Contacts of the helix formed by residues 949 - 970 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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947A ARG 3.7 5.4 + - - +
948A ILE* 1.3 75.1 - - - +
950A HIS* 1.3 65.0 + - - +
951A ILE* 3.8 25.9 - - - +
952A LYS* 3.1 29.3 + - - +
953A LEU* 3.1 21.1 + - - +
1050A TYR* 3.5 7.2 - - - -
1111B ASN* 3.5 22.9 - - + +
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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
----------------------------------------------------------
949A ASP* 1.3 75.2 - - - +
951A ILE* 1.3 61.8 + - - +
953A LEU* 3.2 10.7 + - + +
954A LEU* 3.1 29.6 + - + +
1048A PHE* 3.6 27.6 + + + -
1050A TYR* 3.5 17.4 - - - -
1092A ASP 5.2 0.4 + - - -
1093A GLY* 3.0 32.6 - - - -
1095A PRO* 3.8 20.3 - - + +
1130A MET* 4.0 19.6 - - + +
1111B ASN 3.2 25.9 + - - -
1112B GLN* 4.5 4.0 - - - +
1113B ARG 5.1 3.6 - - - -
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Residues in contact with ILE 951 (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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949A ASP* 3.2 19.9 - - - +
950A HIS* 1.3 75.9 - - + +
952A LYS* 1.3 57.8 + - + +
954A LEU* 3.4 8.4 + - - +
955A GLN* 3.1 24.8 + - + +
1127A ARG* 4.8 17.1 + - + +
1130A MET* 3.9 41.3 - - + +
1131A ALA* 5.5 5.6 - - + -
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Residues in contact with LYS 952 (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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947A ARG* 4.7 8.6 + - - +
948A ILE* 3.8 18.2 - - + +
949A ASP* 3.1 27.7 + - - +
951A ILE* 1.3 74.1 - - + +
953A LEU* 1.3 65.3 + - - +
955A GLN* 3.2 22.2 + - - +
956A TYR* 3.0 37.4 + - + +
987A GLU* 3.0 51.7 + - - +
988A ASN* 3.3 24.9 - - - -
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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
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941A LEU* 3.7 30.3 - - + -
948A ILE* 3.8 9.0 - - + -
949A ASP 3.1 14.9 + - - +
950A HIS* 3.2 19.9 + - + +
952A LYS* 1.3 76.4 - - - +
954A LEU* 1.3 53.8 + - - +
956A TYR* 3.5 10.1 + - + +
957A THR* 2.6 36.3 + - - -
1047A LEU* 3.4 44.7 - - + +
1048A PHE* 4.0 19.7 - - + -
1050A TYR* 3.6 24.7 - - + +
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Residues in contact with LEU 954 (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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950A HIS* 3.1 18.6 + - + +
951A ILE* 3.8 4.0 - - - +
953A LEU* 1.3 73.6 - - - +
955A GLN* 1.3 61.0 + - - +
957A THR* 3.9 7.2 - - - +
958A SER* 2.9 25.8 + - - -
1044A LEU* 4.8 2.7 - - + -
1048A PHE* 3.7 20.6 - - + -
1098A ILE* 3.7 26.2 - - + -
1123A VAL* 3.4 23.8 - - + +
1126A ILE* 3.8 19.3 - - + -
1127A ARG* 3.6 26.4 - - + +
1130A MET* 3.7 29.8 - - - -
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Residues in contact with GLN 955 (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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951A ILE* 3.1 13.3 + - + +
952A LYS* 3.4 35.6 + - - +
954A LEU* 1.3 76.5 - - - +
956A TYR* 1.3 63.2 + - + +
958A SER* 3.4 3.8 + - - -
959A GLN* 3.1 40.3 + - - +
988A ASN* 3.1 39.0 + - - +
1127A ARG* 3.7 30.7 + - - +
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Residues in contact with TYR 956 (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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937A LEU* 3.9 33.4 - - + -
940A TYR* 3.6 23.6 + + - -
948A ILE* 4.0 23.1 - - + +
952A LYS* 3.0 33.9 + - + +
953A LEU* 3.7 15.0 - - + +
