Contacts of the helix formed by residues 946 - 972 (chain B) in PDB entry 1K05
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 PRO 946 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B PRO 4.7 0.4 - - - +
945B ALA* 1.3 87.7 - - - +
947B PRO* 1.3 62.0 - - + +
948B GLU* 3.2 29.6 - - - +
949B GLU* 2.7 52.4 + - + +
950B TYR* 3.3 6.2 + - - -
1013B GLN* 4.9 1.6 - - - +
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Residues in contact with PRO 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B PRO* 1.3 86.1 - - + -
948B GLU* 1.3 63.3 + - + +
950B TYR* 3.4 36.5 - - + +
951B VAL* 2.8 37.4 + - + +
1005B GLN* 4.2 19.5 - - + +
1008B VAL* 4.2 36.3 - - + -
1013B GLN* 4.4 2.7 - - - +
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Residues in contact with GLU 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B PRO* 2.8 34.7 + - - +
947B PRO* 1.3 82.7 - - + +
949B GLU* 1.3 60.2 + - + +
951B VAL* 5.5 0.2 - - - -
952B PRO* 3.0 19.8 - - - +
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Residues in contact with GLU 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B PRO 4.2 3.1 - - - +
945B ALA* 3.2 18.7 - - + +
946B PRO* 2.7 43.4 + - + +
948B GLU* 1.3 77.0 - - + +
950B TYR* 1.3 59.4 + - - +
952B PRO* 2.8 23.1 - - - +
953B MET* 3.1 27.7 - - + +
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Residues in contact with TYR 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B ILE* 3.8 27.1 - - + -
945B ALA* 3.3 30.7 - - + -
946B PRO 3.3 8.6 + - - -
947B PRO* 3.4 29.3 - - + +
949B GLU* 1.3 78.5 - - - +
951B VAL* 1.3 74.9 + - + +
953B MET* 3.0 13.4 + - + +
954B VAL* 3.0 25.8 + - - +
1001B MET* 4.4 10.8 - - + -
1004B ALA* 2.9 49.1 + - + -
1005B GLN* 3.4 2.3 + - + -
1013B GLN* 3.1 17.1 + - - -
1017B LYS* 3.7 11.0 - - - -
1020B MET* 4.0 16.4 - - + -
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Residues in contact with VAL 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B PRO* 2.8 26.6 + - + +
948B GLU* 5.5 0.4 - - - -
950B TYR* 1.3 76.7 - - + +
952B PRO* 1.3 67.5 - - + +
954B VAL* 3.3 4.0 + - - +
955B LYS* 3.0 40.8 + - - +
1001B MET* 3.8 39.1 - - + +
1005B GLN* 3.8 29.2 - - + +
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Residues in contact with PRO 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948B GLU* 3.0 26.2 - - - +
949B GLU* 2.8 22.7 - - - +
951B VAL* 1.3 97.4 - - + +
953B MET* 1.3 60.1 + - - +
955B LYS* 3.1 17.9 + - + +
956B GLU* 2.9 27.5 + - - +
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Residues in contact with MET 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B ALA 5.3 0.5 - - - +
937B GLU* 4.9 7.0 - - + +
938B MET* 3.6 35.5 - - + +
941B LYS* 3.1 51.4 - - + +
942B ILE* 4.5 3.8 - - - -
945B ALA* 5.3 2.2 - - + -
949B GLU* 3.1 33.6 + - + +
950B TYR* 3.0 22.2 + - - +
952B PRO* 1.3 78.3 - - - +
954B VAL* 1.3 62.1 + - - +
956B GLU* 3.4 8.8 + - - +
957B VAL* 3.4 21.7 + - - +
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Residues in contact with VAL 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B MET* 3.3 27.8 - - + -
950B TYR 3.0 12.9 + - - +
951B VAL 3.7 6.1 - - - +
953B MET* 1.3 73.0 - - - +
955B LYS* 1.3 67.1 + - - +
957B VAL* 3.0 13.6 + - - +
958B GLY* 3.0 10.9 + - - -
994B LEU* 4.8 2.9 - - + -
997B LEU* 3.7 26.2 - - + -
998B ILE* 4.7 14.1 - - + -
1001B MET* 3.8 21.8 - - + -
1020B MET* 3.5 24.5 - - + -
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Residues in contact with LYS 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B VAL* 3.0 33.4 + - - +
