Contacts of the helix formed by residues 935 - 957 (chain A) in PDB entry 5UAK
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 LEU 935 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 3.6 43.9 - - + +
304A TYR* 3.8 28.7 - - + -
305A PHE* 5.9 7.0 - - + -
930A GLY 3.4 1.2 + - - -
931A PHE* 3.4 28.0 + - + +
934A GLY* 1.3 74.6 - - - +
936A PRO* 1.4 77.5 - - + +
937A LEU 3.2 3.4 + - - -
938A VAL* 3.5 18.3 + - + +
939A HIS* 4.1 2.3 + - + -
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Residues in contact with PRO 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A VAL* 3.8 20.0 - - + -
865A TRP* 4.6 15.9 - - + -
932A PHE 5.3 2.7 - - - +
934A GLY* 3.7 6.5 - - - +
935A LEU* 1.4 96.0 - - + +
937A LEU* 1.3 55.8 + - - +
938A VAL 3.1 2.7 - - - -
939A HIS* 3.5 21.5 - - + -
940A THR* 2.8 39.8 + - + +
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Residues in contact with LEU 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A LEU* 5.3 0.2 - - - +
862A VAL* 3.8 22.0 - - + +
863A LEU* 5.3 8.1 - - + -
866A CYS* 5.0 18.2 - - + -
934A GLY* 4.1 16.4 - - - +
935A LEU 3.2 1.0 + - - -
936A PRO* 1.3 79.7 - - - +
938A VAL* 1.3 60.9 + - + +
940A THR* 2.7 19.8 + - - +
941A LEU* 3.3 34.4 - - + +
991A ILE* 4.7 0.2 - - + -
992A PHE* 4.1 36.1 - - + +
995A ILE* 4.1 31.0 - - + -
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Residues in contact with VAL 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 3.9 19.1 - - + -
301A TYR* 5.7 7.9 - - + +
304A TYR* 4.3 28.5 - - + -
935A LEU* 3.5 8.8 + - + +
936A PRO 3.1 0.4 - - - -
937A LEU* 1.3 84.5 - - + +
939A HIS* 1.3 53.1 + - - +
941A LEU* 2.9 10.8 + - - +
942A ILE* 2.8 54.7 + - + +
988A PRO* 4.7 20.4 - - + +
989A LEU* 5.7 8.1 - - + -
992A PHE* 4.9 7.9 - - + -
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Residues in contact with HIS 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 3.1 42.0 + - - +
301A TYR* 3.8 23.7 + - + +
858A SER* 6.1 0.2 - - - -
935A LEU* 4.1 2.6 + - + +
936A PRO* 3.0 26.7 + - + +
938A VAL* 1.3 79.2 - - - +
940A THR* 1.3 67.7 + - + +
942A ILE* 4.6 4.3 - - - -
943A THR* 3.2 33.0 + - + +
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Residues in contact with THR 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A HIS* 3.9 0.4 - - - -
858A SER* 3.6 29.2 - - - +
859A LEU* 3.8 30.2 - - - +
862A VAL* 3.8 14.8 - - + +
936A PRO* 2.8 21.3 + - + +
937A LEU* 2.7 27.5 + - - +
939A HIS* 1.3 77.7 - - + +
941A LEU* 1.3 56.9 + - - +
943A THR* 2.5 24.0 + - - -
944A VAL* 3.0 20.8 + - - +
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Residues in contact with LEU 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A TYR* 4.0 23.1 + - + +
859A LEU* 3.7 21.5 - - + -
937A LEU* 3.3 33.7 - - + +
938A VAL* 2.9 8.3 + - - +
940A THR* 1.3 81.0 + - - +
942A ILE* 1.3 61.4 + - - +
944A VAL* 3.4 14.3 + - + +
945A SER* 3.5 12.5 + - - -
983A LEU 5.7 0.2 - - - +
988A PRO* 3.8 45.1 - - + +
991A ILE* 3.9 31.9 - - + -
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Residues in contact with ILE 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.8 21.3 - - + +
296A THR* 4.8 7.4 - - + +
297A ARG* 3.4 60.6 - - + +
300A ALA* 4.1 9.0 - - + -
301A TYR* 5.9 2.9 - - + -
938A VAL* 2.8 42.4 + - + +
939A HIS* 4.6 2.0 - - - -
940A THR 3.3 0.2 - - - -
941A LEU* 1.3 72.2 - - - +