955A GLN* 1.3 77.2 - - + +
957A THR* 1.3 57.4 + - - +
959A GLN* 3.2 10.4 + - - +
960A ILE* 2.9 36.4 + - + +
986A ASN 4.9 1.1 - - - -
987A GLU* 2.8 32.5 + - - +
988A ASN* 4.3 9.9 - - - -
989A ARG 4.5 0.4 - - - -
990A VAL* 3.5 34.5 - - + +
1047A LEU* 4.8 3.4 - - + -
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Residues in contact with THR 957 (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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953A LEU 2.6 23.2 + - - -
954A LEU* 3.5 11.3 - - + -
955A GLN 3.3 0.2 - - - -
956A TYR* 1.3 76.3 - - - +
958A SER* 1.3 61.7 + - - +
960A ILE* 3.3 12.1 + - - +
961A CYS* 3.0 23.4 + - - -
1040A PHE* 3.5 28.3 - - + -
1044A LEU* 3.5 23.1 - - + +
1047A LEU* 3.5 15.0 - - + +
1123A VAL* 3.8 20.0 - - + -
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Residues in contact with SER 958 (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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954A LEU 2.9 17.6 + - - -
955A GLN 3.6 5.6 - - - -
957A THR* 1.3 77.4 - - - +
959A GLN* 1.3 56.7 + - - +
961A CYS* 3.3 8.1 + - - +
962A LYS* 3.0 46.5 + - - +
1120A ALA* 4.7 4.1 + - - +
1123A VAL* 4.1 8.0 - - - +
1124A ASP* 2.6 32.6 + - - -
1127A ARG* 3.6 11.1 + - - -
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Residues in contact with GLN 959 (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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909A ASN* 3.4 42.0 + - - +
955A GLN* 3.1 27.4 + - + +
956A TYR* 3.2 9.9 + - - +
958A SER* 1.3 77.1 - - - +
960A ILE* 1.3 57.1 + - - +
962A LYS* 3.4 4.6 + - + -
963A GLY* 3.0 23.6 + - - -
988A ASN 2.7 24.9 + - - +
989A ARG* 3.4 9.4 - - - +
990A VAL* 2.8 38.2 + - + +
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Residues in contact with ILE 960 (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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909A ASN* 5.6 0.2 - - - -
937A LEU* 4.3 22.4 - - + -
956A TYR 2.9 26.2 + - - +
957A THR* 3.6 10.3 - - - +
958A SER 3.3 0.2 - - - -
959A GLN* 1.3 76.6 - - - +
961A CYS* 1.3 56.4 + - - +
963A GLY* 3.3 1.7 + - - -
964A MET* 2.9 37.9 + - + +
977A LEU* 4.7 7.2 - - + -
982A ILE* 4.2 25.8 - - + -
990A VAL* 4.1 10.3 - - + -
991A LYS 6.2 0.2 - - - -
992A ILE* 4.0 9.1 - - + +
1040A PHE* 4.1 21.3 - - + -
1043A VAL* 4.2 22.9 - - + -
1047A LEU* 4.5 4.5 - - + -
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Residues in contact with CYS 961 (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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957A THR* 3.0 14.0 + - - -
958A SER* 3.3 9.6 + - - +
960A ILE* 1.3 76.5 - - - +
962A LYS* 1.3 57.6 + - - +
964A MET* 3.3 1.7 + - - +
965A GLU* 2.8 29.6 + - - +
1040A PHE* 3.3 37.9 - - - -
1116A PHE* 3.9 28.8 - - + +
1119A LEU* 3.9 23.3 - - - -
1120A ALA* 4.1 13.9 - - + -
1123A VAL* 5.3 0.7 - - - -
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Residues in contact with LYS 962 (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 HIS* 3.7 18.8 + - + +
909A ASN* 4.3 5.6 - - - +
958A SER* 3.0 36.4 + - - +
959A GLN* 3.9 7.9 - - + +
960A ILE 3.3 0.2 - - - -
961A CYS* 1.3 73.2 - - - +
963A GLY* 1.3 64.5 + - - +
965A GLU* 3.5 7.4 + - - +
966A TYR* 3.2 22.5 + - - +
1120A ALA* 4.6 13.9 - - + -
1124A ASP* 3.7 18.9 + - - -
1127A ARG* 5.1 4.0 - - - +
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Residues in contact with GLY 963 (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 HIS* 3.9 16.9 - - - -
909A ASN* 4.4 5.8 - - - -
