Contacts of the strand formed by residues 546 - 554 (chain B) in PDB entry 6ZGI
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 LEU 546 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B LEU* 3.7 27.1 - - + +
541B PHE* 3.8 17.6 - - + +
542B ASN* 3.5 1.0 - - - -
543B PHE* 2.9 37.4 + - + +
544B ASN 3.3 1.4 + - - -
545B GLY* 1.3 76.2 - - - +
547B THR* 1.3 69.6 + - - +
565B PHE* 4.3 28.5 - - + -
567B ARG* 5.5 4.7 - - - +
573B THR* 4.4 27.4 - - + +
587B ILE* 6.0 1.3 - - + -
976C VAL* 6.4 1.3 - - + -
978C ASN* 5.5 7.6 - - + +
979C ASP* 5.1 10.8 - - + +
982C SER* 4.6 4.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
389B ASP* 6.0 1.3 - - + +
541B PHE* 3.2 11.0 - - - +
542B ASN* 3.8 26.0 - - + +
545B GLY 3.6 8.9 + - - +
546B LEU* 1.3 81.0 - - - +
548B GLY* 1.3 59.9 + - - +
978C ASN* 3.3 28.9 + - - +
981C LEU* 5.3 2.6 - - - +
982C SER* 3.9 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B ASN* 3.4 7.1 + - - +
541B PHE* 2.9 45.9 + - - -
547B THR* 1.3 77.0 - - - +
549B THR* 1.3 64.8 + - - -
978C ASN* 4.1 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 3.9 23.8 - - + -
538B CYS* 4.0 11.4 - - - -
539B VAL 3.6 7.9 - - - +
540B ASN* 3.1 27.7 + - - +
541B PHE* 3.6 10.2 - - - -
548B GLY* 1.3 73.5 - - - -
550B GLY* 1.3 62.7 + - - +
587B ILE* 4.6 4.3 - - - +
588B THR 4.8 0.2 - - - +
589B PRO* 5.2 4.0 - - - +
590B CYS* 5.2 0.7 - - - -
745C ASP* 4.8 28.4 + - + +
978C ASN* 5.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LYS 3.3 1.9 - - - +
538B CYS* 4.0 10.8 - - - -
539B VAL* 2.9 37.9 + - - +
541B PHE* 3.8 9.0 - - - -
549B THR* 1.3 79.4 - - - +
551B VAL* 1.3 65.0 + - - -
552B LEU* 5.0 0.4 - - - +
587B ILE* 4.7 1.6 - - - -
588B THR 3.4 12.3 - - - -
589B PRO* 4.9 2.7 - - - -
590B CYS* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B ASN* 3.8 26.9 - - - +
537B LYS* 3.7 3.8 - - - -
538B CYS* 3.7 22.4 - - + +
550B GLY* 1.3 76.2 - - - -
552B LEU* 1.3 67.2 + - - +
553B THR* 4.3 11.9 + - + -
586B ASP 3.4 4.9 - - - +
587B ILE* 3.4 2.1 - - - +
588B THR* 2.9 38.4 + - - +
590B CYS* 4.1 11.7 - - + -
837C TYR* 4.0 20.6 - - + +
841C LEU* 5.2 10.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
326B ILE* 3.8 28.5 - - + -
533B LEU* 3.9 16.6 - - + -
534B VAL 4.1 13.2 - - - +
535B LYS* 3.6 10.7 - - + +
536B ASN 3.2 23.0 + - - +
537B LYS 4.5 2.4 + - - -
539B VAL* 4.7 10.1 - - + -
541B PHE* 4.2 19.1 - - + -
543B PHE* 4.0 18.2 - - + -
551B VAL* 1.3 78.2 - - - +
553B THR* 1.3 64.1 + - - +
576B VAL* 5.4 0.4 - - + -
585B LEU* 4.5 15.0 - - + -
586B ASP 3.3 3.1 - - - +
587B ILE* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B LYS* 5.4 2.9 - - - -
536B ASN* 3.8 20.6 - - - +
551B VAL* 4.3 13.1 + - + +
552B LEU* 1.3 79.4 - - - +
554B GLU* 1.3 66.0 + - - +
585B LEU* 3.3 12.2 - - - +
586B ASP* 2.9 46.8 + - - +
588B THR* 4.8 3.1 + - - +
841C LEU* 5.0 16.4 - - + +
842C GLY* 4.1 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B LYS* 3.5 33.6 + - + +
553B THR* 1.3 79.3 + - - +
555B SER* 1.3 58.4 + - - +
556B ASN* 5.5 2.3 + - - -
583B GLU* 4.8 9.2 - - - +
584B ILE 4.3 4.5 - - - +
585B LEU* 4.4 2.5 - - + -
586B ASP* 4.2 5.4 - - - +
----------------------------------------------------------
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