943A THR* 1.3 59.9 - - - +
945A SER* 2.7 23.9 + - - -
946A LYS* 3.5 7.3 + - - +
984A ASP* 4.4 12.1 - - - +
988A PRO* 5.1 9.2 - - + -
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Residues in contact with THR 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 3.7 22.0 - - - +
856A HIS* 3.0 28.7 + - + +
939A HIS* 3.2 24.6 + - + +
940A THR* 2.5 24.9 + - - -
942A ILE* 1.3 72.4 - - - +
944A VAL* 1.3 59.0 + - - +
946A LYS* 3.3 18.5 + - - +
947A ILE* 2.9 35.6 + - - +
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Residues in contact with VAL 944 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A TYR* 3.8 45.1 - - + +
855A VAL* 4.8 2.9 - - + -
856A HIS* 3.8 26.0 - - + -
859A LEU* 3.9 20.2 - - + -
940A THR 3.0 19.6 + - - +
941A LEU* 3.6 9.9 - - + +
942A ILE 3.3 0.6 - - - -
943A THR* 1.3 75.9 + - - +
945A SER* 1.3 57.0 + - - +
947A ILE* 3.3 7.6 + - - +
948A LEU* 2.8 42.5 + - + +
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Residues in contact with SER 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 5.2 2.8 + - - -
293A LEU* 4.6 2.1 - - - +
852A TYR* 6.0 0.2 - - - -
941A LEU 3.5 6.8 + - - -
942A ILE* 2.7 22.7 + - - -
944A VAL* 1.3 78.6 - - - +
946A LYS* 1.3 52.6 + - - +
948A LEU* 3.8 2.8 - - - +
949A HIS* 2.8 36.3 + - - +
980A ILE* 4.5 6.0 - - - +
983A LEU* 3.8 29.8 - - - +
984A ASP* 2.9 34.8 + - - -
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Residues in contact with LYS 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLU* 4.9 14.6 - - + +
289A ARG* 5.4 7.4 - - + +
290A GLN* 6.1 3.6 - - - -
293A LEU* 4.2 33.7 - - + -
297A ARG* 4.8 11.9 - - - +
942A ILE 3.5 7.6 + - - +
943A THR* 3.3 21.4 + - - +
945A SER* 1.3 80.3 + - - +
947A ILE* 1.3 65.0 + - - +
949A HIS* 3.7 7.3 - - + +
950A HIS* 3.0 31.4 + - - +
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Residues in contact with ILE 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A VAL 4.2 14.6 - - - +
856A HIS* 3.2 40.6 - - + +
943A THR* 2.9 23.9 + - - +
944A VAL* 3.6 5.4 - - - +
946A LYS* 1.3 82.4 - - - +
948A LEU* 1.3 65.8 + - + +
950A HIS* 3.6 8.4 + - + +
951A LYS* 3.3 44.1 + - + +
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Residues in contact with LEU 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A TYR* 4.3 20.9 - - + -
855A VAL* 3.9 29.6 - - + -
944A VAL* 2.8 34.0 + - + +
945A SER* 3.8 5.4 - - - +
947A ILE* 1.3 73.2 - - + +
949A HIS* 1.3 53.8 + - - +
951A LYS* 3.4 11.7 + - - +
952A MET* 2.8 37.2 + - - +
980A ILE* 5.0 3.1 - - + -
983A LEU* 4.6 19.7 - - + -
1160A VAL* 4.8 1.6 - - + -
1163A VAL* 4.8 13.2 - - + -
1164A PHE* 4.3 23.1 - - + -
1167A ILE* 4.5 16.1 - - + +
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Residues in contact with HIS 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 5.3 5.6 - - - -
285A ILE* 4.0 15.4 - - + +
286A GLU* 6.0 3.4 - - + -
289A ARG* 3.2 51.2 + - + +
945A SER 2.8 22.6 + - - +
946A LYS* 3.7 7.0 - - + +
948A LEU* 1.3 72.1 - - - +
950A HIS* 1.3 69.1 + - - +
952A MET* 3.1 2.8 + - - +
953A LEU* 2.9 30.3 + - + +
976A PHE* 3.4 37.4 - + - -
980A ILE* 3.5 29.3 - - + +
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Residues in contact with HIS 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 4.8 17.5 - - + +
286A GLU* 3.3 39.1 + - - +
946A LYS 3.0 19.3 + - - +
