Contacts of the helix formed by residues 901 - 918 (chain B) in PDB entry 3O33
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 901 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899B LYS 3.5 2.2 + - - +
900B LEU* 1.3 77.8 - - - +
902B PRO* 1.3 74.9 - - - +
903B ILE* 3.5 6.4 + - - +
904B ASP* 2.7 37.6 + - - +
905B LYS* 3.0 18.0 + - - +
1003C ASN* 3.5 39.3 - - + +
1004C LEU* 6.0 2.2 - - + -
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Residues in contact with PRO 902 (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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900B LEU 4.6 0.2 - - - +
901B THR* 1.3 88.3 - - - +
903B ILE* 1.3 62.7 + - - +
905B LYS* 3.2 9.2 + - + +
906B ARG* 3.0 53.8 + - - +
1002C LYS* 3.6 28.9 - - + +
1003C ASN* 3.9 9.6 - - - +
1006C PRO* 3.9 16.2 - - + -
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Residues in contact with ILE 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B LEU* 3.6 27.1 - - + +
874B SER* 4.3 20.9 - - - +
901B THR* 3.2 7.5 + - - +
902B PRO* 1.3 78.2 - - + +
904B ASP* 1.3 62.7 + - - +
906B ARG* 3.2 13.8 + - - +
907B LYS* 2.9 52.2 + - + +
1003C ASN* 5.0 16.8 - - - +
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Residues in contact with ASP 904 (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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900B LEU* 4.4 11.0 - - + -
901B THR* 2.7 36.1 + - - +
903B ILE* 1.3 75.7 - - - +
905B LYS* 1.3 65.0 + - - +
907B LYS* 3.2 9.3 + - - +
908B CYS* 3.0 23.0 + - - +
962B PRO* 3.7 22.0 - - + +
965B PHE* 3.8 4.6 - - + -
1005B TYR* 2.7 37.7 + - - +
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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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855B PRO* 5.3 0.8 - - - +
883B ASP* 2.7 33.0 + - - -
900B LEU* 4.0 19.0 - - + +
901B THR 3.0 13.4 + - - +
902B PRO* 3.6 11.2 - - + +
904B ASP* 1.3 76.3 - - - +
906B ARG* 1.3 61.2 + - + +
908B CYS* 3.3 3.8 + - - +
909B GLU* 2.8 58.2 + - - +
952B LEU* 3.8 35.2 - - + +
953B GLN* 4.9 8.0 - - - +
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Residues in contact with ARG 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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868B THR* 4.6 2.3 - - - +
871B ARG* 3.5 29.3 - - - +
872B ASP 4.5 2.2 - - - -
873B LEU* 2.7 44.7 + - + +
874B SER 3.4 16.0 + - - -
876B PRO* 3.3 25.1 - - - +
902B PRO* 3.0 37.4 + - - +
903B ILE* 3.5 20.2 - - - +
905B LYS* 1.3 78.3 - - + +
907B LYS* 1.3 64.4 + - - +
909B GLU* 3.3 21.4 + - - +
910B ARG* 3.0 22.3 + - - +
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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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873B LEU* 4.2 27.8 - - + -
903B ILE* 2.9 32.3 + - - +
904B ASP* 3.2 15.0 + - - +
906B ARG* 1.3 78.5 - - - +
908B CYS* 1.3 57.5 + - - +
910B ARG* 3.1 6.3 + - - +
911B LEU* 2.9 32.4 + - - +
1004B LEU* 3.0 37.1 + - + +
1005B TYR* 3.3 44.6 - - + +
1006B PRO* 5.6 0.4 - - - +
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Residues in contact with CYS 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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904B ASP 3.0 12.9 + - - +
905B LYS 3.3 7.4 + - - +
907B LYS* 1.3 76.5 - - - +
909B GLU* 1.3 57.2 + - - +
911B LEU* 3.3 6.3 + - - +
912B LEU* 2.9 28.5 + - - +
948B ILE* 4.2 10.1 - - - -
952B LEU* 3.7 22.7 - - + -
965B PHE* 3.5 50.2 - - + -
969B PHE* 3.9 13.5 - - - -
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Residues in contact with GLU 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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854B VAL* 3.6 28.9 - - + +
855B PRO* 3.4 33.1 - - + +
868B THR* 3.8 8.0 + - + +
871B ARG* 4.3 7.4 + - - -
883B ASP* 4.4 0.9 - - - +
905B LYS* 2.8 49.8 + - - +
906B ARG* 3.5 28.0 - - - +
907B LYS 3.2 0.2 - - - -
908B CYS* 1.3 76.9 - - - +
910B ARG* 1.3 57.6 + - - +
912B LEU 3.5 0.3 + - - -
913B LEU* 3.0 27.9 + - - +
952B LEU* 3.5 15.3 - - + +
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Residues in contact with ARG 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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868B THR* 3.0 34.1 + - + +
869B PHE* 3.2 23.0 + - + +
870B CYS 4.4 0.2 - - - -
871B ARG 2.6 31.1 + - - -
872B ASP* 4.8 0.2 - - - +
873B LEU* 3.7 36.0 - - - +
906B ARG 3.0 12.9 + - - +
907B LYS* 3.1 8.5 + - - +
909B GLU* 1.3 74.5 - - - +
