Contacts of the helix formed by residues 949 - 970 (chain B) in PDB entry 2B7A
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 ASP 949 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947B ARG 3.7 4.6 + - - +
948B ILE* 1.3 73.8 - - - +
950B HIS* 1.3 66.9 + - - +
951B ILE* 3.6 27.7 - - + +
952B LYS* 3.2 9.0 + - + +
953B LEU* 2.9 31.0 + - - +
1050B TYR* 3.8 2.7 - - - -
1130B MET* 6.3 0.7 - - - -
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Residues in contact with HIS 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949B ASP* 1.3 77.3 + - - +
951B ILE* 1.3 59.7 + - - +
953B LEU* 3.2 9.3 + - + +
954B LEU* 3.0 31.5 + - + +
1048B PHE* 3.5 32.4 + + + -
1050B TYR* 3.9 22.1 + + - -
1092B ASP 5.5 1.2 + - - -
1093B GLY* 3.2 30.0 + - - -
1095B PRO* 4.0 17.0 - - + +
1130B MET* 3.8 19.6 - - + +
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Residues in contact with ILE 951 (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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949B ASP* 3.6 23.6 - - + +
950B HIS* 1.3 78.0 - - - +
952B LYS* 1.3 62.2 + - + +
954B LEU* 3.4 6.0 + - - +
955B GLN* 3.0 26.5 + - - +
1127B ARG* 3.5 38.7 + - + +
1130B MET* 3.8 30.3 - - + +
1131B ALA* 3.9 18.4 - - + +
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Residues in contact with LYS 952 (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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947B ARG 5.7 0.2 - - - +
948B ILE* 3.8 13.0 - - + -
949B ASP* 3.2 23.4 + - + +
951B ILE* 1.3 81.7 - - + +
953B LEU* 1.3 63.5 + - - +
955B GLN* 3.1 26.7 + - - +
956B TYR* 3.1 44.3 + - + +
987B GLU* 3.0 37.3 + - - +
988B ASN* 3.1 21.3 + - - -
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Residues in contact with LEU 953 (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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941B LEU* 3.6 31.4 - - + -
948B ILE* 3.8 8.3 - - + -
949B ASP 2.9 16.0 + - - +
950B HIS* 3.2 9.4 + - + +
952B LYS* 1.3 77.0 - - - +
954B LEU* 1.3 52.7 + - - +
956B TYR* 3.3 14.1 + - + +
957B THR* 2.7 35.4 + - - -
1047B LEU* 3.6 33.7 - - + +
1048B PHE* 3.9 34.8 - - + -
1050B TYR* 3.5 26.9 - - + +
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Residues in contact with LEU 954 (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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950B HIS* 3.0 14.1 + - + +
951B ILE* 3.7 5.2 - - - +
952B LYS 3.2 0.2 - - - -
953B LEU* 1.3 74.1 - - - +
955B GLN* 1.3 60.4 + - - +
957B THR* 3.8 8.1 - - + +
958B SER* 2.9 25.8 + - - -
1044B LEU* 4.7 2.9 - - + -
1048B PHE* 4.0 20.0 - - + -
1098B ILE* 3.7 24.7 - - + -
1101B ILE* 5.9 0.7 - - + -
1123B VAL* 3.3 26.6 - - + +
1126B ILE* 3.8 21.8 - - + -
1127B ARG* 3.6 25.9 - - + -
1130B MET* 3.7 29.2 - - - -
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Residues in contact with GLN 955 (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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951B ILE* 3.0 13.8 + - - +
952B LYS* 3.3 30.1 - - + +
954B LEU* 1.3 74.2 - - - +
956B TYR* 1.3 64.5 + - + +
958B SER* 3.5 2.9 + - - -
959B GLN* 3.2 38.9 + - - +
988B ASN* 3.0 42.3 + - - +
1127B ARG* 3.7 31.1 + - - +
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Residues in contact with TYR 956 (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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937B LEU* 4.2 27.8 - - + -
940B TYR* 3.9 17.4 - + - -
941B LEU* 5.2 0.2 - - + -
948B ILE* 4.1 20.8 - - + +
952B LYS* 3.1 36.7 + - + +
