Contacts of the helix formed by residues 896 - 910 (chain B) in PDB entry 4YZC
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 SER 896 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863B GLU* 2.6 25.1 + - - -
870B VAL* 4.3 3.1 - - - -
874B TRP* 3.2 11.3 + - - -
893B LYS* 3.2 17.5 + - - -
894B GLY 3.5 0.6 - - - -
895B GLY* 1.3 78.3 - - - +
897B VAL* 1.3 62.1 - - - +
898B ARG* 3.3 4.2 + - - +
899B ASP* 3.1 27.1 + - - -
900B LEU 3.1 15.2 + - - -
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Residues in contact with VAL 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B LEU* 3.8 33.2 - - + +
863B GLU* 2.9 15.7 + - - +
866B GLY* 3.5 39.3 - - - +
869B VAL* 4.6 9.2 - - + -
870B VAL* 3.8 13.9 - - + -
895B GLY 4.2 0.4 + - - -
896B SER* 1.3 69.1 - - - +
898B ARG* 1.3 65.9 + - - +
900B LEU* 3.0 5.9 + - - +
901B LEU* 2.9 25.1 + - + +
940B LEU* 4.1 22.4 - - + -
943B HIS* 4.6 3.8 - - + +
944B THR* 4.4 1.3 - - - +
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Residues in contact with ARG 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849B ILE* 3.5 45.2 + - + +
850B GLU* 3.4 33.9 + - - +
851B LYS* 4.0 9.3 - - - +
852B GLU 4.4 1.8 + - - +
854B LEU* 3.5 28.5 - - - +
859B VAL* 3.7 25.8 - - + +
862B LEU* 4.3 7.3 - - + +
863B GLU* 2.8 20.4 + - - +
896B SER* 3.6 2.9 - - - +
897B VAL* 1.3 73.3 - - - +
899B ASP* 1.3 71.2 + - - +
901B LEU* 3.1 6.1 + - - +
902B ARG* 2.8 46.4 + - - +
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Residues in contact with ASP 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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874B TRP* 3.7 3.2 - - + -
891B THR 3.0 11.6 - - - +
892B TYR* 3.7 8.7 - - + -
893B LYS* 2.8 50.7 + - - +
896B SER* 3.1 15.7 + - - +
898B ARG* 1.3 89.0 + - - +
900B LEU* 1.3 58.2 + - - +
902B ARG* 3.2 30.5 + - - +
903B ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B VAL* 6.0 0.2 - - + -
870B VAL* 4.1 18.6 - - + -
874B TRP* 3.6 47.9 - - + +
878B ILE* 5.7 0.2 - - + -
896B SER 3.1 7.0 + - - +
897B VAL* 3.0 10.2 + - - +
899B ASP* 1.3 77.3 - - - +
901B LEU* 1.3 62.7 + - - +
903B ALA* 3.3 3.0 + - + +
904B MET* 3.1 32.5 + - - +
933B PHE* 4.4 24.0 - - + -
937B PHE* 4.2 22.7 - - + -
940B LEU* 4.1 26.9 - - + -
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Residues in contact with LEU 901 (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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842B PHE* 3.7 34.0 - - + +
845B VAL* 3.7 29.8 - - + -
846B SER* 3.4 22.1 + - - -
849B ILE* 4.2 3.6 - - + -
862B LEU* 4.0 21.1 - - + -
897B VAL* 2.9 22.1 + - + +
898B ARG* 3.6 5.4 - - - +
900B LEU* 1.3 72.7 - - - +
902B ARG* 1.3 59.9 + - - +
904B MET* 3.3 16.6 + - - +
905B ARG* 2.8 25.3 + - - +
940B LEU* 4.0 18.8 - - + -
944B THR* 4.1 8.3 - - + +
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Residues in contact with ARG 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B SER* 3.5 13.7 - - - +
850B GLU* 3.3 44.8 + - + +
891B THR* 3.2 33.3 + - - -
892B TYR* 3.2 30.3 + - + -
898B ARG* 2.8 42.4 + - + +
899B ASP* 3.2 23.5 + - - +
901B LEU* 1.3 73.2 - - - +
903B ALA* 1.3 59.4 + - - +
905B ARG* 3.3 2.6 + - - +
906B ASN* 2.8 31.7 + - - +
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Residues in contact with ALA 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874B TRP* 3.9 24.0 - - + -
886B LEU* 4.1 13.5 - - + -
892B TYR* 3.6 20.3 - - + -
899B ASP 3.0 13.3 + - - +
900B LEU* 3.6 10.3 - - + +
901B LEU 3.3 0.2 - - - -
