Contacts of the helix formed by residues 786 - 807 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D ASN 4.1 1.6 + - - -
785D ILE* 1.3 78.1 - - - +
787D SER* 1.3 66.2 + - - -
788D GLN* 3.2 4.0 - - - -
789D TYR* 3.2 23.0 + - - +
790D LEU* 3.2 15.6 + - - +
957D ILE* 3.9 1.1 - - - -
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Residues in contact with SER 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786D GLY* 1.3 71.5 - - - -
788D GLN* 1.3 61.1 + - - +
790D LEU* 3.6 0.6 + - - -
791D LEU* 3.4 29.5 + - - +
951D PRO* 2.8 38.5 + - - +
952D GLN* 4.0 14.1 + - - -
955D LEU* 3.8 16.8 - - - +
957D ILE* 3.5 25.3 - - - +
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Residues in contact with GLN 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786D GLY* 3.2 1.3 - - - -
787D SER* 1.3 80.2 + - - +
789D TYR* 1.3 68.4 + - + +
791D LEU* 3.8 1.2 + - - +
792D ASN* 3.0 66.1 + - - +
948D ALA* 2.8 32.2 + - - +
949D ARG 5.6 0.2 - - - -
951D PRO* 3.7 21.5 - - + +
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Residues in contact with TYR 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777D TYR* 5.8 0.9 - + - -
785D ILE* 3.9 15.3 - - + -
786D GLY* 3.2 18.7 + - - +
788D GLN* 1.3 87.3 - - + +
790D LEU* 1.3 67.3 + - - +
792D ASN* 3.1 8.2 + - - +
793D TRP* 3.0 42.0 + + + +
824D PRO* 3.2 37.8 - - + +
825D GLN* 2.7 31.2 + - + +
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Residues in contact with LEU 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778D VAL* 5.3 0.7 - - + -
785D ILE* 4.1 10.8 - - + +
786D GLY 3.2 18.5 + - - +
787D SER 3.6 1.5 + - - +
788D GLN 3.6 0.2 - - - -
789D TYR* 1.3 78.3 - - - +
791D LEU* 1.3 58.6 + - - +
793D TRP* 3.4 22.2 + - + +
794D CYS* 3.1 32.1 + - - -
883D LEU* 3.1 45.1 - - + +
884D MET* 4.1 15.3 - - + +
886D PHE* 4.2 21.3 - - + -
914D ILE* 4.3 10.3 - - + -
955D LEU* 4.5 6.7 - - + -
957D ILE* 4.0 21.3 - - + -
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Residues in contact with LEU 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787D SER 3.4 12.5 + - - +
788D GLN 4.3 1.3 - - - +
789D TYR 3.3 0.4 - - - -
790D LEU* 1.3 77.3 - - - +
792D ASN* 1.3 63.2 + - - +
794D CYS* 3.4 6.9 - - - +
795D VAL* 3.1 28.1 + - - +
884D MET* 4.7 3.8 - - + -
919D VAL* 4.8 4.3 - - + -
944D PHE* 3.4 33.5 - - + +
947D MET* 3.8 30.1 - - + +
948D ALA* 4.1 14.0 - - + +
951D PRO* 3.9 27.8 - - + +
954D TYR* 4.6 4.0 - - + -
955D LEU* 3.3 31.9 - - + -
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Residues in contact with ASN 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788D GLN* 3.0 53.4 + - - +
789D TYR* 3.1 9.2 + - - +
791D LEU* 1.3 73.8 - - - +
793D TRP* 1.3 63.7 + - + +
794D CYS 3.1 1.1 - - - -
795D VAL* 3.2 7.8 + - - +
796D GLN* 2.8 46.3 + - - +
825D GLN* 6.2 2.7 - - - +
948D ALA* 3.5 12.0 - - - +
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Residues in contact with TRP 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D LEU* 3.9 27.1 - - + -
777D TYR* 3.8 32.3 - + - -
778D VAL* 3.7 21.8 - - + -
785D ILE* 3.8 28.7 - - + -
789D TYR* 3.0 25.9 + + + -
790D LEU* 3.5 29.4 - - + +
792D ASN* 1.3 78.5 - - + +
794D CYS* 1.3 58.0 + - - +
796D GLN* 3.8 13.0 - - - +
797D ILE* 2.8 38.4 + - - +