953B LEU* 3.5 19.3 - - + +
955B GLN* 1.3 73.3 - - + +
957B THR* 1.3 66.9 + - - +
959B GLN* 3.2 12.1 + - - +
960B ILE* 3.0 28.0 + - - +
984B VAL* 6.0 0.2 - - + -
986B ASN 4.7 0.9 - - - -
987B GLU* 2.6 37.2 + - - +
988B ASN 4.2 8.7 - - - -
989B ARG 4.4 0.4 - - - -
990B VAL* 3.6 33.7 - - + +
1047B LEU* 4.9 4.7 - - + -
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Residues in contact with THR 957 (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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953B LEU 2.7 23.8 + - - -
954B LEU* 3.5 12.6 - - + -
956B TYR* 1.3 75.7 - - - +
958B SER* 1.3 55.9 + - - +
960B ILE* 3.2 9.3 + - - +
961B CYS* 2.9 27.6 + - - -
1040B PHE* 3.5 27.6 - - + -
1044B LEU* 3.6 22.4 - - + +
1047B LEU* 3.3 19.5 - - + +
1123B VAL* 3.9 19.3 - - + -
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Residues in contact with SER 958 (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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954B LEU 2.9 17.2 + - - -
955B GLN 3.7 3.6 - - - -
957B THR* 1.3 75.7 - - - +
959B GLN* 1.3 57.9 + - - +
961B CYS* 3.3 8.3 + - - +
962B LYS* 3.0 51.6 + - - +
1120B ALA* 4.6 3.0 + - - +
1123B VAL* 4.0 10.5 - - - +
1124B ASP* 2.6 29.5 + - - -
1127B ARG* 3.6 9.8 + - - -
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Residues in contact with GLN 959 (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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909B ASN* 3.4 41.1 + - - +
955B GLN* 3.2 25.6 + - - +
956B TYR* 3.2 9.4 + - - +
958B SER* 1.3 75.4 - - - +
960B ILE* 1.3 58.0 + - - +
962B LYS* 3.4 3.9 + - + -
963B GLY 3.0 23.2 + - - -
988B ASN 2.8 24.7 + - - +
989B ARG* 3.3 7.8 - - - +
990B VAL* 2.8 38.3 + - + +
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Residues in contact with ILE 960 (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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909B ASN* 5.8 0.4 - - + +
937B LEU* 5.5 2.5 - - + -
956B TYR* 3.0 22.1 + - + +
957B THR* 3.2 8.3 + - - +
959B GLN* 1.3 72.6 - - - +
961B CYS* 1.3 67.2 + - - +
963B GLY* 3.3 2.1 + - - -
964B MET* 2.9 32.7 + - + +
977B LEU* 4.7 9.4 - - + -
982B ILE* 3.7 50.9 - - + -
990B VAL* 3.7 13.2 - - + -
991B LYS* 5.0 0.4 - - - -
992B ILE* 4.1 17.3 - - + +
1040B PHE* 3.9 24.5 - - + -
1043B VAL* 5.0 7.0 - - + -
1047B LEU* 5.8 2.2 - - + -
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Residues in contact with CYS 961 (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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957B THR* 2.9 15.6 + - - +
958B SER* 3.3 9.4 + - - +
960B ILE* 1.3 76.7 - - - +
962B LYS* 1.3 51.4 + - - +
964B MET* 3.2 2.9 + - - +
965B GLU* 2.8 35.3 + - - +
1040B PHE* 3.2 35.9 - - - -
1116B PHE* 3.9 17.6 - - - +
1119B LEU* 3.8 24.9 - - - -
1120B ALA* 4.0 22.7 - - + -
1123B VAL* 4.9 1.1 - - - -
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Residues in contact with LYS 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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907B HIS* 3.6 12.0 + - + +
909B ASN* 4.3 11.0 - - - +
958B SER* 3.0 35.9 + - - +
959B GLN* 3.8 7.6 - - + +
960B ILE 3.3 0.2 - - - -
961B CYS* 1.3 74.4 - - - +
963B GLY* 1.3 64.5 + - - +
965B GLU* 3.5 13.9 + - - +
966B TYR* 3.1 22.2 + - - +
1120B ALA* 4.5 13.5 - - + -
1124B ASP* 3.4 22.2 + - - -
1127B ARG* 4.8 4.0 - - - +
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Residues in contact with GLY 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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907B HIS* 3.8 18.3 - - - -
