Contacts of the helix formed by residues 904 - 920 (chain B) in PDB entry 1ZY5
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 GLU 904 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827B HIS* 3.4 54.2 - - + +
831B ILE 4.9 0.2 - - - +
832B ILE* 3.5 22.8 - - + +
903B ASN* 1.3 91.9 - - - +
905B LYS* 1.3 83.6 + - + +
906B ILE* 3.2 2.2 + - - -
907B ASP* 3.2 12.4 + - - +
908B MET* 4.1 1.5 + - + +
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Residues in contact with LYS 905 (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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903B ASN* 2.8 33.0 + - - +
904B GLU* 1.3 93.4 - - + +
906B ILE* 1.3 61.5 + - - +
907B ASP 3.1 0.2 - - - -
908B MET* 3.0 33.4 + - + +
909B TYR 3.3 4.9 + - - -
966B PRO* 3.5 21.4 + - + +
967B ASN* 5.0 4.9 + - - +
969B ARG* 2.6 48.4 + - + +
970B PRO* 4.3 0.2 - - - +
971B GLY* 3.6 22.4 - - - +
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Residues in contact with ILE 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B ILE* 3.9 22.7 - - + -
834B ARG* 4.0 24.9 - - + +
892B ALA* 3.6 19.9 + - + +
894B GLU* 3.7 20.2 - - - +
895B VAL* 4.3 9.2 - - + -
902B TYR* 3.8 33.2 - - + -
903B ASN 3.5 15.0 - - - +
905B LYS* 1.3 76.8 - - - +
907B ASP* 1.3 67.8 + - - +
909B TYR* 3.2 4.3 + - - +
910B SER* 3.1 24.5 + - - -
969B ARG* 3.6 7.6 - - - +
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Residues in contact with ASP 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823B LEU* 4.0 14.1 - - + +
827B HIS* 2.9 28.3 + - + +
832B ILE* 3.1 11.7 - - - +
833B HIS* 2.9 31.4 + - - +
834B ARG* 3.0 28.2 + - - -
836B LEU* 3.6 10.9 - - + +
904B GLU 3.2 6.7 + - - +
905B LYS 3.1 0.6 - - - -
906B ILE* 1.3 82.1 - - - +
908B MET* 1.3 59.6 + - - +
910B SER* 3.3 9.2 + - - -
911B LEU* 2.9 28.3 + - - +
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Residues in contact with MET 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B LEU* 3.8 17.5 - - + -
823B LEU* 4.2 6.7 - - - -
827B HIS* 4.1 14.8 - - + -
904B GLU* 4.3 2.2 - - + +
905B LYS* 3.0 28.7 + - + +
907B ASP* 1.3 78.3 - - - +
909B TYR* 1.3 56.7 + - - +
911B LEU* 3.3 12.7 - - + +
912B GLY 2.9 21.0 + - - -
961B LEU* 3.5 34.0 - - + +
969B ARG* 4.7 7.2 - - + -
970B PRO 3.6 24.5 - - - +
971B GLY* 3.9 1.6 - - - +
972B ALA* 3.7 38.6 - - - +
975B LEU* 4.4 0.9 - - + -
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Residues in contact with TYR 909 (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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890B TYR 4.0 7.0 - - - -
891B VAL 3.7 13.2 - - - -
892B ALA* 3.9 15.0 - - + -
893B THR* 3.6 31.9 - - + +
905B LYS 3.3 2.4 + - - -
906B ILE 3.2 9.6 + - - +
907B ASP 3.2 0.2 - - - -
908B MET* 1.3 75.4 - - - +
910B SER* 1.3 60.6 + - - +
912B GLY* 2.5 27.5 + - - -
913B ILE* 3.1 25.8 + - + +
936B ARG* 3.5 34.3 + - - +
961B LEU 3.2 12.7 + - - +
962B ILE* 3.7 37.6 + - + +
963B ASP 4.2 2.5 - - - -
964B HIS* 5.2 0.7 + - - -
969B ARG* 3.6 31.4 - - - +
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Residues in contact with SER 910 (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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834B ARG 5.8 1.9 - - - -
836B LEU* 3.5 37.5 + - - +
890B TYR* 2.8 28.8 + - - +
891B VAL* 5.0 0.7 - - - -
892B ALA 5.1 0.5 + - - -
906B ILE 3.1 10.2 + - - -
907B ASP* 3.5 9.7 + - - -
909B TYR* 1.3 79.7 - - - +
911B LEU* 1.3 57.2 + - - +
913B ILE* 3.3 5.0 + - - +
914B ILE* 2.9 33.5 + - - +
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Residues in contact with LEU 911 (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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816B PHE* 3.7 36.3 - - + -
819B ILE* 3.7 31.4 - - + -
820B LEU* 4.0 22.7 - - + -
823B LEU* 3.9 20.4 - - + -
836B LEU* 4.2 6.7 - - + +
907B ASP 2.9 13.7 + - - +
908B MET* 3.3 18.4 - - + +
910B SER* 1.3 74.3 - - - +
912B GLY* 1.3 65.4 + - - +
914B ILE* 4.2 12.3 - - + -
915B PHE* 2.8 24.6 + - - +
918B MET* 6.0 0.2 - - - -
961B LEU* 4.4 3.6 - - + -
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Residues in contact with GLY 912 (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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908B MET 2.9 6.3 + - - -
909B TYR 2.5 17.1 + - - -
911B LEU* 1.3 73.2 - - - +
913B ILE* 1.3 62.3 + - - +
915B PHE* 3.3 3.7 + - - +
916B PHE* 3.3 13.5 + - - +
958B ILE* 4.0 14.0 - - - +
961B LEU* 3.7 21.3 - - - +
962B ILE* 3.6 18.2 - - - -