821D VAL* 6.1 0.4 - - + -
824D PRO* 3.0 29.6 + - + -
825D GLN* 4.6 1.2 - - - +
827D VAL* 3.9 24.5 - - + +
883D LEU* 4.0 13.7 - - + -
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Residues in contact with CYS 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790D LEU 3.1 23.4 + - - -
791D LEU* 3.4 10.5 - - - +
792D ASN 3.1 0.2 - - - -
793D TRP* 1.3 78.1 - - - +
795D VAL* 1.3 59.6 + - - +
797D ILE* 3.5 4.0 + - - -
798D ALA* 3.2 14.2 + - - +
876D TYR* 2.7 24.8 + - - +
880D VAL* 3.9 17.7 - - - -
883D LEU* 4.5 8.7 - - - -
884D MET* 3.4 28.3 - - - -
944D PHE* 3.5 26.9 - - + -
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Residues in contact with VAL 795 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791D LEU 3.1 16.6 - - - +
792D ASN* 3.2 8.5 + - - +
794D CYS* 1.3 74.8 - - - +
796D GLN* 1.3 62.5 + - + +
798D ALA* 3.3 5.3 + - - +
799D LYS* 2.8 63.7 + - + +
941D ILE* 4.4 6.3 - - + +
944D PHE* 3.5 37.2 - - + +
945D SER* 3.5 17.0 - - - +
948D ALA* 4.3 6.3 - - + -
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Residues in contact with GLN 796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749D HIS* 3.3 45.4 + - + +
792D ASN* 2.8 34.7 + - + +
793D TRP* 3.8 6.8 - - - +
795D VAL* 1.3 79.0 - - + +
797D ILE* 1.3 63.2 + - - +
799D LYS* 3.4 7.5 + - + -
800D GLY* 3.0 18.5 + - - -
825D GLN 2.8 27.8 + - - -
826D HIS* 3.3 1.4 - - - -
827D VAL* 2.7 41.5 + - + -
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Residues in contact with ILE 797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D LEU* 4.1 5.8 - - + -
793D TRP 2.8 28.3 + - - +
794D CYS* 4.0 1.3 - - - +
795D VAL 3.2 0.2 - - - -
796D GLN* 1.3 76.4 - - - +
798D ALA* 1.3 58.3 + - - +
801D MET* 3.0 24.9 + - + +
814D LEU* 4.1 16.8 - - + -
819D VAL* 3.8 35.0 - - + -
827D VAL* 4.3 5.2 - - + -
829D ILE* 3.0 27.8 - - + +
876D TYR* 3.8 26.2 - - + -
879D THR* 4.1 11.7 - - + -
880D VAL* 6.3 0.7 - - + -
883D LEU* 4.1 22.7 - - + -
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Residues in contact with ALA 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794D CYS 3.2 17.6 + - - +
795D VAL* 3.7 4.0 - - - +
796D GLN 3.2 0.2 - - - -
797D ILE* 1.3 74.9 - - - +
799D LYS* 1.3 55.4 + - - +
800D GLY 3.2 0.2 - - - -
801D MET* 3.7 5.6 - - - +
802D ASN* 2.7 37.4 + - - +
876D TYR* 3.8 17.9 - - + +
937D PHE* 4.1 9.6 - - + +
940D LEU* 4.3 5.8 - - + -
941D ILE* 3.8 29.3 - - + +
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Residues in contact with LYS 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D ASN* 4.4 7.2 + - - +
749D HIS* 4.0 24.2 + - + +
795D VAL* 2.8 55.5 + - + +
796D GLN* 3.7 5.4 - - + +
798D ALA* 1.3 72.3 - - - +
800D GLY* 1.3 57.8 + - - +
802D ASN* 3.4 1.9 + - - +
803D TYR* 2.9 28.2 + - - +
941D ILE* 3.8 29.8 - - + -
945D SER* 4.9 3.0 + - - -
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Residues in contact with GLY 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D ASN* 4.0 2.2 - - - -
749D HIS* 3.8 11.1 - - - +
750D VAL* 3.5 23.2 - - - +
796D GLN 3.0 11.4 + - - -
799D LYS* 1.3 77.4 - - - +
801D MET* 1.3 60.6 + - - +
803D TYR* 3.1 5.4 + - - +
804D LEU* 3.1 20.7 + - - +
829D ILE* 3.7 18.4 - - - -