909B ASN* 4.5 4.3 - - - -
910B ILE* 4.0 8.0 - - - +
959B GLN 3.0 14.5 + - - -
960B ILE 3.7 2.9 - - - -
962B LYS* 1.3 75.2 - - - +
964B MET* 1.3 56.7 + - - +
966B TYR* 3.3 6.2 + - - +
967B LEU* 3.1 27.2 + - - +
992B ILE* 3.9 15.9 - - - -
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Residues in contact with MET 964 (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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960B ILE* 2.9 22.2 + - + +
961B CYS 3.6 3.8 - - - +
963B GLY* 1.3 74.8 - - - +
965B GLU* 1.3 64.4 + - - +
967B LEU* 3.3 31.0 + - + +
968B GLY* 3.1 18.0 + - - -
972B TYR 5.5 0.9 - - - +
974B HIS* 4.0 3.6 - - + -
977B LEU* 3.8 28.0 - - + -
992B ILE* 3.7 16.4 - - + -
1036B ASP* 3.3 39.9 - - + +
1116B PHE* 3.7 39.4 - - + -
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Residues in contact with GLU 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 CYS 2.8 18.6 + - - +
962B LYS* 3.6 16.2 - - - +
963B GLY 3.4 0.2 - - - -
964B MET* 1.3 72.4 - - - +
966B TYR* 1.3 60.9 + - - +
968B GLY* 3.3 10.6 + - - -
969B THR* 3.4 19.7 + - + +
1116B PHE* 4.1 8.6 - - + +
1117B ARG* 3.7 45.9 - - + +
1120B ALA* 4.3 13.7 - - - +
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Residues in contact with TYR 966 (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 SER 3.8 0.5 + - - -
905B LEU* 3.6 21.8 - - + -
906B GLN* 3.0 42.0 + - - +
907B HIS* 3.7 26.7 - + + -
910B ILE* 3.5 20.9 - - + -
962B LYS 3.1 13.5 + - - +
963B GLY 3.4 7.4 - - - +
964B MET 3.2 0.2 - - - -
965B GLU* 1.3 74.6 - - - +
967B LEU* 1.3 61.5 + - - +
969B THR* 2.6 32.5 + - + -
970B LYS* 3.4 37.0 + - - +
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Residues in contact with LEU 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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905B LEU* 3.6 37.2 - - + -
910B ILE* 4.5 3.1 - - + -
963B GLY 3.1 16.2 + - - +
964B MET* 3.5 35.9 - - + +
966B TYR* 1.3 75.3 - - - +
968B GLY* 1.3 58.4 + - - +
970B LYS* 3.0 20.0 + - - +
972B TYR* 3.0 46.9 + - + +
974B HIS* 3.9 23.1 - - + +
992B ILE* 5.2 1.1 - - + -
995B PHE* 3.8 22.7 - - + -
998B THR* 5.2 0.2 - - + -
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Residues in contact with GLY 968 (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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964B MET 3.1 12.6 + - - -
965B GLU 3.3 6.9 + - - -
966B TYR 3.2 0.8 - - - -
967B LEU* 1.3 77.8 - - - +
969B THR* 1.3 56.9 + - - +
971B ARG* 3.0 23.3 + - - +
972B TYR 4.4 5.3 + - - -
1033B VAL* 5.0 15.7 - - - +
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Residues in contact with THR 969 (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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965B GLU* 3.5 16.4 - - + +
966B TYR* 2.6 31.6 + - + +
968B GLY* 1.3 75.5 - - - +
970B LYS* 1.3 63.7 + - - +
971B ARG* 3.3 5.4 - - - +
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Residues in contact with LYS 970 (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 SER* 3.0 27.1 + - - +
905B LEU* 4.1 6.7 - - + -
966B TYR* 3.4 45.1 + - - +
967B LEU 3.0 8.6 + - - +
969B THR* 1.3 81.2 - - - +
971B ARG* 1.3 69.7 + - - +
972B TYR* 3.4 43.7 + - + +
1000B VAL* 4.4 4.9 - - - +
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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) + - + + + + + -
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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