Contacts of the helix formed by residues 910 - 933 (chain M) in PDB entry 2O5J
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 LYS 910 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M PHE* 4.7 0.2 - - - -
551M GLU* 4.6 9.1 + - - -
552M HIS* 6.3 1.6 - - + -
886M LEU* 6.3 0.9 - - - -
906M PHE 4.4 14.5 + - - -
907M ASP* 5.6 2.4 + - - +
908M GLY 5.2 4.4 + - - +
909M ALA* 1.3 80.5 + - - +
911M GLU* 1.3 72.6 + - + +
912M PRO* 3.4 17.7 - - + -
913M GLU* 2.8 30.4 + - - +
914M ILE* 3.0 14.5 - - - +
1063N GLU* 5.7 6.5 + - + +
1064N GLY* 5.0 15.4 - - - +
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Residues in contact with GLU 911 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552M HIS* 6.1 1.6 - - + -
886M LEU* 4.9 15.8 - - + +
910M LYS* 1.3 74.5 - - + +
912M PRO* 1.3 71.4 - - + +
914M ILE* 3.3 9.1 + - - +
915M LYS* 2.9 39.8 + - - +
951N ILE* 2.9 18.9 - - + +
1062N ARG* 2.6 65.6 + - - +
1063N GLU* 4.5 9.1 - - - +
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Residues in contact with PRO 912 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910M LYS* 3.2 20.9 - - + -
911M GLU* 1.3 93.6 - - + +
913M GLU* 1.3 67.2 + - - +
915M LYS* 3.0 22.7 + - + +
916M GLU* 3.0 11.9 + - - +
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Residues in contact with GLU 913 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M LYS* 4.9 13.0 + - - +
6M PHE* 3.5 37.0 - - + -
910M LYS* 2.8 23.9 + - - +
912M PRO* 1.3 79.5 - - - +
914M ILE* 1.3 57.2 + - - +
916M GLU* 3.0 27.7 - - + +
917M LEU* 3.1 18.3 - - + +
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Residues in contact with ILE 914 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M PHE* 4.9 2.2 - - + -
549M PHE* 5.5 3.8 - - + -
886M LEU* 5.5 13.7 - - + +
889M HIS* 4.4 17.3 - - + +
890M LEU* 4.3 25.8 - - + +
909M ALA* 3.3 33.0 - - + -
910M LYS 3.0 28.9 + - - +
911M GLU* 3.6 9.4 - - - +
913M GLU* 1.3 73.9 - - + +
915M LYS* 1.3 70.0 + - + +
916M GLU 3.0 2.2 + - - -
917M LEU* 3.1 9.1 + - - +
918M LEU* 2.8 43.8 + - + +
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Residues in contact with LYS 915 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911M GLU* 2.9 36.1 + - - +
912M PRO* 3.3 9.6 - - + +
914M ILE* 1.3 78.9 - - + +
916M GLU* 1.3 52.2 + - - +
918M LEU* 3.3 7.5 - - + +
919M ALA* 2.9 16.1 + - - +
968M LEU* 2.9 60.6 - - + +
969M GLN* 5.6 2.9 - - - +
951N ILE* 4.9 15.5 - - - -
952N ASP* 5.9 5.4 - - - +
1062N ARG* 5.5 5.0 - - - +
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Residues in contact with GLU 916 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M LYS* 5.4 5.7 + - - +
912M PRO 3.0 10.5 + - - +
913M GLU* 3.0 25.6 - - + +
915M LYS* 1.3 74.1 - - - +
917M LEU* 1.3 77.8 + - + +
919M ALA* 2.9 28.7 + - - +
920M GLN* 3.1 12.9 + - - +
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Residues in contact with LEU 917 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M LYS* 4.7 18.8 - - + +
6M PHE* 3.7 30.5 - - + -
890M LEU* 3.8 19.5 - - + -
893M ALA* 4.1 15.7 - - + -
897M LEU* 3.9 13.5 - - + +
899M GLN* 5.8 1.6 - - - +
901M TYR* 4.0 14.1 - - + +
913M GLU 3.1 13.0 - - - +
914M ILE* 3.1 6.8 + - - +
916M GLU* 1.3 91.3 - - + +