910A ILE* 4.1 4.0 - - - +
959A GLN 3.0 14.1 + - - -
960A ILE 3.3 3.5 + - - -
961A CYS 3.3 0.2 - - - -
962A LYS* 1.3 77.2 - - - +
964A MET* 1.3 55.7 + - - +
966A TYR* 3.3 6.2 + - - +
967A LEU* 3.1 29.3 + - - +
992A ILE* 3.7 16.8 - - - -
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Residues in contact with MET 964 (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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960A ILE* 2.9 23.5 + - + +
961A CYS 3.7 4.0 - - - +
963A GLY* 1.3 73.5 - - - +
965A GLU* 1.3 66.0 + - - +
967A LEU* 3.2 23.8 + - + +
968A GLY* 3.0 19.8 + - - -
972A TYR 5.4 0.4 - - - +
974A HIS* 3.9 8.7 - - + -
977A LEU* 3.7 33.7 - - + -
992A ILE* 3.7 19.3 - - + -
1036A ASP* 3.2 39.5 - - + +
1116A PHE* 3.7 31.4 - - + -
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Residues in contact with GLU 965 (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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961A CYS 2.8 16.5 + - - +
962A LYS* 3.8 8.5 - - - +
963A GLY 3.4 0.2 - - - -
964A MET* 1.3 75.3 - - - +
966A TYR* 1.3 62.3 + - - +
968A GLY* 3.2 5.4 + - - +
969A THR* 3.1 24.8 + - - -
1033A VAL* 6.2 0.3 - - - +
1115A SER* 5.9 0.9 - - - -
1116A PHE* 4.0 21.9 + - + +
1117A ARG* 3.9 49.9 + - - +
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Residues in contact with TYR 966 (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 SER 3.8 0.3 + - - -
905A LEU* 3.6 19.7 - - + -
906A GLN* 3.0 42.8 + - - +
907A HIS* 3.6 27.4 - + + -
910A ILE* 3.4 22.7 - - + -
962A LYS 3.2 14.9 + - - +
963A GLY 3.4 7.9 - - - +
965A GLU* 1.3 75.7 - - - +
967A LEU* 1.3 61.9 + - - +
969A THR* 2.9 36.9 - - + +
970A LYS* 3.5 36.0 + - - +
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Residues in contact with LEU 967 (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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905A LEU* 3.6 40.6 - - + -
910A ILE* 3.7 13.2 - - + -
963A GLY 3.1 15.5 + - - +
964A MET* 3.2 34.3 + - + +
966A TYR* 1.3 74.1 - - - +
968A GLY* 1.3 57.6 + - - +
970A LYS* 3.1 13.2 + - - +
972A TYR* 3.0 44.7 + - + +
974A HIS* 3.9 25.6 - - + +
992A ILE* 4.9 1.6 - - + -
995A PHE* 3.9 17.7 - - + -
998A THR* 5.0 1.1 - - + -
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Residues in contact with GLY 968 (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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964A MET 3.0 13.6 + - - -
965A GLU* 3.2 8.2 + - - -
967A LEU* 1.3 71.7 - - - +
969A THR* 1.3 59.4 + - - +
970A LYS 3.1 2.2 - - - -
971A ARG* 3.0 23.7 + - - +
972A TYR 4.3 7.4 - - - -
1033A VAL* 4.7 19.2 - - - +
1116A PHE* 6.5 0.2 - - - -
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Residues in contact with THR 969 (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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965A GLU* 3.1 16.8 + - - -
966A TYR* 2.9 37.7 - - + +
967A LEU 3.2 0.6 - - - -
968A GLY* 1.3 76.5 - - - +
970A LYS* 1.3 68.2 + - + +
971A ARG* 3.4 3.9 - - - +
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Residues in contact with LYS 970 (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 SER* 2.7 31.0 + - - +
905A LEU* 4.2 11.2 - - + -
906A GLN* 5.9 1.2 - - - +
966A TYR* 3.5 34.5 + - - +
967A LEU 3.1 7.8 + - - +
968A GLY 3.1 0.6 - - - -
969A THR* 1.3 89.4 - - + +
971A ARG* 1.3 70.0 + - - +
972A TYR* 3.2 34.8 + - + +
1000A VAL* 4.3 4.3 - - - +
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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