Contacts of the helix formed by residues 786 - 807 (chain A) 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 GLY 786 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A ASN 4.3 0.4 + - - -
785A ILE* 1.3 78.6 - - - +
787A SER* 1.3 68.4 + - - -
788A GLN* 3.1 3.4 - - - -
789A TYR* 2.8 24.5 + - - +
790A LEU* 3.1 11.5 + - - +
957A ILE* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A GLY* 1.3 70.0 - - - -
788A GLN* 1.3 64.1 + - - +
791A LEU* 3.0 28.9 + - - +
951A PRO* 3.2 34.3 - - - -
952A GLN* 3.2 21.7 + - - -
955A LEU* 3.7 27.0 + - - +
957A ILE* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A GLY 2.9 2.4 + - - -
787A SER* 1.3 79.6 - - - +
789A TYR* 1.3 70.1 + - + +
791A LEU 4.0 0.3 - - - -
792A ASN* 3.1 61.3 + - - +
948A ALA* 3.0 33.5 + - - +
951A PRO* 3.6 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A TYR* 5.7 1.6 - + - -
785A ILE* 3.9 17.5 - - + -
786A GLY* 2.8 15.0 + - - +
788A GLN* 1.3 87.3 - - + +
790A LEU* 1.3 65.6 + - - +
792A ASN* 3.2 7.8 + - - +
793A TRP* 3.0 42.1 + + + +
824A PRO* 3.2 38.1 - - + -
825A GLN* 2.7 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A VAL* 5.5 1.3 - - + -
785A ILE* 4.2 13.2 - - + +
786A GLY 3.1 9.2 + - - +
787A SER 3.9 0.4 - - - +
789A TYR* 1.3 80.4 - - - +
791A LEU* 1.3 62.4 - - - +
793A TRP* 3.2 21.9 + - + +
794A CYS* 3.1 26.3 + - - -
883A LEU* 3.6 40.3 - - + +
884A MET* 4.4 7.6 - - + +
886A PHE* 4.3 9.9 - - + -
914A ILE* 4.2 13.7 - - + -
955A LEU* 3.5 21.1 - - + -
957A ILE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A SER 3.0 10.0 + - - +
788A GLN 4.4 0.4 - - - +
790A LEU* 1.3 80.7 - - - +
792A ASN* 1.3 59.5 + - - +
794A CYS* 3.4 5.0 + - - +
795A VAL* 3.1 30.3 + - - +
884A MET* 4.1 13.2 - - + -
919A VAL* 4.9 3.6 - - + -
944A PHE* 3.7 32.2 - - + +
947A MET* 3.8 22.4 - - + +
948A ALA* 3.9 17.9 - - + +
951A PRO* 3.6 32.5 - - + +
954A TYR* 4.5 3.1 - - + -
955A LEU* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A GLN* 3.1 50.9 + - - +
789A TYR* 3.6 9.0 - - - +
790A LEU 3.2 0.2 - - - -
791A LEU* 1.3 73.3 - - - +
793A TRP* 1.3 58.0 + - + +
794A CYS 3.1 1.8 - - - -
795A VAL* 3.2 7.3 + - - +
796A GLN* 2.8 52.1 + - + +
825A GLN* 6.2 3.2 - - - +
948A ALA* 3.7 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A LEU* 3.9 26.7 - - + -
777A TYR* 3.8 33.0 - + - -
778A VAL* 3.7 21.5 - - + -
785A ILE* 3.8 28.5 - - + -
789A TYR* 3.0 30.3 + + + -
790A LEU* 3.5 22.4 - - + +
792A ASN* 1.3 78.3 - - + +
794A CYS* 1.3 54.6 + - - +
796A GLN* 3.8 13.2 - - - -
797A ILE* 2.8 40.7 + - - +
821A VAL* 6.0 0.4 - - + -
824A PRO* 3.0 28.8 + - + -
825A GLN* 4.6 1.2 - - - +
827A VAL* 3.8 25.8 - - + +
883A LEU* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A LEU 3.1 14.8 + - - -
791A LEU* 3.5 9.6 - - - +
792A ASN 3.1 0.6 - - - -
793A TRP* 1.3 79.4 - - - +
795A VAL* 1.3 59.1 + - - +
797A ILE* 3.5 3.5 + - - -
798A ALA* 3.2 13.9 + - - +
876A TYR* 2.7 25.7 + - - +
880A VAL* 3.8 19.1 - - - -
883A LEU* 4.5 9.4 - - - -
884A MET* 3.4 33.4 - - - -
944A PHE* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LEU 3.1 17.5 - - - +
792A ASN* 3.2 10.3 + - - +
794A CYS* 1.3 72.8 - - - +
796A GLN* 1.3 63.8 + - + +
798A ALA* 3.2 6.1 + - - +
799A LYS* 2.8 64.1 + - + +
941A ILE* 4.4 5.4 - - + +
944A PHE* 3.5 36.1 - - + +
945A SER* 3.7 18.6 - - - +
948A ALA* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A HIS* 3.3 44.8 - - + +
792A ASN* 2.8 32.8 + - - +
793A TRP* 3.8 7.5 - - - +
795A VAL* 1.3 80.3 - - + +
797A ILE* 1.3 61.5 + - - +
799A LYS* 3.4 7.6 + - + +
800A GLY 3.0 18.4 + - - -
825A GLN 2.9 27.4 + - - -
826A HIS* 3.3 3.5 - - - -
