Contacts of the helix formed by residues 883 - 901 (chain B) in PDB entry 6MZL
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 PHE 883 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASP* 5.1 7.4 - - - -
327B THR 4.7 2.2 - - - -
328B ASN* 3.2 28.9 - - - -
847B ARG* 4.3 21.8 - - + -
848B HIS* 4.2 7.8 + + + -
882B HIS* 1.3 83.1 - - - +
884B VAL* 1.3 80.0 + - + +
885B ASP* 3.1 40.4 - - + -
886B ILE* 3.7 22.5 - - + +
887B ARG* 3.2 22.8 + - - +
222K PRO* 4.0 20.0 - - + +
223K TYR* 4.2 23.1 - - + -
226K ALA* 4.2 15.5 - - + -
227K LEU* 6.0 4.7 - - + -
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Residues in contact with VAL 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP* 4.7 14.1 - - - +
311B GLU* 6.1 6.1 - - + -
328B ASN* 5.4 8.7 - - - +
882B HIS 4.0 0.2 + - - -
883B PHE* 1.3 82.9 - - + +
885B ASP* 1.3 63.1 - - - +
887B ARG* 2.9 10.1 + - - +
888B ILE* 2.6 58.7 + - + +
919B VAL* 5.0 16.2 - - + -
921B TYR* 4.6 14.1 - - + -
922B VAL* 4.9 9.4 - - + -
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Residues in contact with ASP 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN* 4.9 6.3 + - - -
847B ARG* 3.3 36.3 + - + +
852B VAL* 3.7 16.6 - - + +
883B PHE* 3.1 28.6 - - + -
884B VAL* 1.3 82.0 - - - +
886B ILE* 1.3 66.0 + - - +
888B ILE* 3.3 13.9 - - + +
889B ALA* 3.0 24.4 + - - +
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Residues in contact with ILE 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B ARG 4.4 1.8 - - - +
848B HIS* 3.5 48.2 - - + +
851B THR* 4.8 7.9 - - + -
852B VAL* 3.9 11.4 - - + +
855B LEU* 4.3 12.7 - - + +
877B TYR* 4.0 34.3 - - + +
882B HIS* 4.1 13.5 - - + +
883B PHE* 3.7 25.4 - - + +
885B ASP* 1.3 77.5 - - - +
887B ARG* 1.3 58.0 + - - +
889B ALA* 3.1 4.4 + - - +
890B ALA* 2.9 27.5 + - - +
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Residues in contact with ARG 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B TYR 3.5 10.5 - - - +
878B ALA* 3.5 18.0 + - - +
879B GLU 2.8 23.9 + - - +
880B TYR* 2.7 61.2 + - - +
882B HIS* 5.0 3.6 + - + +
883B PHE 3.2 19.4 + - - +
884B VAL* 2.9 6.4 + - - +
886B ILE* 1.3 77.8 - - - +
888B ILE* 1.3 58.5 + - - +
890B ALA* 3.3 2.3 + - - +
891B LEU* 3.0 43.0 + - + +
913B MET* 4.8 11.1 - - - +
917B ASP* 4.5 18.8 + - - +
919B VAL* 4.3 13.0 - - - +
922B VAL* 4.3 18.6 - - + +
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Residues in contact with ILE 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ARG* 6.0 2.0 - - - +
884B VAL* 2.6 26.5 + - + +
885B ASP* 3.3 22.9 - - + +
887B ARG* 1.3 74.0 - - - +
889B ALA* 1.3 61.9 + - + +
891B LEU* 3.3 9.4 + - + +
892B GLU* 3.0 41.5 + - + +
921B TYR* 3.8 24.2 - - + +
922B VAL* 5.1 7.6 - - + -
925B LYS* 3.6 44.2 - - + -
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Residues in contact with ALA 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B VAL* 3.8 31.4 - - + +
855B LEU* 5.1 7.1 - - + +
856B ARG* 4.4 17.4 - - + +
885B ASP 3.0 16.4 + - - +
886B ILE 3.8 2.9 - - - +
888B ILE* 1.3 77.0 - - + +
890B ALA* 1.3 59.8 + - - +
892B GLU* 3.3 13.6 + - - +
893B ALA* 2.9 28.3 + - - +
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Residues in contact with ALA 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B LEU* 5.0 6.4 - - + +
874B PHE* 3.5 27.3 - - - +
877B TYR* 3.5 33.0 - - + +
878B ALA* 3.9 3.1 - - - +
886B ILE 2.9 10.1 + - - +
887B ARG 3.3 3.8 + - - +
889B ALA* 1.3 79.0 - - - +
891B LEU* 1.3 57.1 + - - +
893B ALA* 3.2 7.4 + - - +
894B VAL* 2.9 31.0 + - - +
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Residues in contact with LEU 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B ALA* 3.7 22.4 - - + -
887B ARG* 3.0 31.6 + - + +
888B ILE* 3.7 8.3 - - + +
889B ALA 3.2 0.2 - - - -
890B ALA* 1.3 74.6 - - - +
892B GLU* 1.3 65.4 + - + +
894B VAL* 3.4 16.3 - - + +
895B VAL* 2.9 31.8 + - + +
909B TRP* 4.6 2.0 - - + -
910B LEU* 4.4 13.2 - - + -
913B MET* 4.2 17.0 - - + -
922B VAL* 4.5 12.3 - - + +
925B LYS 6.2 0.7 - - - -
926B ILE* 3.7 35.9 - - + +
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Residues in contact with GLU 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ARG* 4.0 25.5 + - - +
888B ILE* 3.0 30.5 + - + +