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Residues in contact with MET 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D ILE* 3.0 25.0 + - + +
798D ALA 3.7 0.7 - - - +
800D GLY* 1.3 75.4 - - - +
802D ASN* 1.3 58.6 + - - +
804D LEU* 3.4 18.2 + - + +
805D GLU* 2.8 28.8 + - - +
809D LEU 5.8 0.7 - - - +
811D HIS* 3.9 18.6 - - + +
814D LEU* 3.7 22.9 - - + -
829D ILE* 3.6 16.2 - - + -
872D ASP* 3.7 40.2 - - + +
937D PHE* 3.4 40.2 - - + -
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Residues in contact with ASN 802 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696C SER* 3.4 26.5 + - - -
798D ALA 2.7 21.9 + - - +
799D LYS 3.7 2.7 - - - +
801D MET* 1.3 71.2 - - - +
803D TYR* 1.3 58.7 + - - +
805D GLU* 3.7 11.1 + - - +
806D ASP* 2.9 48.2 + - - +
936D LYS* 6.0 1.2 - - - +
937D PHE* 3.8 12.2 - - + +
938D ARG* 4.0 24.9 - - - +
941D ILE* 3.4 25.2 - - + +
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Residues in contact with TYR 803 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703C TYR* 4.8 15.7 - - - -
744D SER 3.9 0.3 + - - -
745D VAL* 3.8 16.2 - - + -
746D ASP* 2.9 38.9 + - - +
747D ASN* 3.6 35.2 - - + +
750D VAL* 4.0 9.9 - - + -
799D LYS 2.9 14.1 + - - +
800D GLY 3.1 8.0 + - - +
802D ASN* 1.3 76.5 - - - +
804D LEU* 1.3 57.0 + - + +
806D ASP* 2.9 13.6 + - + +
807D ARG* 2.6 84.1 + - + +
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Residues in contact with LEU 804 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745D VAL* 4.3 8.1 - - + -
750D VAL* 4.3 13.9 - - + -
800D GLY 3.1 15.1 + - - +
801D MET* 3.6 29.8 - - + +
803D TYR* 1.3 76.7 - - + +
805D GLU* 1.3 67.0 + - - +
807D ARG* 3.1 5.4 + - - +
808D ARG 2.9 4.9 + - - -
809D LEU* 2.8 50.8 + - + +
811D HIS* 4.3 6.7 - - + -
829D ILE* 4.9 4.0 - - + -
832D PHE* 3.7 56.1 - - + -
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Residues in contact with GLU 805 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724C ARG* 2.9 45.7 + - - +
801D MET 2.8 21.4 + - - +
802D ASN* 3.7 13.0 + - - +
803D TYR 3.2 0.2 - - - -
804D LEU* 1.3 73.0 - - - +
806D ASP* 1.3 57.4 + - - +
808D ARG* 2.7 22.7 + - - -
809D LEU 4.1 0.4 + - - -
869D HIS* 3.6 42.4 - - + +
870D GLN* 5.1 2.1 - - - +
936D LYS* 3.0 37.0 + - - -
937D PHE* 3.8 22.4 - - + +
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Residues in contact with ASP 806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696C SER* 4.0 6.2 + - - -
700C GLY 5.1 1.4 - - - -
701C THR* 2.8 28.1 + - - +
724C ARG* 3.4 42.0 + - + +
802D ASN* 2.9 33.3 + - - +
803D TYR* 3.4 12.9 - - + +
805D GLU* 1.3 77.5 - - - +
807D ARG* 1.3 62.0 + - + +
808D ARG* 3.1 5.2 + - - +
938D ARG* 6.2 0.3 - - - -
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Residues in contact with ARG 807 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741D VAL* 4.3 13.3 - - - +
744D SER* 2.7 42.4 + - - -
745D VAL* 3.6 8.1 - - - +
803D TYR* 2.6 79.0 + - + +
804D LEU 3.1 7.2 + - - +
806D ASP* 1.3 72.5 - - + +
808D ARG* 1.3 76.1 + - - +
809D LEU* 3.5 21.2 + - + +
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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) + - + + + + + -
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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