902B ARG* 1.3 76.8 - - - +
904B MET* 1.3 56.5 + - + +
906B ASN* 3.3 1.4 + - - +
907B LYS* 2.9 36.9 + - + +
933B PHE* 5.4 3.8 - - + -
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Residues in contact with MET 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B LEU* 4.6 11.0 - - + -
842B PHE* 3.5 39.0 - - + -
900B LEU* 3.1 18.8 + - - +
901B LEU* 3.6 15.3 - - - +
902B ARG 3.3 0.2 - - - -
903B ALA* 1.3 72.8 - - - +
905B ARG* 1.3 65.7 + - - +
908B LYS* 3.0 27.1 + - - +
929B PHE* 3.5 7.6 - - + -
930B VAL* 5.2 1.6 - - + -
933B PHE* 3.5 61.5 - - + -
940B LEU* 3.9 20.4 - - - -
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Residues in contact with ARG 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A GLN* 5.1 0.2 - - - +
905A ARG* 3.4 26.7 - - - +
909A HIS* 3.7 10.9 + - - +
842B PHE 5.4 0.4 - - - +
843B GLN* 3.5 44.8 + - - +
846B SER* 3.4 16.2 - - - +
847B ASP* 2.6 41.0 + - - +
850B GLU* 6.0 1.3 - - - +
901B LEU 2.8 21.0 + - - +
902B ARG* 3.6 4.5 - - - +
904B MET* 1.3 72.2 - - - +
906B ASN* 1.3 62.7 + - - +
908B LYS* 3.7 9.7 - - - +
909B HIS* 3.2 54.8 + - - +
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Residues in contact with ASN 906 (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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892B TYR* 3.4 18.7 + - - +
902B ARG 2.8 17.5 + - - +
903B ALA 3.8 2.2 - - - +
905B ARG* 1.3 78.9 - - - +
907B LYS* 1.3 70.4 + - + +
909B HIS* 3.3 1.5 + - - -
910B HIS* 2.9 63.0 + - - +
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Residues in contact with LYS 907 (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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882B LEU* 4.2 24.9 - - + -
885B ASP* 2.4 40.7 + - - +
886B LEU* 3.7 26.0 - - + -
888B LYS* 5.3 4.4 - - - +
892B TYR* 5.8 0.7 - - - -
903B ALA* 2.9 22.1 + - + +
904B MET* 4.9 0.7 - - - -
906B ASN* 1.3 84.4 + - + +
908B LYS* 1.3 57.8 + - - +
911B TYR* 3.2 27.8 - - - +
914B LEU* 3.5 32.0 - - + +
918B VAL* 4.8 0.2 - - + -
922B LEU* 5.2 2.5 - - + -
929B PHE* 3.9 20.0 - - + -
933B PHE* 5.5 2.9 - - + -
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Residues in contact with LYS 908 (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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839B LEU* 4.0 32.0 + - + +
840B GLN* 3.5 14.5 + - - +
843B GLN* 2.5 41.3 + - + +
904B MET 3.0 18.6 + - - +
905B ARG* 3.7 11.4 - - - +
906B ASN 3.1 0.2 - - - -
907B LYS* 1.3 76.8 - - - +
909B HIS* 1.3 67.0 + - - +
911B TYR* 3.3 17.8 + - - +
925B LEU* 3.9 25.3 - - + +
926B PRO* 6.2 0.9 - - - -
929B PHE* 3.7 14.3 - - + -
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Residues in contact with HIS 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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847A ASP* 3.6 28.4 + - + -
850A GLU 6.1 1.6 - - - -
905A ARG* 4.0 17.4 + - - -
905B ARG* 3.2 37.5 + - - +
906B ASN* 3.3 4.0 + - - +
908B LYS* 1.3 81.5 - - - +
910B HIS* 1.3 87.3 + + + +
911B TYR 3.5 0.5 + - - -
912B ARG* 4.9 2.3 + - - +
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Residues in contact with HIS 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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906B ASN* 2.9 54.1 + - - +
907B LYS 4.1 0.4 - - - -
909B HIS* 1.3 100.9 + + + +
911B TYR* 1.3 53.9 + - - +
912B ARG* 3.1 4.0 - - - -
913B GLU* 2.7 36.4 + - + +
914B LEU* 3.3 22.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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