Contacts of the helix formed by residues 786 - 807 (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 GLY 786 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B ASN 4.1 1.8 + - - -
785B ILE* 1.3 80.4 - - - +
787B SER* 1.3 63.6 - - - -
788B GLN* 3.3 4.0 + - - -
789B TYR* 3.6 11.0 + - - +
790B LEU* 3.5 21.8 + - - +
957B ILE* 3.8 3.1 - - - -
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Residues in contact with SER 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B GLY* 1.3 70.5 - - - -
788B GLN* 1.3 64.8 + - - +
790B LEU* 3.6 0.4 + - - -
791B LEU* 3.2 30.0 + - - +
951B PRO* 2.7 40.2 - - - +
952B GLN* 3.6 13.0 + - - +
955B LEU* 3.8 25.0 - - - +
957B ILE* 3.5 23.8 - - - +
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Residues in contact with GLN 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B GLY* 3.3 1.3 - - - -
787B SER* 1.3 80.7 + - - +
789B TYR* 1.3 71.4 + - + +
791B LEU* 3.7 0.6 + - - -
792B ASN* 3.1 62.5 + - - +
948B ALA* 2.9 27.3 + - - +
951B PRO* 3.2 23.5 - - + +
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Residues in contact with TYR 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B TYR* 5.7 0.9 - + - -
785B ILE* 3.9 15.9 - - + -
786B GLY* 3.6 14.5 + - - +
787B SER 3.3 0.4 - - - -
788B GLN* 1.3 86.7 - - + +
790B LEU* 1.3 65.8 + - - +
792B ASN* 3.2 8.8 + - - +
793B TRP* 3.0 42.6 + + + -
824B PRO* 3.2 37.9 - - + +
825B GLN* 2.7 30.9 + - + +
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Residues in contact with LEU 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B VAL* 5.4 0.9 - - + -
785B ILE* 4.2 7.4 - - + +
786B GLY 3.5 15.8 + - - +
787B SER 3.9 1.3 - - - +
788B GLN 3.5 0.4 - - - -
789B TYR* 1.3 78.6 - - - +
791B LEU* 1.3 62.7 + - - +
793B TRP* 3.4 20.5 + - + +
794B CYS* 3.2 28.2 + - - -
883B LEU* 3.4 42.2 - - + +
884B MET* 4.4 6.1 - - + +
886B PHE* 4.1 21.8 - - + -
914B ILE* 4.2 13.0 - - + -
955B LEU* 3.9 15.7 - - + -
957B ILE* 4.0 20.2 - - + -
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Residues in contact with LEU 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B SER 3.2 13.6 + - - +
788B GLN 4.2 1.3 - - - +
790B LEU* 1.3 76.2 - - - +
792B ASN* 1.3 62.9 + - - +
794B CYS* 3.3 5.0 + - - +
795B VAL* 3.2 27.2 + - - +
884B MET* 4.2 5.8 - - + -
919B VAL* 4.8 7.6 - - + -
944B PHE* 3.7 30.0 - - + +
947B MET* 4.1 16.6 - - + +
948B ALA* 4.0 15.9 - - + +
951B PRO* 3.9 29.8 - - + +
954B TYR* 4.5 4.9 - - + -
955B LEU* 3.2 35.4 - - + -
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Residues in contact with ASN 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B GLN* 3.1 52.4 + - - +
789B TYR* 3.6 9.0 - - - +
791B LEU* 1.3 71.8 - - - +
793B TRP* 1.3 62.3 + - + +
794B CYS 3.1 1.6 - - - -
795B VAL* 3.2 7.7 + - - +
796B GLN* 2.9 45.9 + - + +
825B GLN* 6.3 1.8 - - - +
948B ALA* 3.6 12.0 - - - +
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Residues in contact with TRP 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B LEU* 3.9 26.9 - - + -
777B TYR* 3.8 32.3 - + - -
778B VAL* 3.7 21.5 - - + -
785B ILE* 3.9 29.4 - - + -
789B TYR* 3.0 31.0 + + + +
790B LEU* 3.6 22.9 - - + +
792B ASN* 1.3 79.2 - - + +
794B CYS* 1.3 53.7 + - - +