952B PRO* 3.2 18.7 - - + +
954B VAL* 1.3 77.3 - - - +
956B GLU* 1.3 65.4 + - + +
958B GLY* 2.9 4.7 + - - -
959B LEU* 2.8 25.3 + - + +
962B ARG* 4.6 8.1 + - - +
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Residues in contact with GLU 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B ALA* 4.5 10.0 - - + +
952B PRO 2.9 15.8 + - - +
953B MET* 3.6 11.9 - - - +
955B LYS* 1.3 74.7 - - - +
957B VAL* 1.3 57.5 + - - +
959B LEU* 3.3 30.4 + - - +
960B ALA* 2.8 30.8 + - - +
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Residues in contact with VAL 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU* 3.8 9.5 - - + +
934B ALA* 3.9 34.1 - - + +
935B VAL* 4.1 11.4 - - + +
938B MET* 4.2 17.9 - - + -
953B MET 3.4 15.0 - - - +
954B VAL* 3.0 9.9 + - - +
956B GLU* 1.3 75.8 - - - +
958B GLY* 1.3 52.9 + - - +
960B ALA* 3.0 5.5 + - - +
961B LEU* 2.7 32.7 + - - +
997B LEU* 4.0 11.9 - - + -
1027B LEU* 3.7 29.2 - - + -
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Residues in contact with GLY 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954B VAL 3.0 8.2 + - - -
955B LYS* 2.9 8.0 + - - -
957B VAL* 1.3 73.1 - - - +
959B LEU* 1.3 66.5 + - - +
961B LEU* 3.0 3.3 + - - +
962B ARG* 3.0 38.9 + - - +
994B LEU* 3.8 29.5 - - - +
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Residues in contact with LEU 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955B LYS* 2.8 17.2 + - + +
956B GLU* 3.5 36.3 - - - +
958B GLY* 1.3 72.4 - - - +
960B ALA* 1.3 65.1 + - - +
962B ARG* 3.3 19.8 + - + +
963B THR* 3.2 32.8 + - - +
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Residues in contact with ALA 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B ASN* 5.3 2.1 - - - +
930B GLY 4.7 1.8 - - - -
931B LEU* 3.8 31.3 - - + +
934B ALA* 4.4 6.1 - - + -
956B GLU 2.8 14.2 + - - +
957B VAL* 3.1 12.1 - - - +
959B LEU* 1.3 80.6 - - + +
961B LEU* 1.3 63.6 + - - +
962B ARG 3.3 0.2 + - - -
963B THR* 3.3 8.6 + - - -
964B LEU* 3.1 21.0 + - - +
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Residues in contact with LEU 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU* 3.8 19.7 - - + +
957B VAL 2.7 15.8 + - - +
958B GLY* 3.0 11.0 + - - +
960B ALA* 1.3 71.1 - - - +
962B ARG* 1.3 58.9 + - + +
964B LEU* 3.1 8.3 + - + +
965B LEU* 2.8 51.1 + - + +
990B LEU* 4.0 27.8 - - + +
991B ASN* 4.0 8.7 - - - +
994B LEU* 3.8 34.3 - - + -
1027B LEU* 3.8 23.3 - - + -
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Residues in contact with ARG 962 (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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955B LYS* 4.6 10.1 + - - +
958B GLY* 3.0 36.0 + - - +
959B LEU* 3.6 19.2 - - + +
961B LEU* 1.3 74.3 - - + +
963B THR* 1.3 69.2 + - - +
965B LEU* 2.8 11.9 + - + -
966B ALA* 2.6 27.0 + - - +
994B LEU* 4.1 13.7 - - - +
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Residues in contact with THR 963 (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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923B LYS* 6.1 0.7 - - + -
927B ASN* 2.9 33.8 + - - +
959B LEU* 3.2 20.8 + - - +
960B ALA* 3.5 10.6 - - - -
962B ARG* 1.3 75.8 - - - +
964B LEU* 1.3 64.3 + - - +
966B ALA* 3.3 7.1 + - - +
967B THR* 2.9 22.0 + - - +
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Residues in contact with LEU 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B VAL* 3.8 8.1 - - + +
927B ASN* 3.1 36.7 - - + +
928B VAL* 3.5 29.2 - - + +
931B LEU* 3.8 28.0 - - + -