827A VAL* 2.7 40.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A LEU* 4.1 14.1 - - + -
793A TRP 2.8 27.7 + - - +
794A CYS* 3.9 4.7 - - - +
795A VAL 3.2 0.2 - - - -
796A GLN* 1.3 76.1 - - - +
798A ALA* 1.3 56.5 - - - +
801A MET* 3.0 28.1 + - + +
814A LEU* 4.3 14.8 - - + -
819A VAL* 3.9 34.5 - - + -
827A VAL* 4.3 5.2 - - + -
829A ILE* 3.2 21.2 - - + +
876A TYR* 3.8 23.3 - - + -
879A THR* 4.2 11.7 - - + -
880A VAL* 6.3 1.1 - - + -
883A LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A CYS 3.2 17.4 + - - +
795A VAL* 3.6 4.0 - - - +
797A ILE* 1.3 76.2 - - - +
799A LYS* 1.3 59.3 + - - +
800A GLY 3.2 0.2 - - - -
801A MET* 3.6 5.5 - - - +
802A ASN* 2.7 33.1 + - - +
876A TYR* 3.8 17.6 - - + +
937A PHE* 4.0 8.1 - - + +
940A LEU* 4.2 5.2 - - + -
941A ILE* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ASN* 4.4 6.8 + - - +
749A HIS* 3.9 27.3 - - + +
795A VAL* 2.8 53.9 + - + +
796A GLN* 3.7 5.2 - - + +
798A ALA* 1.3 72.1 - - - +
800A GLY* 1.3 57.8 + - - +
802A ASN* 3.3 1.9 + - - +
803A TYR* 2.9 28.9 + - - +
941A ILE* 3.8 31.2 - - + +
945A SER* 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ASN* 4.0 5.4 - - - -
749A HIS* 3.8 14.7 - - - +
750A VAL* 3.7 9.8 - - - +
796A GLN 3.0 11.6 + - - -
799A LYS* 1.3 78.0 - - - +
801A MET* 1.3 60.2 + - - +
803A TYR* 3.1 5.7 + - - +
804A LEU* 3.1 25.3 + - - +
829A ILE* 3.8 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A ILE* 3.0 26.1 + - + +
798A ALA 3.2 0.9 + - - +
800A GLY* 1.3 76.0 - - - +
802A ASN* 1.3 57.6 + - - +
804A LEU* 3.4 19.8 + - + +
805A GLU* 2.8 27.7 + - - +
809A LEU 5.9 0.4 - - - +
811A HIS* 4.0 13.7 - - + -
814A LEU* 3.9 24.9 - - + -
829A ILE* 3.6 15.0 - - + +
872A ASP* 3.7 39.5 - - + +
937A PHE* 3.5 41.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A ALA 2.7 21.3 + - - +
799A LYS 3.6 4.9 - - - +
801A MET* 1.3 69.7 - - - +
803A TYR* 1.3 65.9 + - - +
805A GLU* 4.2 10.5 + - - -
806A ASP* 2.8 48.0 + - - +
936A LYS* 6.0 1.2 - - - +
937A PHE* 3.8 12.2 - - + +
938A ARG* 3.9 26.6 - - - +
941A ILE* 3.4 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A SER 3.9 0.3 + - - -
745A VAL* 3.8 16.2 - - + -
746A ASP* 2.9 40.0 + - - +
747A ASN* 3.5 34.8 - - + +
750A VAL* 3.8 9.6 - - + -
799A LYS 2.9 13.5 + - - +
800A GLY 3.1 7.8 + - - +
802A ASN* 1.3 74.6 - - - +
804A LEU* 1.3 56.2 + - + +
806A ASP* 2.9 14.5 + - + +
807A ARG* 2.6 83.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A VAL* 4.1 6.5 - - + -
750A VAL* 4.1 14.4 - - + -
800A GLY 3.1 14.5 + - - +
801A MET* 3.6 30.3 - - + +
803A TYR* 1.3 80.7 - - + +
805A GLU* 1.3 64.8 + - - +
807A ARG* 3.1 5.4 + - - +
808A ARG 3.0 4.7 + - - -
809A LEU* 2.8 52.3 + - + +
811A HIS* 4.4 7.2 - - + -
829A ILE* 4.7 4.5 - - + -
832A PHE* 3.7 57.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A MET 2.8 20.4 + - - +
802A ASN* 3.7 11.3 + - - +
804A LEU* 1.3 73.9 - - - +
806A ASP* 1.3 61.1 + - - +
808A ARG* 2.7 28.2 + - - +
809A LEU 4.1 0.4 + - - -
869A HIS* 3.6 51.0 + - + +
870A GLN* 5.0 2.4 - - - +
873A VAL* 5.9 0.2 - - - +
936A LYS* 3.0 36.2 + - - -
937A PHE* 3.8 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ASN* 2.8 37.5 + - - +
803A TYR* 3.4 12.7 - - + +
805A GLU* 1.3 80.1 - - - +
807A ARG* 1.3 61.8 + - + +
808A ARG* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A VAL* 4.7 7.5 + - - +
744A SER* 2.7 45.2 + - - -
745A VAL* 3.6 6.5 - - - +
803A TYR* 2.6 77.6 + - + +
804A LEU 3.1 7.4 + - - +
806A ASP* 1.3 71.2 - - + +
808A ARG* 1.3 77.1 + - - +
809A LEU* 3.5 21.2 + - + +
----------------------------------------------------------
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