947A ILE* 3.7 9.0 - - + +
948A LEU 3.3 0.2 - - - -
949A HIS* 1.3 83.6 - - - +
951A LYS* 1.3 68.9 + - + +
953A LEU* 4.0 4.1 + - - +
954A HIS* 3.4 28.3 + + + +
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Residues in contact with LYS 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A VAL* 5.1 13.1 + - - +
947A ILE* 3.3 41.0 + - + +
948A LEU* 3.9 12.5 - - - +
949A HIS 3.3 0.2 - - - -
950A HIS* 1.3 87.1 - - + +
952A MET* 1.3 60.0 + - - +
954A HIS* 3.4 6.6 + - - +
955A SER* 2.8 32.7 + - - -
1164A PHE* 6.5 1.6 - - - -
1167A ILE* 4.7 23.1 - - + +
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Residues in contact with MET 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A LEU 2.8 23.0 + - - +
949A HIS* 3.6 5.8 - - - +
951A LYS* 1.3 71.7 - - - +
953A LEU* 1.3 52.7 + - - +
955A SER* 3.0 4.7 + - - -
956A VAL* 2.8 38.5 + - + +
975A ARG* 4.5 6.1 - - + +
976A PHE* 3.7 43.7 - - + +
980A ILE* 4.3 16.2 - - - -
1163A VAL* 3.7 36.1 - - + -
1166A PHE* 4.0 39.8 - - + +
1167A ILE* 4.0 14.7 - - + +
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Residues in contact with LEU 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 5.5 4.3 - - + -
265A MET* 5.5 9.9 - - + -
281A MET 4.3 6.5 - - - +
282A GLU* 3.7 38.6 - - + +
285A ILE* 5.1 15.0 - - + -
949A HIS* 2.9 24.9 + - + +
950A HIS* 4.2 4.5 - - - +
952A MET* 1.3 75.7 - - - +
954A HIS* 1.3 61.8 + - - +
956A VAL* 3.5 6.2 + - + +
957A LEU* 3.4 36.0 + - + +
976A PHE* 3.8 31.8 - - + -
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Residues in contact with HIS 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLU* 6.3 1.3 - - + +
282A GLU* 3.2 40.0 + - - +
950A HIS* 3.4 25.1 + + + +
951A LYS* 3.4 7.8 + - - +
952A MET 3.2 0.4 - - - -
953A LEU* 1.3 79.8 - - - +
955A SER* 1.3 52.3 + - - +
957A LEU* 2.7 26.7 - - - +
958A GLN* 4.1 22.3 - - + +
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Residues in contact with SER 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A LYS 2.8 17.3 + - - -
952A MET 3.0 4.2 + - - -
954A HIS* 1.3 73.5 - - - +
956A VAL* 1.3 61.2 - - - +
957A LEU 3.0 11.0 - - - +
958A GLN 4.2 6.3 - - - +
959A ALA* 4.2 0.5 - - - +
1166A PHE 2.9 18.5 + - - -
1167A ILE* 2.8 34.3 + - - -
1169A MET* 3.9 22.7 + - - +
1171A THR* 5.4 6.6 - - - +
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Residues in contact with VAL 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 4.2 24.9 - - + -
269A ILE* 5.8 4.3 - - + +
952A MET* 2.8 27.3 + - + +
953A LEU* 3.7 13.9 - - + +
954A HIS 3.4 0.4 - - - -
955A SER* 1.3 74.9 - - - +
957A LEU* 1.3 68.9 + - + +
959A ALA* 3.8 12.8 - - - +
964A LEU* 4.2 20.8 - - + +
972A ILE* 4.8 7.2 - - + -
976A PHE* 4.4 16.6 - - + -
1166A PHE* 3.8 29.4 - - + -
1169A MET* 5.0 3.1 - - - +
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Residues in contact with LEU 957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A MET* 4.0 31.6 - - + -
269A ILE* 5.6 10.8 - - + -
272A VAL* 4.1 24.5 - - + -
273A LYS* 6.1 4.5 - - + +
277A TRP 4.2 6.7 - - - +
278A GLU* 3.5 27.8 - - - +
281A MET* 5.7 1.3 - - + -
282A GLU* 5.4 6.3 - - + +
953A LEU* 3.4 30.0 + - + +
954A HIS* 2.7 20.2 - - - +
955A SER* 3.0 10.0 - - - +
956A VAL* 1.3 88.3 - - + +
958A GLN* 1.3 70.9 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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