Contacts of the helix formed by residues 773 - 781 (chain B) in PDB entry 3LZB
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 CYS 773 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ITI 3.7 18.4 - - + +
771B PHE 4.3 1.0 - - - +
772B GLY* 1.3 74.6 - - - +
774B LEU* 1.3 66.8 + - - +
775B LEU* 3.3 10.5 - - - -
776B ASP* 3.6 39.8 + - - +
777B TYR* 3.3 19.8 + - - +
816B ALA 3.9 2.0 - - - +
817B ARG* 3.5 29.8 - - - +
819B VAL 3.3 9.2 - - - +
820B LEU* 4.3 2.5 - - + +
821B VAL* 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 774 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B CYS* 1.3 70.0 - - - +
775B LEU* 1.3 60.9 + - - +
777B TYR* 3.2 4.0 + - + +
778B VAL* 2.8 40.8 + - + +
793B TRP* 3.9 45.8 - - + -
797B ILE* 4.0 13.2 - - + -
816B ALA* 3.8 5.8 - - + +
819B VAL* 2.6 41.0 + - + +
821B VAL* 3.7 21.4 - - + +
827B VAL* 4.3 5.6 - - + -
883B LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 775 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B CYS* 3.3 8.2 - - - -
774B LEU* 1.3 79.1 - - - +
776B ASP* 1.3 59.5 + - - +
778B VAL* 3.2 7.0 - - + +
779B ARG* 2.8 64.7 + - - +
816B ALA* 3.4 26.0 + - + +
817B ARG* 4.0 18.8 - - + +
856B TRP* 6.1 1.3 - - + -
882B GLU* 4.0 23.8 - - + +
887B GLY* 3.6 31.4 - - - -
888B SER 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 776 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ITI 4.4 20.4 - - - +
771B PHE 5.9 1.1 - - - +
773B CYS* 3.6 26.6 + - - +
775B LEU* 1.3 82.6 - - - +
777B TYR* 1.3 69.5 + - - +
779B ARG* 3.0 17.0 + - - +
780B GLU* 2.8 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 777 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B PHE* 3.9 38.0 + + + +
773B CYS 3.3 11.6 + - - +
774B LEU* 3.2 11.1 + - + +
776B ASP* 1.3 80.1 - - - +
778B VAL* 1.3 62.9 + - - +
780B GLU* 3.2 8.7 + - - -
781B HIS* 2.8 68.0 + + - -
785B ILE* 4.5 4.3 - - + -
789B TYR* 5.7 1.5 - + - -
793B TRP* 3.8 35.2 - + - -
821B VAL* 3.9 17.5 - - + -
824B PRO* 3.4 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 778 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B LEU* 2.8 32.8 + - + +
775B LEU* 3.2 14.4 - - + +
777B TYR* 1.3 68.8 - - - +
779B ARG* 1.3 70.8 + - - +
781B HIS 3.3 2.1 - - - +
782B LYS* 3.0 22.5 + - - -
785B ILE* 3.6 13.5 - - + +
790B LEU* 5.4 0.4 - - + -
793B TRP* 3.7 30.3 - - + -
882B GLU 4.6 4.3 - - - +
883B LEU* 4.2 15.3 - - + +
886B PHE* 3.6 12.9 - - + +
887B GLY* 3.6 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 779 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B LEU* 2.8 54.2 + - - +
776B ASP* 3.6 16.4 + - - +
778B VAL* 1.3 75.0 - - - +
780B GLU* 1.3 63.6 + - - +
782B LYS* 2.8 46.9 + - - +
886B PHE 3.9 6.7 - - - -
887B GLY* 2.5 47.0 + - - -
888B SER 4.7 4.4 + - - -
889B LYS* 4.9 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 780 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ITI 4.5 16.0 - - - +
776B ASP* 2.8 33.0 + - - +
777B TYR* 3.5 16.2 - - - +
779B ARG* 1.3 74.0 - - - +
781B HIS* 1.3 74.8 + - + +
782B LYS 3.3 1.5 + - - -
784B ASN* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 781 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B PHE* 5.6 0.8 - + - -
777B TYR* 2.8 71.1 + + - -
778B VAL 3.3 3.4 - - - -
779B ARG 3.2 0.2 - - - -
780B GLU* 1.3 91.9 + - + +
782B LYS* 1.3 63.0 + - - +
783B ASP 3.4 2.2 - - - -
784B ASN* 3.1 36.2 + - + +
785B ILE* 3.0 35.0 - - + +
----------------------------------------------------------
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