Contacts of the helix formed by residues 868 - 885 (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 THR 868 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A VAL* 3.7 18.9 - - - +
860A GLU* 5.0 2.6 + - - -
866A ILE* 4.0 20.4 - - + +
867A TYR* 1.3 81.2 - - - +
869A HIS* 1.3 63.8 + - - +
870A GLN* 3.2 19.4 + - - +
871A SER* 2.7 27.4 + - - -
872A ASP* 3.1 6.6 + - - -
931A ALA* 5.2 2.1 - - - +
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Residues in contact with HIS 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLU* 3.6 61.9 + - + +
808A ARG* 4.0 8.9 - - - +
809A LEU 3.1 39.6 + - - -
810A VAL* 3.7 14.4 - - + +
868A THR* 1.3 76.2 - - - +
870A GLN* 1.3 61.7 + - - +
872A ASP* 3.3 12.7 + - - +
873A VAL* 3.0 28.9 + - - +
937A PHE* 3.8 4.8 - - + -
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Residues in contact with GLN 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLU* 5.0 2.1 - - - +
868A THR* 3.1 10.4 + - - +
869A HIS* 1.3 87.5 - - - +
871A SER* 1.3 62.7 + - - +
873A VAL* 3.2 18.3 + - - +
874A TRP 3.3 6.8 + - - -
931A ALA* 3.1 41.1 + - + +
932A ASP* 4.2 11.3 - - - +
934A ARG* 3.1 46.7 + - - +
935A PRO 3.1 16.7 + - - +
936A LYS* 4.4 18.7 - - - +
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Residues in contact with SER 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A VAL* 4.9 0.3 - - - +
858A ALA* 4.0 7.7 + - - +
860A GLU* 3.9 12.6 - - - -
861A SER* 3.7 21.7 + - - -
866A ILE 4.3 2.0 - - - -
867A TYR* 3.5 9.5 - - - +
868A THR* 2.7 39.1 + - - -
870A GLN* 1.3 74.8 - - - +
872A ASP* 1.3 66.7 + - - +
874A TRP* 3.2 12.8 + - - +
875A SER* 3.2 16.9 + - - -
934A ARG* 3.9 8.2 - - - +
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Residues in contact with ASP 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A MET* 3.7 19.8 - - + +
809A LEU 4.6 1.2 - - - +
810A VAL* 3.4 12.4 - - - +
811A HIS* 2.8 35.8 + - - +
812A ARG* 3.2 24.6 + - - -
814A LEU* 3.9 6.7 - - - +
868A THR 3.1 11.4 + - - +
869A HIS* 3.4 15.2 + - - +
870A GLN 3.3 0.2 - - - -
871A SER* 1.3 74.5 + - - +
873A VAL* 1.3 60.7 + - - +
875A SER* 3.3 8.4 + - - -
876A TYR* 2.8 29.1 + - - +
937A PHE* 3.7 5.8 - - + -
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Residues in contact with VAL 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A HIS 3.0 18.3 + - - +
870A GLN* 3.4 19.1 - - - +
871A SER 3.1 0.4 - - - -
872A ASP* 1.3 79.1 - - - +
874A TRP* 1.3 63.0 + - - +
876A TYR* 3.0 12.0 + - - +
877A GLY 3.0 10.7 + - - -
926A CYS* 3.7 31.3 - - + +
934A ARG* 4.1 8.7 - - + -
935A PRO* 3.2 28.9 - - + +
937A PHE* 3.7 32.5 - - + +
940A LEU* 4.3 4.9 - - + -
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Residues in contact with TRP 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A LYS 5.5 1.2 + - - -
856A TRP 3.6 18.8 - - - -
857A MET 3.4 8.1 + - - -
