
544B ILE* 1.3 71.4 + - + +
546B SER* 2.4 27.5 + - - -
547B THR* 3.2 9.3 + - - -
574B GLU* 2.8 51.8 - - + +
577B CYS* 4.2 8.8 - - + +
608B TYR* 3.8 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ARG* 3.5 27.1 - - + +
516B PHE* 3.6 25.0 - - + +
528B PHE* 3.4 27.4 - - + -
541B GLY* 3.8 9.0 - - - +
542B MET 3.1 0.8 - - - -
543B GLU* 1.3 94.7 - - + +
545B TYR* 1.3 63.4 + - - +
546B SER 3.2 1.1 - - - -
547B THR* 3.3 12.2 + - - -
548B THR* 2.9 30.1 + - - -
608B TYR* 4.5 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLU* 4.1 20.6 + - + +
528B PHE* 3.4 54.7 - + + -
529B SER* 3.9 22.2 + - - -
532B ARG* 5.0 9.6 - - + +
542B MET* 3.4 26.1 - - + +
544B ILE* 1.3 80.7 - - - +
546B SER* 1.3 58.8 + - - +
548B THR* 3.1 4.6 + - - -
549B LEU* 2.9 33.6 + - + +
557B ALA* 5.8 5.0 - - + +
561B LEU* 5.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B MET 3.1 11.6 + - - -
543B GLU* 2.4 23.7 + - - -
545B TYR* 1.3 78.0 - - - +
547B THR* 1.3 58.7 + - - +
549B LEU* 3.1 9.3 + - - +
550B TRP* 2.9 27.1 + - - +
558B LEU* 5.2 6.9 - - - +
561B LEU* 5.9 8.1 - - - -
577B CYS* 4.0 6.8 + - - +
578B ALA* 3.7 36.8 - - - -
581B ASN* 4.1 7.9 - - - +
612B LEU* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B GLU 3.2 11.5 + - - -
544B ILE* 3.6 10.1 - - - -
545B TYR 3.2 0.6 - - - -
546B SER* 1.3 79.9 + - - +
548B THR* 1.3 61.2 + - - +
550B TRP* 3.6 14.6 - - + +
551B HIS* 3.1 28.3 + - + +
581B ASN* 5.3 1.3 - - - -
608B TYR* 2.6 30.9 + - - +
612B LEU* 4.5 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PHE* 4.3 10.2 - - - +
521B TYR* 3.4 33.6 - - + +
524B ALA* 4.0 8.4 - - + +
525B GLU* 4.0 23.8 - - + +
528B PHE* 3.9 11.8 - - - -
544B ILE 2.9 21.0 + - - -
545B TYR* 3.1 14.1 + - + -
547B THR* 1.3 76.4 - - - +
549B LEU* 1.3 61.3 + - - +
550B TRP 3.1 1.4 + - - -
551B HIS* 3.4 3.9 + - - +
552B LEU* 3.2 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B TYR* 2.9 21.2 + - + +
546B SER* 3.5 10.8 - - - +
548B THR* 1.3 73.1 - - - +
550B TRP* 1.3 52.8 + - - +
552B LEU* 2.6 25.5 - - - +
554B LYS* 3.3 25.1 + - + +
557B ALA* 5.1 4.5 - - + -
558B LEU* 4.2 26.2 - - + +
585B LEU* 3.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B SER 2.9 14.4 + - - +
547B THR* 3.6 17.5 - - + +
548B THR 3.1 0.2 - - - -
549B LEU* 1.3 76.4 - - - +
551B HIS* 1.3 68.6 + - + +
552B LEU 2.9 13.1 - - - +
553B GLN* 4.2 4.2 - - - +
558B LEU* 5.9 0.2 - - - -
581B ASN* 3.4 33.9 - - + -
584B SER* 3.3 25.4 + - - -
585B LEU* 3.6 33.0 - - + +
680B HIS* 5.7 0.7 - - - -
681B ILE* 3.9 27.4 - - + -
684B VAL* 3.7 32.8 - - + +
685B GLN* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B TYR* 5.3 8.3 - - + -
547B THR* 3.1 16.5 + - + +
548B THR* 4.0 4.7 - - - +
550B TRP* 1.3 87.6 - - + +
552B LEU* 1.3 64.5 + - - +
553B GLN* 3.6 3.6 + - - +
680B HIS* 3.9 36.1 - - + +
684B VAL* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B TYR* 5.2 13.7 - - + +
522B MET* 6.5 0.2 - - - -
548B THR* 3.2 14.9 + - + +
549B LEU* 2.6 29.6 - - - +
550B TRP 2.9 7.8 - - - -
551B HIS* 1.3 76.5 - - - +
553B GLN* 1.3 58.1 + - - +
554B LYS* 3.4 5.8 - - + +
----------------------------------------------------------
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