918M LEU* 1.3 57.1 + - - +
920M GLN* 3.0 13.0 + - + +
921M ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 918 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889M HIS* 3.1 31.9 - - + +
892M LEU* 3.9 8.7 - - + -
893M ALA* 3.6 16.4 - - + +
914M ILE* 2.8 27.3 + - + +
915M LYS* 3.3 10.5 - - + +
917M LEU* 1.3 78.6 - - - +
919M ALA* 1.3 62.2 + - - +
921M ALA* 3.0 2.9 + - - -
922M PHE 2.9 10.6 + - - -
967M PHE* 2.9 49.1 - - + +
968M LEU* 3.1 31.2 - - + +
970M GLY* 4.2 9.4 - - - +
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Residues in contact with ALA 919 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915M LYS 2.9 14.0 + - - +
916M GLU* 3.0 19.1 - - - +
918M LEU* 1.3 76.7 - - - +
920M GLN* 1.3 58.0 + - - +
922M PHE* 3.5 18.3 + - - +
923M GLU* 3.9 5.5 + - - +
964M LYS* 4.5 19.2 + - - +
968M LEU* 3.7 14.1 - - + +
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Residues in contact with GLN 920 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897M LEU* 3.2 33.0 - - + +
899M GLN* 5.0 1.2 + - - -
916M GLU* 3.1 15.7 + - - +
917M LEU* 3.0 19.2 + - + +
919M ALA* 1.3 76.0 - - - +
921M ALA* 1.3 60.9 + - - +
923M GLU* 3.5 13.1 + - - +
924M VAL* 3.4 21.0 + - - +
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Residues in contact with ALA 921 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892M LEU 4.7 0.2 - - - +
893M ALA* 4.0 26.0 - - - +
896M PHE* 4.2 11.0 - - + +
897M LEU* 3.6 9.8 - - + +
917M LEU 2.9 11.9 + - - +
918M LEU 3.0 7.6 + - - +
920M GLN* 1.3 76.0 - - - +
922M PHE* 1.3 64.0 + - - +
924M VAL* 3.0 4.0 + - - +
925M TYR* 2.8 25.8 + - - +
967M PHE* 3.6 19.5 - - + -
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Residues in contact with PHE 922 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918M LEU 2.9 11.2 + - - +
919M ALA* 3.6 10.8 - - - +
920M GLN 3.3 0.4 - - - -
921M ALA* 1.3 75.3 - - - +
923M GLU* 1.3 69.9 + - - +
925M TYR* 4.2 9.0 - + - -
926M PHE* 2.6 78.6 + + + -
930M LYS* 4.6 4.9 - - - -
960M GLU* 3.6 35.9 - - - -
963M LEU* 4.4 5.6 - - + -
964M LYS* 3.0 56.3 - - + +
967M PHE* 4.0 20.6 - + + -
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Residues in contact with GLU 923 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919M ALA 3.9 4.8 + - - +
920M GLN* 3.5 14.0 + - - +
921M ALA 3.1 0.4 - - - -
922M PHE* 1.3 93.4 - - + +
924M VAL* 1.3 60.1 + - + +
927M GLY* 2.7 52.7 + - - +
928M LYS 3.6 1.2 + - - -
930M LYS* 4.8 9.4 + - - +
964M LYS* 5.2 3.1 + - - +
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Residues in contact with VAL 924 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896M PHE* 3.2 32.5 - - + +
897M LEU* 3.6 18.8 - - + -
920M GLN* 3.4 20.0 - - - +
921M ALA 3.0 5.2 + - - +
923M GLU* 1.3 81.2 - - + +
925M TYR* 1.3 62.2 + - - +
928M LYS* 3.6 19.0 - - + +
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Residues in contact with TYR 925 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861M LEU* 3.6 27.3 - - + +
862M PRO* 3.1 39.5 - - + +
863M ASP* 5.1 3.4 - - + -
896M PHE* 4.4 29.8 - + + -
921M ALA 2.8 16.5 + - - +
922M PHE* 3.4 8.7 - + - +
924M VAL* 1.3 80.7 - - - +
926M PHE* 1.3 69.9 + + + +
928M LYS* 4.5 1.6 - - - +