858A ALA* 3.4 23.3 - - + -
859A LEU* 4.2 15.5 - - + -
870A GLN 3.3 5.2 + - - +
871A SER 3.2 12.0 + - - +
873A VAL* 1.3 77.5 - - - +
875A SER* 1.3 56.5 + - - +
877A GLY* 2.9 18.4 + - - -
878A VAL* 3.2 17.7 + - + +
891A TYR* 5.0 5.5 + - - -
903A LEU* 4.0 31.8 - - + +
908A ARG* 4.0 13.2 - - - -
926A CYS 3.4 12.3 + - - +
927A TRP* 3.1 49.8 + + + -
928A MET 3.1 24.5 - - - -
929A ILE* 4.6 3.4 - - + -
934A ARG* 3.4 26.0 - - - +
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Residues in contact with SER 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A ARG 5.1 5.4 + - - -
813A ASP* 5.7 0.4 - - - -
814A LEU* 3.5 30.7 + - - +
856A TRP* 3.0 26.6 + - - +
857A MET* 4.6 3.5 - - - +
871A SER 3.2 11.6 + - - -
872A ASP* 3.7 11.6 + - - -
873A VAL 3.3 0.2 - - - -
874A TRP* 1.3 77.6 - - - +
876A TYR* 1.3 57.0 + - - +
878A VAL* 3.2 6.1 + - - +
879A THR* 2.8 32.0 + - - -
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Residues in contact with TYR 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A CYS* 2.7 34.8 + - - +
797A ILE* 3.8 29.2 - - + -
798A ALA* 3.8 17.2 - - + +
801A MET* 4.6 0.2 - - + -
814A LEU* 3.6 13.0 - - + -
872A ASP 2.8 15.2 + - - +
873A VAL 3.2 9.9 - - - +
874A TRP 3.0 0.2 - - - -
875A SER* 1.3 74.9 - - - +
877A GLY* 1.3 61.6 + - - +
879A THR* 3.1 5.7 + - + -
880A VAL* 2.9 47.5 + - + +
926A CYS* 4.2 4.7 - - - -
937A PHE* 3.7 19.1 - + + -
940A LEU* 3.7 26.9 - - + -
944A PHE* 3.6 24.8 - + - -
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Residues in contact with GLY 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A VAL 3.0 6.5 + - - -
874A TRP 2.9 8.4 + - - -
876A TYR* 1.3 80.0 - - - +
878A VAL* 1.3 54.6 + - - +
880A VAL* 3.5 7.0 + - - +
881A TRP* 3.0 26.2 + - - +
923A MET* 3.9 7.1 - - - +
926A CYS* 4.0 17.7 - - - -
927A TRP* 3.5 19.9 - - - -
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Residues in contact with VAL 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A LYS 3.8 15.9 - - - +
856A TRP* 3.4 30.5 - - + +
874A TRP* 3.2 23.6 + - + +
875A SER 3.6 6.3 - - - +
876A TYR 3.2 0.4 - - - -
877A GLY* 1.3 72.1 - - - +
879A THR* 1.3 61.1 + - - +
881A TRP* 3.0 9.8 + - + +
882A GLU* 2.8 27.5 + - + +
890A PRO* 3.8 25.4 - - + -
891A TYR* 5.3 2.0 - - - +
909A LEU* 4.2 13.5 - - + -
927A TRP* 3.7 16.6 - - - +
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Residues in contact with THR 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A ILE* 4.2 26.2 - - + -
814A LEU* 3.5 24.0 + - + +
815A ALA* 3.5 7.8 - - - +
816A ALA* 3.6 25.6 - - + +
819A VAL* 4.7 2.2 - - + -
875A SER 2.8 15.2 + - - -
876A TYR* 3.3 11.9 - - + -
878A VAL* 1.3 76.2 - - - +
880A VAL* 1.3 63.4 + - + +
882A GLU* 3.1 14.5 + - - +
883A LEU* 3.0 27.4 + - + +
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Residues in contact with VAL 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A CYS* 3.8 13.9 - - - -