911B LEU* 1.3 66.9 + - - +
913B LEU* 3.1 2.5 + - - +
914B PHE* 2.8 55.2 + - + -
1004B LEU* 4.2 22.0 - - + +
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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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907B LYS 2.9 18.2 + - - +
908B CYS* 3.6 6.7 - - - +
910B ARG* 1.3 75.6 - - - +
912B LEU* 1.3 63.1 + - - +
914B PHE* 3.4 6.1 + - - +
915B LEU* 3.1 28.2 + - - +
965B PHE* 4.0 23.8 - - + -
969B PHE* 3.9 14.1 - - + -
997B PHE* 3.9 22.9 - - + -
1000B LEU* 3.8 32.3 - - + +
1001B LEU* 3.8 24.9 - - + +
1004B LEU* 3.7 22.0 - - + -
1005B TYR* 4.9 2.9 - - + -
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Residues in contact with LEU 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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854B VAL* 3.9 21.5 - - + -
908B CYS 2.9 20.5 + - - +
909B GLU 3.7 3.8 - - - +
911B LEU* 1.3 76.1 - - - +
913B LEU* 1.3 57.9 + - - +
915B LEU* 3.2 4.3 + - - +
916B TYR* 2.9 37.2 + - + -
945B LEU* 3.8 31.4 - - + +
948B ILE* 3.9 15.7 - - + -
949B LYS* 3.6 29.6 - - + +
952B LEU* 4.1 13.0 - - + -
969B PHE* 3.4 29.4 - - + -
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Residues in contact with LEU 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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831B VAL* 3.8 26.0 - - + -
848B PHE* 3.9 11.9 - - + -
852B CYS 4.1 3.6 - - - +
853B HIS* 3.9 16.2 - - + +
854B VAL* 4.0 24.6 - - + +
868B THR* 3.7 27.6 - - + +
869B PHE* 3.4 35.2 - - + -
909B GLU 3.0 17.9 + - - +
910B ARG 3.7 4.3 - - - +
912B LEU* 1.3 75.3 - - - +
914B PHE* 1.3 63.2 + - - +
916B TYR* 3.3 1.5 + - + -
917B CYS* 3.0 29.9 + - - -
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Residues in contact with PHE 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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846B LYS* 5.9 1.3 - - - -
869B PHE* 3.6 26.7 - + + -
910B ARG* 2.8 52.6 + - + +
911B LEU* 3.6 3.8 - - - +
913B LEU* 1.3 77.6 - - - +
915B LEU* 1.3 62.2 + - - +
917B CYS* 3.3 3.7 + - - +
918B HIS* 3.1 16.6 + - - -
996B TYR* 3.3 33.8 + - + -
1000B LEU* 3.4 42.0 - - + -
1004B LEU* 5.6 4.0 - - + -
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Residues in contact with LEU 915 (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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911B LEU 3.1 14.3 + - - +
912B LEU 3.8 3.4 - - - +
914B PHE* 1.3 73.3 - - - +
916B TYR* 1.3 63.6 + - - +
918B HIS* 3.1 11.0 + - - +
921B SER* 2.8 24.7 - - - -
945B LEU* 3.9 19.5 - - + -
969B PHE* 3.5 37.0 - - + -
973B PHE* 4.2 13.2 - - + -
993B LEU* 3.6 33.4 - - + +
996B TYR* 3.6 19.1 - - + -
997B PHE* 3.9 19.7 - - + -
1000B LEU* 4.4 2.5 - - + -
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Residues in contact with TYR 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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831B VAL* 3.8 39.7 - - + +
852B CYS 5.0 2.7 - - - -
854B VAL* 3.9 23.8 - - + -
912B LEU* 2.9 30.8 + - + +
913B LEU* 3.7 7.2 - - + +
915B LEU* 1.3 77.1 - - - +
917B CYS* 1.3 59.5 + - - +
918B HIS 3.8 0.9 - - - +
921B SER* 2.9 17.6 + - - -
925B GLN* 3.6 44.5 + - + -
926B ASP* 5.5 0.2 + - - -
945B LEU* 3.8 27.7 + - + +
946B SER* 3.2 33.6 + - - -
949B LYS* 4.1 16.2 - - + +
950B LYS* 4.6 0.9 + - - -
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Residues in contact with CYS 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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830B ALA* 3.5 41.1 - - - +
831B VAL* 3.7 18.1 - - - +
833B GLN* 5.1 3.6 + - - -
846B LYS* 3.9 13.2 - - - +
848B PHE* 4.3 0.2 - - - -
869B PHE* 3.9 17.9 - - + -
913B LEU* 3.0 24.6 + - - +
914B PHE* 3.8 4.0 - - - +
916B TYR* 1.3 73.8 - - - +
918B HIS* 1.3 68.6 + - - +
919B GLU* 3.5 4.7 + - - +
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Residues in contact with HIS 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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914B PHE 3.1 11.1 + - - +
915B LEU 3.1 14.1 + - - +
916B TYR 3.8 1.0 - - - +
917B CYS* 1.3 77.2 - - - +
919B GLU* 1.3 69.8 + - + +
920B MET* 3.1 46.1 + - + +
921B SER* 3.2 17.7 + - - -
992B LYS* 4.7 21.3 + - + +
993B LEU* 3.6 18.0 - - + +
996B TYR* 3.4 49.3 - + + +
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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
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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