Contacts of the helix formed by residues 704 - 715 (chain Z) in PDB entry 5L4K
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 704 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698Z SER 4.5 3.4 - - - +
699Z VAL 4.6 9.4 - - - +
700Z SER* 5.4 1.1 - - - -
701Z ASN 3.6 23.6 - - - +
702Z PRO* 5.0 0.7 - - + -
703Z ARG* 1.3 73.4 - - - +
705Z ASN* 1.3 61.3 + - - +
706Z ILE 3.0 8.2 + - - +
707Z LEU* 3.7 30.7 + - + +
708Z ASP* 4.2 4.5 + - - +
738Z ASN* 3.7 38.8 - - + +
742Z ALA* 3.4 23.4 - - + +
745Z LEU* 5.1 0.3 - - - +
746Z ARG* 4.9 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 705 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673Z ARG* 3.5 20.5 - - - +
703Z ARG* 3.4 16.4 + - - +
704Z LEU* 1.3 76.2 + - - +
706Z ILE* 1.3 58.9 + - - +
707Z LEU 3.6 0.4 - - - -
708Z ASP* 4.0 11.6 - - + +
709Z THR* 3.1 27.7 + - - +
742Z ALA* 3.7 5.4 - - - +
745Z LEU* 3.1 30.9 - - + +
787Z LEU* 4.4 15.6 + - + +
788Z MET* 4.0 10.5 - - - +
789Z SER* 3.5 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 706 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668Z ALA 5.7 0.2 - - - +
669Z GLU* 4.3 5.2 - - - +
672Z LEU* 4.0 20.9 - - + +
673Z ARG* 3.7 27.6 - - + +
694Z LEU* 4.5 1.6 - - + +
698Z SER* 3.4 41.7 - - - +
701Z ASN* 5.3 0.9 - - + -
702Z PRO 3.4 12.1 - - - +
703Z ARG* 2.9 28.3 - - + +
704Z LEU 3.0 1.2 - - - -
705Z ASN* 1.3 76.3 - - - +
707Z LEU* 1.3 63.1 + - + +
708Z ASP 3.2 1.1 - - - -
709Z THR* 3.1 8.2 + - - +
710Z LEU* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 707 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695Z ALA* 3.6 38.4 - - + +
698Z SER* 3.3 33.4 - - - +
699Z VAL* 4.1 9.2 - - + +
704Z LEU* 3.7 31.4 - - + +
706Z ILE* 1.3 79.6 - - + +
708Z ASP* 1.3 56.2 + - - +
710Z LEU* 4.1 5.0 - - + +
711Z SER* 2.8 35.9 + - - -
729Z MET* 3.8 31.4 - - + -
746Z ARG* 4.5 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 708 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704Z LEU 4.2 2.9 + - - +
705Z ASN* 4.0 16.7 - - - +
706Z ILE 3.2 0.2 - - - -
707Z LEU* 1.3 77.8 - - - +
709Z THR* 1.3 58.8 + - + +
711Z SER* 3.1 5.5 + - - -
712Z LYS* 2.8 61.6 + - - +
729Z MET* 4.7 1.5 - - - +
745Z LEU* 3.2 57.9 - - + +
746Z ARG* 4.9 2.1 - - + +
748Z LEU* 4.8 3.2 - - - +
749Z ALA* 3.4 12.7 - - - +
787Z LEU* 3.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 709 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673Z ARG* 3.5 7.5 + - + -
676Z GLY* 3.4 31.6 - - - +
677Z HIS* 3.0 46.4 - - + +
680Z ARG* 4.5 3.1 - - - +
705Z ASN 3.1 17.4 + - - +
706Z ILE* 3.1 13.6 + - - -
708Z ASP* 1.3 76.5 - - + +
710Z LEU* 1.3 60.0 + - - +
712Z LYS* 3.7 20.8 + - - +
713Z PHE* 3.7 11.1 + - - +
784Z ASP* 5.2 0.2 - - - -