929M ARG* 3.2 28.3 + - + +
967M PHE* 4.0 22.4 - + + -
972M VAL* 3.8 28.3 - - + +
973M VAL 5.3 0.3 + - - -
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Residues in contact with PHE 926 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922M PHE* 2.6 50.3 + + + +
925M TYR* 1.3 83.2 - + + +
927M GLY* 1.3 61.3 + - - +
928M LYS 3.4 0.4 - - - -
929M ARG* 3.4 17.4 - - + +
930M LYS* 3.1 55.0 + - + +
934M PHE 5.4 0.9 - - - -
935M GLY* 4.6 18.6 - - - -
936M VAL* 4.1 20.9 - - + -
940M GLU* 4.8 4.3 - - - -
960M GLU* 4.7 12.3 - - + -
963M LEU* 3.8 26.0 - - + -
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Residues in contact with GLY 927 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922M PHE 3.5 0.6 + - - -
923M GLU* 2.7 52.1 + - - +
926M PHE* 1.3 73.8 - - - +
928M LYS* 1.3 59.8 + - - +
930M LYS* 3.2 18.8 + - - +
931M GLY* 3.3 10.6 + - - -
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Residues in contact with LYS 928 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923M GLU 3.6 4.8 + - - -
924M VAL* 3.6 17.6 + - - +
925M TYR 4.5 2.2 - - - +
926M PHE 3.4 0.2 - - - -
927M GLY* 1.3 74.4 + - - +
929M ARG* 1.3 53.4 + - + +
931M GLY* 3.9 6.3 - - - -
932M GLU* 2.6 68.8 + - - +
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Residues in contact with ARG 929 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K GLN* 3.2 28.3 + - - +
198K ARG* 4.3 22.7 + - - +
862M PRO* 3.2 39.1 + - - +
863M ASP* 3.8 10.6 - - + +
925M TYR* 3.2 28.0 + - + +
926M PHE* 3.4 27.4 - - + +
928M LYS* 1.3 76.3 - - + +
930M LYS* 1.3 60.0 + - - +
932M GLU* 4.1 9.9 - - - +
933M GLY 3.5 4.2 + - - -
934M PHE* 2.8 38.9 + - - +
935M GLY 3.2 25.7 + - - -
940M GLU* 3.4 12.7 + - - -
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Residues in contact with LYS 930 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922M PHE* 4.6 7.6 - - - -
923M GLU* 4.8 7.8 + - - +
926M PHE* 3.1 53.0 + - + +
927M GLY* 3.2 13.0 + - - +
929M ARG* 1.3 77.1 - - - +
931M GLY* 1.3 60.3 + - - +
933M GLY* 3.5 11.8 + - - -
934M PHE 3.9 7.0 + - - +
935M GLY* 6.4 0.2 - - - -
960M GLU* 3.8 26.4 + - - -
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Residues in contact with GLY 931 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927M GLY 3.3 8.7 + - - -
928M LYS* 3.8 9.4 - - - -
930M LYS* 1.3 77.1 - - - +
932M GLU* 1.3 62.8 + - - +
933M GLY* 2.9 8.5 + - - -
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Residues in contact with GLU 932 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K TYR* 3.4 27.4 + - + +
22K GLU* 3.8 14.6 - - - +
198K ARG* 3.1 35.5 + - - +
200K TRP* 4.6 5.9 - - - -
928M LYS* 2.6 67.8 + - - +
929M ARG* 4.0 7.0 + - - +
930M LYS 3.5 0.4 - - - -
931M GLY* 1.3 70.9 - - - +
933M GLY* 1.3 56.9 + - - +
934M PHE 4.0 0.4 - - - -
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Residues in contact with GLY 933 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K GLU* 5.1 1.6 - - - -
929M ARG 3.5 1.8 + - - -
930M LYS 3.5 7.6 + - - -
931M GLY 2.9 7.7 + - - -
932M GLU* 1.3 80.7 - - - +
934M PHE* 1.3 80.7 + - - +
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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