Contacts of the helix formed by residues 901 - 918 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899A LYS 3.5 4.2 + - - +
900A LEU* 1.3 78.1 - - - +
902A PRO* 1.3 74.8 - - - +
903A ILE* 3.5 9.0 + - - +
904A ASP* 2.8 36.3 + - - +
905A LYS* 3.1 17.2 + - - +
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Residues in contact with PRO 902 (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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900A LEU 4.3 1.6 - - - +
901A THR* 1.3 88.7 - - - +
903A ILE* 1.3 61.3 + - + +
905A LYS* 3.4 9.8 + - + +
906A ARG* 3.0 55.3 + - - +
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Residues in contact with ILE 903 (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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873A LEU* 3.7 25.6 - - + +
874A SER* 4.3 21.8 - - - +
901A THR* 3.2 8.4 - - - +
902A PRO* 1.3 80.4 - - + +
904A ASP* 1.3 62.8 + - - +
906A ARG* 3.3 12.9 + - - +
907A LYS* 2.9 52.1 + - + +
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Residues in contact with ASP 904 (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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900A LEU* 4.5 9.4 - - + -
901A THR* 2.8 35.2 + - - +
903A ILE* 1.3 78.0 - - - +
905A LYS* 1.3 65.4 + - - +
907A LYS* 3.3 8.1 + - - +
908A CYS 3.1 17.7 + - - -
962A PRO* 3.7 21.3 - - + +
965A PHE* 3.6 13.0 - - + -
1005A TYR* 2.7 37.6 + - - +
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Residues in contact with LYS 905 (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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855A PRO* 5.1 3.8 - - - +
900A LEU* 4.2 18.1 - - + +
901A THR 3.1 12.4 + - - +
902A PRO* 3.6 12.6 - - + +
903A ILE 3.3 0.2 - - - -
904A ASP* 1.3 75.2 - - - +
906A ARG* 1.3 59.6 + - + +
908A CYS* 3.2 3.5 + - - +
909A GLU* 2.9 60.8 + - - +
952A LEU* 3.7 39.4 - - + +
953A GLN* 5.0 7.3 - - - +
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Residues in contact with ARG 906 (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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868A THR* 4.7 2.9 - - - +
871A ARG* 3.3 31.1 - - - +
872A ASP 4.2 4.5 - - - -
873A LEU* 2.6 47.9 + - + +
874A SER 3.1 16.6 + - - -
876A PRO* 3.4 25.6 - - - +
879A GLU* 5.9 1.2 + - - -
902A PRO* 3.0 47.8 + - - +
903A ILE* 3.6 8.8 - - - +
905A LYS* 1.3 79.6 - - + +
907A LYS* 1.3 56.1 + - - +
909A GLU* 3.4 14.4 + - - +
910A ARG* 3.0 27.4 + - - +
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Residues in contact with LYS 907 (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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873A LEU* 4.1 27.1 - - + -
903A ILE* 2.9 33.5 + - - +
904A ASP* 3.6 12.5 + - - +
905A LYS 3.2 0.2 - - - -
906A ARG* 1.3 74.0 - - - +
908A CYS* 1.3 61.7 + - - +
910A ARG* 3.3 2.0 + - - +
911A LEU* 2.9 33.6 + - - +
1004A LEU* 2.7 43.7 + - + +
1005A TYR* 3.4 44.0 - - + +
1006A PRO* 5.5 0.4 - - - +
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Residues in contact with CYS 908 (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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904A ASP 3.1 6.5 + - - +
905A LYS 3.6 7.6 - - - +
907A LYS* 1.3 73.8 - - - +
909A GLU* 1.3 60.4 + - - +
911A LEU* 3.6 9.6 - - - +
912A LEU* 2.9 34.7 + - - +
948A ILE* 4.3 9.4 - - - -
952A LEU* 3.6 23.8 - - + -
959A TYR* 5.2 0.2 - - - -
965A PHE* 3.6 51.5 - - + -
969A PHE* 3.9 13.5 - - - -
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Residues in contact with GLU 909 (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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854A VAL* 3.3 31.8 - - + +
855A PRO* 3.4 34.5 - - + +
868A THR* 3.9 8.4 + - + +
871A ARG* 4.1 8.3 + - - -
905A LYS* 2.9 52.5 + - - +
906A ARG* 3.6 25.4 - - - +
907A LYS 3.2 0.2 - - - -
908A CYS* 1.3 77.4 - - - +
910A ARG* 1.3 60.1 + - - +
912A LEU 3.5 0.2 + - - -
913A LEU* 3.1 21.1 + - - +
952A LEU* 3.5 17.1 - - + +
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Residues in contact with ARG 910 (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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868A THR* 3.1 27.3 + - + +
869A PHE* 3.4 25.2 + - + -
870A CYS 4.7 0.2 - - - -
871A ARG 2.7 29.9 + - - -
872A ASP* 4.8 0.4 - - - +
873A LEU* 3.6 36.9 - - - +
906A ARG 3.0 15.0 + - - +
907A LYS* 3.6 6.7 - - - +
908A CYS 3.2 0.2 - - - -
909A GLU* 1.3 76.6 - - - +
911A LEU* 1.3 65.5 + - - +