796B GLN* 3.8 12.7 - - - -
797B ILE* 2.8 41.2 + - - +
821B VAL* 6.2 0.4 - - + -
824B PRO* 3.0 30.8 + - + -
825B GLN* 4.7 0.9 - - - +
827B VAL* 3.9 24.5 - - + +
883B LEU* 4.0 13.5 - - + -
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Residues in contact with CYS 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B LEU 3.2 20.0 + - - -
791B LEU* 3.4 9.9 - - - +
793B TRP* 1.3 80.7 - - - +
795B VAL* 1.3 59.8 + - - +
797B ILE* 3.5 3.5 + - - -
798B ALA* 3.2 14.0 + - - +
876B TYR* 2.7 24.5 + - - +
880B VAL* 3.9 18.4 - - - -
883B LEU* 4.4 8.7 - - - -
884B MET* 3.4 28.9 - - - -
944B PHE* 3.5 27.4 - - + -
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Residues in contact with VAL 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LEU 3.2 17.0 + - - +
792B ASN* 3.5 9.4 - - - +
794B CYS* 1.3 72.7 - - - +
796B GLN* 1.3 63.2 + - + +
798B ALA* 3.2 6.0 + - - +
799B LYS* 2.8 63.4 + - + +
941B ILE* 4.5 6.7 - - + +
944B PHE* 3.5 37.0 - - + +
945B SER* 3.7 17.7 - - - +
948B ALA* 4.4 5.4 - - + -
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Residues in contact with GLN 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B HIS* 3.3 43.9 - - + +
792B ASN* 2.9 33.0 + - + +
793B TRP* 3.8 7.6 - - - +
795B VAL* 1.3 80.6 - - + +
797B ILE* 1.3 58.1 + - - +
799B LYS* 3.4 6.2 + - + -
800B GLY* 3.0 23.7 + - - -
825B GLN* 2.9 27.8 + - - +
826B HIS* 3.3 1.8 - - - -
827B VAL* 2.7 42.3 + - + -
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Residues in contact with ILE 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B LEU* 4.0 15.0 - - + -
793B TRP 2.8 29.0 + - - +
794B CYS* 4.6 1.1 - - - -
796B GLN* 1.3 75.9 - - - +
798B ALA* 1.3 57.1 + - - +
801B MET* 3.0 27.7 + - - +
814B LEU* 4.3 11.9 - - + -
819B VAL* 3.8 36.8 - - + -
827B VAL* 4.3 4.9 - - + -
829B ILE* 3.3 21.9 - - + +
876B TYR* 3.7 26.7 - - + -
879B THR* 4.2 11.7 - - + -
880B VAL* 6.3 0.9 - - + -
883B LEU* 4.1 14.8 - - + -
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Residues in contact with ALA 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B CYS 3.2 16.9 + - - +
795B VAL* 3.6 4.5 - - - +
797B ILE* 1.3 74.6 - - - +
799B LYS* 1.3 59.9 + - - +
800B GLY 3.2 1.8 - - - -
801B MET* 3.7 5.1 - - - +
802B ASN* 2.7 32.6 + - - +
876B TYR* 3.8 17.9 - - + +
937B PHE* 4.0 7.2 - - + +
940B LEU* 4.2 8.7 - - + -
941B ILE* 3.8 28.2 - - + +
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Residues in contact with LYS 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747B ASN* 4.4 6.3 + - - +
749B HIS* 4.0 25.5 + - + +
795B VAL* 2.8 56.1 + - + +
796B GLN* 3.7 5.6 - - + +
798B ALA* 1.3 72.6 - - - +
800B GLY* 1.3 58.5 + - - +
802B ASN* 3.3 2.1 + - - +
803B TYR* 2.9 28.4 + - - +
941B ILE* 3.8 29.8 - - + +
945B SER* 5.0 1.6 - - - -
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Residues in contact with GLY 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ASN* 4.0 2.2 - - - -
749B HIS* 3.8 15.4 - - - +
750B VAL* 3.5 27.6 - - - +
796B GLN 3.0 13.6 + - - -
797B ILE 3.9 2.0 - - - -
799B LYS* 1.3 77.7 - - - +
801B MET* 1.3 60.8 + - - +
803B TYR* 3.1 5.5 + - - +
804B LEU* 3.1 20.8 + - - +
829B ILE* 4.1 4.5 - - - -