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Residues in contact with ILE 913 (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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889B MET* 3.9 17.7 - - + +
890B TYR* 3.6 27.8 - - + -
909B TYR* 3.1 31.2 + - + +
910B SER 3.6 6.1 - - - +
912B GLY* 1.3 73.5 - - - +
914B ILE* 1.3 65.5 + - - +
916B PHE* 3.0 17.8 + - + +
917B GLU* 3.2 16.0 + - - +
932B LEU* 4.4 25.1 - - + +
935B LEU* 4.9 15.9 - - + -
936B ARG* 4.3 13.9 - - + -
962B ILE* 3.7 15.2 - - + +
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Residues in contact with ILE 914 (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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796B LEU* 3.5 30.1 - - + -
800B ILE* 4.8 0.2 - - - +
819B ILE* 5.0 3.6 - - + -
836B LEU* 3.7 26.7 - - + +
837B LYS* 3.7 23.8 - - - +
838B PRO* 3.9 19.5 - - + -
841B ILE* 3.8 11.7 - - + -
890B TYR* 3.9 7.0 - - + -
910B SER 2.9 21.5 + - - +
911B LEU* 3.7 8.5 - - + +
913B ILE* 1.3 76.0 - - - +
915B PHE* 1.3 62.7 + - - +
917B GLU* 3.1 21.0 + - - +
918B MET* 3.1 19.4 + - - +
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Residues in contact with PHE 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B TYR* 3.5 44.4 - + + -
813B TRP* 3.6 33.4 - + - -
816B PHE* 3.4 36.1 - + + -
911B LEU* 2.8 21.0 + - - +
912B GLY* 3.8 5.2 - - - +
914B ILE* 1.3 75.0 - - - +
916B PHE* 1.3 60.9 + - - +
918B MET* 3.2 21.5 + - + -
919B ILE* 3.2 19.1 + - + +
954B GLU* 3.5 24.7 - - + -
957B ILE* 5.1 2.5 - - + -
958B ILE* 3.7 23.6 - - + -
961B LEU* 5.5 0.2 - - + -
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Residues in contact with PHE 916 (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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912B GLY 3.3 7.8 + - - +
913B ILE* 3.0 14.0 + - + +
915B PHE* 1.3 79.4 - - - +
917B GLU* 1.3 53.6 + - - +
919B ILE* 2.9 11.9 + - + +
920B TYR* 2.6 66.9 + + + +
922B PHE* 3.6 26.7 - + - -
931B ILE* 3.8 3.6 - - + -
932B LEU* 3.8 18.4 - - + -
935B LEU* 3.6 33.2 - - + -
942B PHE* 4.5 12.8 - + - -
943B PRO* 3.9 22.9 - - + -
946B PHE* 4.7 7.4 - + - -
958B ILE* 4.0 21.2 - - + +
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Residues in contact with GLU 917 (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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800B ILE* 3.7 29.9 - - + +
801B HIS* 5.8 3.3 + - + -
806B ASN* 5.8 0.2 - - - +
838B PRO* 3.7 9.6 - - - +
890B TYR* 2.5 36.5 + - - -
913B ILE* 3.2 10.3 + - + +
914B ILE* 3.1 8.5 + - - +
916B PHE* 1.3 77.5 - - - +
918B MET* 1.3 59.2 - - - +
919B ILE 3.6 0.2 + - - -
920B TYR 4.0 17.7 + - - +
921B PRO* 4.9 2.1 - - - +
922B PHE* 4.3 14.2 - - + -
928B ARG* 2.8 39.4 + - - -
932B LEU* 3.8 13.5 - - + +
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Residues in contact with MET 918 (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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796B LEU* 4.1 13.0 - - + -
800B ILE* 3.8 18.8 - - + -
805B LEU* 3.6 31.6 - - + +
806B ASN* 3.1 24.8 + - - -
812B TYR* 3.7 20.4 - - + +
815B LEU* 3.7 30.3 - - + -
816B PHE* 4.3 5.4 - - - +
819B ILE* 4.7 7.9 - - + -
911B LEU* 6.0 0.4 - - - -
914B ILE* 3.2 29.2 - - + +
915B PHE* 3.4 24.5 - - + +
916B PHE 3.0 1.0 - - - -
917B GLU* 1.3 78.5 - - - +
919B ILE* 1.3 62.5 + - + +
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Residues in contact with ILE 919 (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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806B ASN* 3.2 24.1 - - - +
812B TYR* 3.9 38.4 - - + -
915B PHE* 3.5 19.1 - - + +
916B PHE* 2.9 16.3 + - + +
918B MET* 1.3 81.1 - - - +
920B TYR* 1.3 58.8 + - + +
921B PRO* 3.6 1.9 - - - +
946B PHE* 3.8 29.8 - - + -
951B MET* 3.9 25.2 - - - +
954B GLU* 3.9 15.0 - - + +
958B ILE* 3.8 26.7 - - + -
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Residues in contact with TYR 920 (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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806B ASN* 4.8 0.2 - - - -
916B PHE* 2.6 44.6 + + + +
917B GLU 4.0 6.9 - - - +
918B MET 3.7 0.6 - - - -
919B ILE* 1.3 76.7 - - + +
921B PRO* 1.3 79.8 - - + +
922B PHE* 3.3 30.7 - + - -
927B GLU* 4.5 6.4 + - - -
931B ILE* 3.7 24.9 - - + +
943B PRO* 3.7 17.9 - - + +
945B ASP* 2.6 38.8 + - - -
946B PHE* 4.0 24.2 - + - -
951B MET* 5.8 1.3 - - + -
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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) + - + + + + + -
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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