913A LEU* 3.2 2.2 + - - +
914A PHE* 2.9 58.1 + - + -
1004A LEU* 4.3 19.6 - - + +
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Residues in contact with LEU 911 (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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907A LYS 2.9 22.5 + - - +
908A CYS* 3.3 6.0 + - - +
910A ARG* 1.3 76.1 - - - +
912A LEU* 1.3 63.3 + - - +
914A PHE* 3.4 6.9 + - - +
915A LEU* 3.1 28.6 + - - +
965A PHE* 3.9 23.1 - - + -
969A PHE* 4.1 12.3 - - + -
997A PHE* 4.1 23.3 - - + -
1000A LEU* 3.7 30.7 - - + +
1001A LEU* 3.9 28.5 - - + +
1004A LEU* 3.6 17.5 - - + -
1005A TYR* 4.9 2.7 - - + -
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Residues in contact with LEU 912 (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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854A VAL* 4.0 17.3 - - + -
908A CYS* 2.9 19.9 + - - +
909A GLU 3.7 4.0 - - - +
910A ARG 3.2 0.2 - - - -
911A LEU* 1.3 77.4 - - - +
913A LEU* 1.3 56.6 + - - +
915A LEU* 3.2 4.6 + - - +
916A TYR* 2.8 39.6 + - + -
945A LEU* 3.9 26.2 - - + +
948A ILE* 3.8 15.9 - - + -
949A LYS* 3.6 30.3 - - + +
952A LEU* 4.0 18.2 - - + -
969A PHE* 3.5 28.5 - - + -
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Residues in contact with LEU 913 (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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831A VAL* 4.2 9.2 - - + -
848A PHE* 4.0 19.5 - - + -
852A CYS 4.2 9.4 - - - +
853A HIS* 4.0 14.4 - - + +
854A VAL* 3.4 30.7 - - + +
868A THR* 3.7 28.0 - - + -
869A PHE* 3.3 34.8 - - + +
909A GLU 3.1 10.4 + - - +
910A ARG* 3.2 4.9 + - - +
912A LEU* 1.3 75.3 - - - +
914A PHE* 1.3 66.7 - - - +
916A TYR* 3.6 2.8 - - + +
917A CYS* 2.9 30.0 + - - -
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Residues in contact with PHE 914 (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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869A PHE* 3.4 29.3 - + - -
910A ARG* 2.9 54.6 + - + +
911A LEU* 3.6 2.7 - - - +
913A LEU* 1.3 78.3 - - - +
915A LEU* 1.3 62.4 + - - +
917A CYS* 3.3 3.7 + - - +
918A HIS* 3.2 20.3 + - - +
996A TYR* 3.2 29.2 + - + -
1000A LEU* 3.4 42.0 - - + -
1004A LEU* 5.8 3.6 - - + -
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Residues in contact with LEU 915 (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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911A LEU 3.1 11.7 + - - +
912A LEU 3.2 6.3 + - - +
914A PHE* 1.3 77.2 - - - +
916A TYR* 1.3 66.6 + - - +
918A HIS* 3.0 12.3 + - - +
921A SER* 2.9 22.2 + - - -
945A LEU* 3.9 19.3 - - + -
969A PHE* 3.6 36.1 - - + -
973A PHE* 4.7 9.0 - - + -
993A LEU* 3.7 22.0 - - + -
996A TYR* 3.7 26.2 - - + -
997A PHE* 4.1 24.5 - - + -
1000A LEU* 4.4 4.9 - - + -
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Residues in contact with TYR 916 (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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831A VAL* 4.0 36.5 - - + +
852A CYS 5.0 4.9 - - - -
854A VAL* 4.4 9.6 - - + -
912A LEU* 2.8 39.2 + - + +
913A LEU* 3.6 7.6 - - + +
915A LEU* 1.3 74.6 - - - +
917A CYS* 1.3 60.7 + - - +
918A HIS 3.9 0.9 - - - +
921A SER* 3.4 4.9 + - - -
925A GLN* 3.4 56.4 + - + -
926A ASP* 5.3 1.2 + - - -
945A LEU* 3.8 22.9 - - + -
946A SER* 3.2 33.8 + - - -
949A LYS* 4.0 25.6 - - + +
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Residues in contact with CYS 917 (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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830A ALA* 3.6 40.3 - - + +
831A VAL* 3.8 17.3 - - - -
846A LYS* 5.4 4.9 - - - +
848A PHE* 4.4 0.7 - - - -
869A PHE* 4.1 21.3 - - + -
913A LEU* 2.9 23.6 + - - +
914A PHE 3.8 5.2 - - - +
915A LEU 3.1 0.2 - - - -
916A TYR* 1.3 75.9 - - - +
918A HIS* 1.3 60.6 + - - +
919A GLU* 3.8 1.7 + - - -
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Residues in contact with HIS 918 (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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914A PHE 3.2 10.7 + - - +
915A LEU 3.0 10.4 + - - +
916A TYR 3.9 1.2 - - - +
917A CYS* 1.3 78.9 - - - +
919A GLU* 1.3 71.0 + - + +
920A MET* 3.0 50.9 - - + +
921A SER* 2.9 24.3 + - - -
922A LEU* 4.5 0.7 + - - +
925A GLN* 4.9 0.3 + - - -
992A LYS* 5.1 6.3 + - + +
993A LEU* 4.0 15.2 - - + +
996A TYR* 3.5 45.2 - + + -
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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