787Z LEU* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 710 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672Z LEU 5.2 0.4 - - - +
675Z PHE* 4.5 0.4 - - + -
676Z GLY* 3.6 17.5 - - - +
679Z LEU* 3.6 27.6 - - + -
691Z PRO* 3.7 16.0 - - + +
694Z LEU* 3.3 52.5 - - + +
695Z ALA* 3.5 12.1 - - + +
706Z ILE* 2.9 34.6 + - + +
707Z LEU* 4.1 4.9 - - + +
709Z THR* 1.3 75.5 - - - +
711Z SER* 1.3 60.2 + - - +
713Z PHE* 3.1 6.6 + - - +
714Z SER* 2.9 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 711 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707Z LEU 2.8 24.3 + - - -
708Z ASP 3.6 3.4 - - - -
710Z LEU* 1.3 77.6 - - - +
712Z LYS* 1.3 57.8 + - - +
713Z PHE 3.2 0.7 + - - -
714Z SER* 4.5 3.6 - - - +
715Z HIS* 3.1 29.3 + - - +
722Z SER* 4.0 6.1 + - - -
725Z SER* 5.4 2.6 - - - -
726Z ILE* 3.7 23.7 - - - +
729Z MET* 3.2 23.4 - - - +
749Z ALA* 4.0 12.6 - - - -
753Z ALA* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 712 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680Z ARG* 3.6 29.9 + - - +
708Z ASP* 2.8 52.8 + - - +
709Z THR* 3.7 14.8 - - - +
710Z LEU 3.2 0.4 - - - -
711Z SER* 1.3 72.3 - - - +
713Z PHE* 1.3 53.3 + - - +
715Z HIS* 2.6 29.6 + - - -
748Z LEU* 5.2 6.0 - - + +
749Z ALA* 4.4 10.3 - - + +
752Z HIS* 3.7 28.4 - - + +
753Z ALA* 5.5 0.2 - - - -
762Z VAL* 4.4 2.3 - - - +
784Z ASP* 2.5 40.0 + - - +
787Z LEU* 3.4 14.1 - - - +
800Z LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 713 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650Z GLN* 5.2 0.4 - - - -
679Z LEU* 3.0 45.3 - - + -
680Z ARG* 3.6 17.7 - - + +
683Z GLU* 3.1 26.3 - - - +
684Z PRO* 3.4 33.4 - - + -
686Z LEU 3.9 21.3 - - - -
687Z ARG* 3.8 24.2 + - + -
691Z PRO* 3.9 27.6 - - + -
709Z THR 3.7 4.9 + - - +
710Z LEU 3.1 6.1 + - - +
712Z LYS* 1.3 78.8 - - - +
714Z SER* 1.3 74.7 + - - +
715Z HIS* 3.0 6.1 + - - -
716Z ASP 3.2 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 714 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687Z ARG* 4.3 18.5 + - - +
688Z ARG 5.1 0.2 + - - -
691Z PRO* 3.4 28.5 - - - +
692Z LEU 5.1 1.4 + - - -
710Z LEU 2.9 14.9 + - - -
711Z SER* 3.7 4.5 + - - -
713Z PHE* 1.3 87.2 - - - +
715Z HIS* 1.3 64.9 + - - +
716Z ASP* 3.0 4.7 + - - +
721Z VAL* 3.8 28.2 - - - +
722Z SER* 4.5 6.3 - - - -
725Z SER* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 715 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711Z SER 3.1 12.7 + - - +
712Z LYS* 2.6 44.5 + - - +
713Z PHE 3.5 4.5 + - - -
714Z SER* 1.3 79.2 - - - +
716Z ASP* 1.3 89.6 + - - +
717Z ALA 2.8 11.1 + - - +
718Z ASP 4.4 1.2 - - - +
719Z PRO* 3.8 16.8 - - + +
720Z GLU 4.9 0.9 + - - -
721Z VAL* 5.6 0.9 + - - +
722Z SER* 3.6 21.7 + - - +
752Z HIS* 4.6 5.8 - + - -
753Z ALA* 2.6 54.7 + - + -
762Z VAL* 3.7 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