Contacts of the helix formed by residues 674 - 688 (chain O) in PDB entry 5Z3U
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 THR 674 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671O LEU* 2.4 46.4 + - - +
673O GLN* 1.3 67.1 - - - +
675O LYS* 1.3 57.2 + - - +
678O ARG* 2.5 54.0 + - + +
744O TYR* 5.6 1.3 - - - +
944O LYS* 5.3 7.9 - - + -
952O PHE* 6.0 1.7 - - - -
982O ARG* 5.8 0.4 - - - -
986O VAL* 4.3 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 675 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672O ASP* 2.6 37.5 + - - +
674O THR* 1.3 74.0 - - - +
676O ASP* 1.3 77.1 + - - +
679O ILE* 2.9 42.2 + - + +
744O TYR* 3.1 31.2 - - + +
985O LYS* 4.8 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 676 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672O ASP* 2.9 14.8 + - - +
673O GLN* 5.3 1.1 - - - -
675O LYS* 1.3 94.2 - - - +
677O THR* 1.3 70.7 + - - +
679O ILE* 3.2 6.5 + - - +
680O THR* 3.0 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 677 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673O GLN* 2.4 47.5 + - + +
676O ASP* 1.3 74.5 - - - +
678O ARG* 1.3 77.6 + - - +
680O THR* 2.9 19.7 + - - +
681O HIS* 2.9 16.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 678 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673O GLN* 4.6 4.7 - - - +
674O THR* 2.5 46.9 + - + +
677O THR* 1.3 108.8 + - - +
679O ILE* 1.3 61.1 + - - +
681O HIS* 3.5 29.7 + - - +
682O LEU* 2.9 28.5 + - - +
685O GLN* 5.0 1.7 + - - +
744O TYR* 6.0 0.4 - - - -
944O LYS* 4.5 28.8 + - + +
948O SER* 5.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 679 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675O LYS* 2.9 33.7 + - + +
676O ASP* 3.8 7.0 - - - +
678O ARG* 1.3 73.9 - - - +
680O THR* 1.3 67.5 + - + +
681O HIS 3.0 1.1 - - - -
682O LEU* 2.7 36.6 + - + +
683O LEU* 3.0 8.8 + - + +
743O ASP 5.7 4.0 - - - +
744O TYR* 3.4 38.1 - - + -
747O VAL* 3.5 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 680 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676O ASP* 3.0 16.8 + - + +
677O THR* 2.9 23.0 + - - +
679O ILE* 1.3 77.4 - - + +
681O HIS* 1.3 54.7 + - - +
683O LEU* 3.2 25.1 - - + +
684O ARG* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 681 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677O THR* 2.9 21.5 + - + +
678O ARG* 3.5 34.4 + - - +
679O ILE 3.0 0.2 - - - -
680O THR* 1.3 74.8 - - - +
682O LEU* 1.3 53.9 + - - +
684O ARG* 3.2 24.7 - - + +
685O GLN* 2.7 65.6 + - - +
689O PHE* 4.3 12.3 - + - -
943O PRO* 4.6 20.0 - - + +
944O LYS* 4.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 682 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678O ARG 2.9 22.1 + - - +
679O ILE* 2.7 42.3 + - + +
681O HIS* 1.3 67.9 - - - +
683O LEU* 1.3 55.4 + - - +
685O GLN* 3.1 19.0 + - - +
686O THR* 2.6 40.9 + - + +
744O TYR* 4.4 8.5 - - + -
747O VAL* 4.0 13.5 - - + +
748O ALA* 3.5 39.7 - - + -
786O LEU* 4.9 11.0 - - + -
942O LEU* 6.0 6.3 - - + -
989O PRO* 5.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 683 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679O ILE* 3.0 13.3 + - + +
680O THR* 3.2 27.8 - - + +
682O LEU* 1.3 74.7 - - - +
684O ARG* 1.3 62.8 + - + +
686O THR* 3.3 4.3 - - - -
687O ASN* 2.9 34.8 + - - +
688O ALA* 3.7 0.5 + - - +
747O VAL* 4.7 16.1 - - + +
750O ARG* 3.2 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 684 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680O THR* 2.9 25.6 + - - +
681O HIS* 3.1 31.1 + - + +
683O LEU* 1.3 75.1 - - - +
685O GLN* 1.3 60.3 + - - +
688O ALA* 2.9 18.1 + - - +
689O PHE* 2.8 42.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 685 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678O ARG* 5.2 1.8 + - - +
681O HIS* 2.7 66.3 + - - +
682O LEU* 3.1 24.7 - - - +
684O ARG* 1.3 71.1 - - - +
686O THR* 1.3 61.2 + - - +
689O PHE* 3.0 16.1 + - + -
690O LEU* 2.6 32.2 + - - +
785O HIS 5.4 0.2 - - - +
786O LEU* 4.0 19.2 - - + +
942O LEU* 5.8 4.6 - - - +
943O PRO* 3.6 37.9 - - + +
944O LYS* 4.7 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 686 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682O LEU* 2.6 28.4 + - + +
683O LEU* 3.0 12.1 + - - +
685O GLN* 1.3 80.2 - - - +
687O ASN* 1.3 73.8 + - - +
690O LEU* 3.2 26.3 - - - +
747O VAL 5.6 2.5 - - - +
748O ALA 4.8 2.5 - - - +
750O ARG* 5.0 10.6 - - - -
784O ASN* 3.2 37.0 - - + +
785O HIS* 4.3 7.0 - - - -
786O LEU* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 687 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683O LEU* 2.9 20.6 + - - +
686O THR* 1.3 88.2 + - - +
688O ALA* 1.3 65.2 + - + +
690O LEU* 4.5 8.4 - - - +
750O ARG* 3.4 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 688 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683O LEU 3.7 0.6 + - - +
684O ARG* 2.9 32.9 + - + +
687O ASN* 1.3 82.1 - - + +
689O PHE* 1.3 67.9 + - + +
690O LEU* 4.9 1.9 - - - +
----------------------------------------------------------
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