889B ALA* 3.5 13.8 - - - +
891B LEU* 1.3 75.3 - - - +
893B ALA* 1.3 61.1 + - - +
895B VAL* 3.4 8.6 + - - +
896B ASP* 3.1 25.3 + - - +
925B LYS* 5.4 6.0 - - + +
929B MET* 3.7 43.3 - - + +
933B ASN* 5.9 0.7 + - - -
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Residues in contact with ALA 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B LEU* 5.2 4.3 - - + +
856B ARG* 6.1 1.8 - - + -
859B ARG* 3.2 34.3 - - + +
874B PHE* 3.9 25.1 - - + -
889B ALA 2.9 14.5 + - - +
890B ALA* 3.4 10.1 - - - +
891B LEU 3.2 0.2 - - - -
892B GLU* 1.3 76.3 - - - +
894B VAL* 1.3 57.1 + - - +
896B ASP* 3.1 3.5 + - - -
897B TYR* 2.9 23.8 + - - +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PRO* 4.5 22.9 - - + +
874B PHE* 4.9 11.9 - - + -
875B LYS* 5.6 4.3 - - + +
878B ALA* 5.6 1.8 - - + -
890B ALA 2.9 20.1 + - - +
891B LEU* 3.4 26.2 - - + +
893B ALA* 1.3 76.1 - - - +
895B VAL* 1.3 62.0 + - + +
897B TYR* 3.8 9.2 - - + -
898B THR* 2.9 40.0 + - - +
906B GLU* 4.8 16.2 - - + +
909B TRP* 4.8 12.3 - - + -
910B LEU* 5.3 6.7 - - + +
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Residues in contact with VAL 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B LEU* 2.9 22.4 + - + +
892B GLU* 3.5 8.1 - - - +
894B VAL* 1.3 77.2 - - + +
896B ASP* 1.3 58.4 + - - +
898B THR* 3.3 6.8 + - - -
899B LYS* 2.8 25.3 + - - +
910B LEU* 4.1 18.8 - - + -
926B ILE* 4.8 6.3 - - + +
929B MET* 3.7 16.4 - - + +
930B LEU* 3.8 31.6 - - + +
933B ASN* 3.3 29.3 - - + +
935B PRO* 5.0 1.9 - - - +
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Residues in contact with ASP 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859B ARG* 3.0 29.9 + - - +
863B LYS* 3.2 23.8 + - - +
892B GLU 3.1 12.5 + - - +
893B ALA* 3.1 4.4 + - - +
895B VAL* 1.3 73.2 - - - +
897B TYR* 1.3 65.0 + - - +
899B LYS* 3.2 24.8 + - - +
900B VAL* 3.0 22.2 + - - +
933B ASN* 3.8 26.3 + - - +
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Residues in contact with TYR 897 (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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859B ARG* 3.3 27.0 - - - +
862B GLN* 3.8 6.1 - - - -
869B SER* 2.8 44.5 + - - -
870B ASP* 3.9 2.0 + - - -
871B PRO* 3.4 42.1 - - + +
874B PHE* 5.9 2.5 - + + -
893B ALA 2.9 10.1 + - - +
894B VAL* 3.3 16.4 - - + +
895B VAL 3.2 0.2 - - - -
896B ASP* 1.3 77.0 - - - +
898B THR* 1.3 65.8 + - - +
901B ASP* 2.9 60.2 + - + +
903B SER* 3.9 24.6 - - - -
906B GLU* 5.3 1.6 - - + -
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Residues in contact with THR 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B VAL* 2.9 21.7 + - - +
895B VAL* 3.9 5.4 - - - -
897B TYR* 1.3 81.1 - - - +
899B LYS* 1.3 61.8 + - - +
901B ASP 2.8 14.5 - - - +
902B ARG* 4.6 2.5 - - - -
903B SER* 3.3 28.3 + - - +
906B GLU* 4.6 4.5 - - - +
907B LEU* 3.7 34.8 + - + -
910B LEU* 5.8 3.8 - - - +
930B LEU* 6.4 0.7 - - - -
935B PRO* 3.3 19.9 - - + +
936B PHE* 5.5 2.9 - - + -
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Residues in contact with LYS 899 (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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863B LYS* 6.1 0.2 - - - +
895B VAL 2.8 14.9 + - - +
896B ASP* 3.2 28.5 + - - +
897B TYR 3.1 0.4 - - - -
898B THR* 1.3 80.7 - - - +
900B VAL* 1.3 80.3 + - + +
901B ASP 3.4 1.2 - - - +
902B ARG* 5.3 0.3 - - - -
933B ASN* 4.9 15.3 + - + +
934B PRO* 3.4 28.1 - - - +
935B PRO* 3.8 14.9 - - + +
937B THR* 6.1 0.2 - - - -
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Residues in contact with VAL 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859B ARG* 4.7 8.3 - - - +
863B LYS* 5.2 11.0 - - + +
896B ASP* 3.0 10.8 + - - +
899B LYS* 1.3 100.3 - - + +
901B ASP* 1.3 67.0 + - - +
902B ARG* 3.8 2.9 + - - +
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Residues in contact with ASP 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859B ARG* 5.4 0.6 - - - +
869B SER* 3.8 14.6 + - - +
897B TYR* 2.9 60.5 + - + +
898B THR* 2.8 24.8 - - - +
899B LYS 3.4 0.9 - - - +
900B VAL* 1.3 79.2 - - - +
902B ARG* 1.3 74.8 + - - +
903B SER* 3.4 7.7 + - - -
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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