960B ALA 3.1 9.5 + - - +
961B LEU* 3.3 10.8 - - + +
962B ARG 3.1 0.8 - - - -
963B THR* 1.3 77.9 - - - +
965B LEU* 1.3 58.7 + - - +
967B THR* 3.0 6.6 + - - -
968B VAL* 2.8 42.2 + - + +
990B LEU* 4.2 20.6 - - + -
1031B ALA* 4.4 7.0 - - + -
1034B LEU* 4.7 5.4 - - + -
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Residues in contact with LEU 965 (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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961B LEU* 2.8 51.4 + - + +
962B ARG* 2.8 12.4 + - + +
964B LEU* 1.3 68.6 - - + +
966B ALA* 1.3 66.8 + - - +
968B VAL* 2.9 9.0 + - + +
969B ASP* 2.9 31.0 + - - +
987B GLN* 3.7 39.2 + - + +
990B LEU* 4.0 18.6 - - + -
991B ASN* 4.0 20.9 - - - +
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Residues in contact with ALA 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962B ARG 2.6 18.8 + - - +
963B THR* 3.5 9.2 - - + +
965B LEU* 1.3 71.8 - - - +
967B THR* 1.3 63.8 + - - +
969B ASP* 3.0 29.5 + - - +
970B GLU* 3.2 15.3 + - + +
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Residues in contact with THR 967 (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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923B LYS* 3.8 32.2 - - + +
924B VAL* 3.8 23.8 - - + +
927B ASN* 2.9 23.7 + - - +
963B THR* 2.9 9.1 + - - +
964B LEU 3.2 9.0 - - - +
966B ALA* 1.3 76.8 - - - +
968B VAL* 1.3 63.5 + - - +
970B GLU* 3.0 28.3 + - - +
971B THR* 3.1 17.8 + - - +
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Residues in contact with VAL 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B VAL* 4.8 5.4 - - + -
964B LEU* 2.8 35.8 + - + +
965B LEU* 2.9 8.5 + - + +
967B THR* 1.3 73.8 - - - +
969B ASP* 1.3 61.4 + - - +
971B THR* 3.1 7.5 + - - -
972B ILE* 3.0 24.4 + - + +
983B ILE* 3.7 20.0 - - + -
987B GLN* 3.5 20.6 - - + +
1034B LEU* 3.7 22.4 - - + -
1038B ILE* 3.6 26.2 - - + -
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Residues in contact with ASP 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965B LEU* 2.9 25.9 + - - +
966B ALA* 3.1 14.3 - - - +
968B VAL* 1.3 77.8 - - - +
970B GLU* 1.3 56.7 + - + +
972B ILE* 3.5 11.3 + - - +
973B PRO* 3.0 26.0 - - - +
987B GLN* 3.1 19.3 + - - +
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Residues in contact with GLU 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A PRO 4.6 9.8 - - - +
974A LEU* 3.7 38.5 - - + +
966B ALA* 3.4 14.8 - - - +
967B THR* 3.0 20.6 + - - +
969B ASP* 1.3 76.6 - - + +
971B THR* 1.3 60.5 + - - +
973B PRO* 3.7 7.6 - - - +
974B LEU* 4.7 3.5 - - - +
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Residues in contact with THR 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A MET* 6.2 0.7 - - - -
1046A LEU* 6.0 1.3 - - + -
924B VAL* 3.8 15.9 - - + +
967B THR* 3.1 13.5 + - - +
968B VAL* 3.1 12.5 + - + -
969B ASP 3.1 0.6 - - - -
970B GLU* 1.3 77.8 - - - +
972B ILE* 1.3 68.4 + - - +
973B PRO* 3.2 3.1 - - - -
974B LEU* 2.8 22.7 + - + +
975B LEU* 3.5 30.4 - - + +
1038B ILE* 4.2 15.7 - - + -
1042B ARG* 4.8 10.7 + - - +
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Residues in contact with ILE 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B VAL* 3.0 20.9 + - + +
969B ASP* 3.8 15.3 - - - +
971B THR* 1.3 73.8 - - - +
973B PRO* 1.3 64.1 - - + +
975B LEU* 2.8 29.7 + - + +
980B HIS* 3.2 52.3 + - + +
983B ILE* 4.1 23.3 - - + -
984B GLU* 4.4 16.2 - - + +
987B GLN* 3.8 24.0 - - - +
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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