797A ILE* 6.3 0.7 - - + -
876A TYR* 2.9 55.0 + - + +
877A GLY* 3.7 6.5 - - - +
879A THR* 1.3 76.0 - - + +
881A TRP* 1.3 59.1 + - - +
883A LEU* 3.0 12.9 + - + +
884A MET* 2.8 59.8 + - + +
919A VAL* 5.3 1.1 - - + -
923A MET* 4.0 19.5 - - + -
944A PHE* 4.4 9.0 - - + -
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Residues in contact with TRP 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A GLY 3.0 10.1 + - - +
878A VAL* 3.0 14.0 + - - +
880A VAL* 1.3 76.9 - - - +
882A GLU* 1.3 68.0 + - - +
884A MET* 3.2 3.7 + - - -
885A THR* 3.0 42.1 + - + +
888A SER* 3.6 24.9 - - - -
889A LYS 3.6 15.3 - - - -
890A PRO* 3.3 34.3 - - + -
891A TYR 4.6 1.3 - - - -
909A LEU* 3.7 30.0 - - + +
910A PRO* 2.7 47.9 + - + -
912A PRO* 3.7 11.2 - - + +
923A MET* 3.0 35.9 - - + -
927A TRP* 4.4 0.9 - + + -
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Residues in contact with GLU 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A LEU* 4.0 17.1 - - + +
815A ALA* 4.9 0.5 - - - +
816A ALA* 3.0 41.8 + - + +
817A ARG* 4.9 0.3 + - - +
856A TRP* 3.0 42.1 + - + +
878A VAL* 2.8 19.1 + - + +
879A THR* 3.1 13.1 + - - +
881A TRP* 1.3 79.9 - - + +
883A LEU* 1.3 61.2 + - - +
885A THR* 3.1 7.9 + - - -
886A PHE 3.0 3.3 + - - -
887A GLY* 2.7 35.1 + - - -
888A SER 4.2 14.8 - - - +
890A PRO* 4.6 1.5 - - + +
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Residues in contact with LEU 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774A LEU* 3.8 27.4 - - + -
778A VAL* 4.2 17.1 - - + +
790A LEU* 3.6 26.5 - - + +
793A TRP* 4.0 29.2 - - + -
794A CYS* 4.5 16.4 - - - -
797A ILE* 4.1 17.5 - - + -
816A ALA* 4.1 15.5 - - + -
879A THR* 3.0 17.7 + - + +
880A VAL* 3.0 10.6 + - + +
882A GLU* 1.3 81.0 - - - +
884A MET* 1.3 60.5 + - + +
885A THR 3.1 0.2 - - - -
886A PHE* 2.9 22.9 + - - -
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Residues in contact with MET 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A LEU* 4.4 13.9 - - + -
791A LEU* 4.1 20.4 - - + -
794A CYS* 3.4 33.7 - - - -
880A VAL* 2.8 31.3 + - + +
881A TRP* 3.8 4.7 - - - +
883A LEU* 1.3 74.8 - - + +
885A THR* 1.3 59.1 + - - +
886A PHE* 3.9 3.3 + - - -
912A PRO* 3.9 11.1 - - + +
913A PRO* 5.6 0.7 - - - +
914A ILE* 2.8 33.9 - - + +
915A CYS* 3.6 23.1 - - - -
919A VAL* 4.5 6.3 - - + -
923A MET* 4.8 2.0 - - - -
944A PHE* 4.6 0.7 - - + -
955A LEU* 3.4 31.2 - - + -
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Residues in contact with THR 885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A TRP* 3.0 45.4 + - + +
882A GLU* 3.1 10.4 + - - -
883A LEU 3.1 0.2 - - - -
884A MET* 1.3 74.8 - - - +
886A PHE* 1.3 75.2 + - - +
888A SER* 3.1 37.3 + - - -
912A PRO* 3.7 22.4 - - + -
913A PRO* 5.4 4.3 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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