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Residues in contact with MET 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ILE* 3.0 24.3 + - + +
798B ALA 3.7 0.7 - - - +
800B GLY* 1.3 74.8 - - - +
802B ASN* 1.3 57.8 + - - +
804B LEU* 3.4 21.0 + - + +
805B GLU* 2.8 28.2 + - - +
809B LEU 5.8 0.7 - - - +
811B HIS* 4.0 13.0 - - + +
814B LEU* 3.6 34.3 - - + -
829B ILE* 4.0 12.1 - - + +
872B ASP* 3.7 39.7 - - + +
937B PHE* 3.4 37.5 - - + -
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Residues in contact with ASN 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B ALA 2.7 21.7 + - - +
799B LYS 3.6 4.3 - - - +
801B MET* 1.3 70.3 - - - +
803B TYR* 1.3 67.1 + - - +
805B GLU* 3.3 11.0 + - - +
806B ASP* 2.9 47.5 + - - +
936B LYS* 5.9 1.0 - - - +
937B PHE* 3.8 11.8 - - + +
938B ARG* 4.0 32.0 - - - +
941B ILE* 3.5 24.4 - - + +
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Residues in contact with TYR 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A LYS* 6.3 1.3 - - + -
693A VAL* 4.8 21.3 - - + -
744B SER 3.9 0.3 + - - -
745B VAL* 3.8 15.5 - - + -
746B ASP* 2.9 39.7 + - - +
747B ASN* 3.5 33.9 - - + +
750B VAL* 4.2 9.4 - - + -
799B LYS 2.9 13.9 + - - +
800B GLY 3.1 7.6 + - - +
802B ASN* 1.3 76.2 - - - +
804B LEU* 1.3 55.6 + - + +
806B ASP* 2.9 12.1 + - + +
807B ARG* 2.6 83.8 + - + +
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Residues in contact with LEU 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745B VAL* 4.2 5.6 - - + -
750B VAL* 4.1 20.0 - - + -
800B GLY 3.1 16.2 + - - +
801B MET* 3.6 29.4 - - + +
803B TYR* 1.3 73.6 - - + +
805B GLU* 1.3 66.3 + - - +
807B ARG* 3.1 5.6 + - - +
808B ARG 3.0 4.9 + - - -
809B LEU* 2.8 49.1 + - + +
811B HIS* 4.4 7.2 - - + -
829B ILE* 4.5 4.5 - - + -
832B PHE* 3.8 52.7 - - + -
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Residues in contact with GLU 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A SER* 4.7 6.1 + - - -
801B MET 2.8 21.6 + - - +
802B ASN* 3.7 11.2 + - - +
803B TYR 3.2 0.2 - - - -
804B LEU* 1.3 73.2 - - - +
806B ASP* 1.3 60.7 + - - +
808B ARG* 2.7 27.4 + - - +
809B LEU 4.1 0.6 + - - -
869B HIS* 3.6 49.9 + - + +
870B GLN* 5.0 2.4 - - - +
873B VAL* 5.8 0.2 - - - +
936B LYS* 3.0 38.4 + - - -
937B PHE* 3.8 22.6 - - + +
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Residues in contact with ASP 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A VAL* 3.2 30.5 - - + +
694A LEU 4.1 3.6 - - - +
695A GLY* 3.3 18.7 + - - -
696A SER* 3.3 42.1 + - - +
701A THR* 4.1 5.4 + - - +
703A TYR* 5.1 1.6 + - - -
802B ASN* 2.9 36.1 + - - +
803B TYR* 2.9 12.8 + - + +
805B GLU* 1.3 78.0 - - - +
807B ARG* 1.3 57.7 + - - +
808B ARG* 3.3 9.9 + - - +
938B ARG* 6.2 0.2 - - - -
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Residues in contact with ARG 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A VAL* 3.5 27.0 - - + +
703A TYR* 6.0 0.2 - - - -
741B VAL* 4.6 10.3 + - - +
744B SER* 2.7 45.8 + - - -
745B VAL* 3.6 5.1 - - - +
803B TYR* 2.6 70.3 + - + +
804B LEU 3.1 6.7 + - - +
806B ASP* 1.3 75.0 - - - +
808B ARG* 1.3 77.2 + - - +
809B LEU* 3.5 23.0 + - + +
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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