Contacts of the helix formed by residues 986 - 1009 (chain A) in PDB entry 3MPX
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 GLY 986 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955A LEU* 3.4 36.4 - - - +
983A ARG* 3.5 8.2 + - - +
984A GLU 3.2 1.0 - - - -
985A GLN* 1.3 76.2 + - - +
987A PHE* 1.3 55.6 + - - +
988A ASP 3.0 9.1 + - - -
989A HIS* 3.2 30.9 + - - +
990A HIS 4.1 0.3 + - - -
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Residues in contact with PHE 987 (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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955A LEU* 4.6 2.7 - - + -
956A HIS* 4.5 2.5 - + - -
959A ILE* 3.9 19.3 - - + -
980A PHE* 3.7 32.8 - + - -
983A ARG* 3.1 30.3 + - + +
984A GLU 3.4 5.1 + - - +
986A GLY* 1.3 71.5 - - - +
988A ASP* 1.3 62.6 + - - +
989A HIS 3.3 0.7 - - - -
990A HIS* 3.2 31.9 - + + +
991A ALA 3.2 4.9 + - - -
1043A LEU* 3.6 24.0 - - + -
1046A TYR* 3.5 36.6 - + - -
1073A LEU* 3.7 18.6 - - + -
1074A ILE* 4.4 8.7 - - + -
1077A VAL* 3.6 25.6 - - + +
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Residues in contact with ASP 988 (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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984A GLU* 3.3 21.1 + - - +
985A GLN* 3.3 22.0 + - - +
986A GLY 3.0 1.2 - - - -
987A PHE* 1.3 77.3 - - - +
989A HIS* 1.4 58.4 + - + +
991A ALA* 3.2 11.6 + - - +
992A THR* 2.9 33.7 + - - +
1077A VAL* 5.6 2.4 - - - +
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Residues in contact with HIS 989 (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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948A GLU* 2.9 31.6 + - - +
951A ALA* 3.6 31.0 - - + +
952A ILE* 4.1 17.0 - - + +
985A GLN* 3.8 16.5 + - + +
986A GLY* 3.2 23.9 + - - +
988A ASP* 1.4 73.8 - - + +
990A HIS* 1.4 53.0 + - - +
992A THR* 3.3 3.6 + - - -
993A HIS* 2.8 36.9 + - - +
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Residues in contact with HIS 990 (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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5A UNX 3.0 29.3 - - - -
907A TYR* 3.6 21.1 - - - -
952A ILE* 3.7 18.2 - - + +
955A LEU* 3.7 23.3 - - + -
956A HIS* 2.8 26.4 + + - -
987A PHE* 3.2 26.1 + + - +
988A ASP 3.3 0.2 - - - -
989A HIS* 1.4 77.6 - - - +
991A ALA* 1.3 55.5 + - - +
993A HIS* 3.2 1.3 + - - -
994A ILE* 2.9 30.9 + - - +
1039A VAL* 4.0 8.9 + - + -
1042A ARG* 5.6 0.2 - - + -
1043A LEU* 3.6 22.0 - - + +
1077A VAL* 3.6 15.7 - - + -
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Residues in contact with ALA 991 (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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987A PHE 3.2 8.1 + - - +
988A ASP* 3.2 19.2 + - - +
990A HIS* 1.3 77.6 - - - +
992A THR* 1.3 58.3 + - - +
994A ILE* 3.5 7.4 + - - +
995A LEU* 3.0 39.4 + - + +
1076A LYS 6.0 0.2 - - - +
1077A VAL* 3.6 21.2 - - + +
1080A ARG* 4.7 6.6 - - + +
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Residues in contact with THR 992 (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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944A GLN* 6.0 0.4 - - - +
948A GLU* 3.3 24.9 - - - +
988A ASP* 2.9 17.7 + - - +
989A HIS* 3.6 5.4 - - - -
991A ALA* 1.3 73.1 - - - +
993A HIS* 1.4 62.3 + - - +
995A LEU* 3.5 13.4 + - - +
996A GLN* 2.8 49.9 + - - +
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Residues in contact with HIS 993 (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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5A UNX 2.7 25.2 - - - -
945A GLY* 4.0 12.1 - - - -
948A GLU* 4.0 12.1 - - + -
949A LEU* 3.9 11.4 - - + +
952A ILE* 3.9 11.4 - - + +
989A HIS 2.8 20.6 + - - +
990A HIS 3.2 0.2 + - - -
992A THR* 1.4 69.9 - - - +
994A ILE* 1.3 53.1 + - - +
996A GLN* 3.3 5.0 + - - +
997A PHE* 2.9 61.0 + + - -
1000A TYR* 2.7 39.5 + + - -
1036A LEU* 4.6 1.8 - - + -
1039A VAL* 3.8 23.8 - - + +
1040A VAL* 4.1 1.0 - - + +
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Residues in contact with ILE 994 (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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5A UNX 4.0 4.7 - - - -
990A HIS 2.9 22.3 + - - +
991A ALA* 3.6 3.4 - - - +
993A HIS* 1.3 75.9 - - - +
995A LEU* 1.4 63.2 + - - +
997A PHE* 3.3 23.5 + - - +
1040A VAL* 3.8 21.3 - - + -
1043A LEU* 3.8 24.9 - - + -
1077A VAL* 3.8 20.4 - - + +
1080A ARG* 3.4 40.8 - - + +
1081A ALA* 3.4 16.4 - - + +
1084A SER* 4.1 8.1 - - - +
1085A MSE 3.9 12.4 - - + +
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Residues in contact with LEU 995 (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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991A ALA* 3.0 33.2 + - + +
992A THR* 3.7 12.8 - - - +
993A HIS 3.4 0.2 - - - -
994A ILE* 1.4 73.5 - - - +
996A GLN* 1.3 59.5 + - + +
1080A ARG* 4.7 10.8 - - + -
1084A SER* 3.7 30.6 - - - +
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Residues in contact with GLN 996 (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 GLU 4.9 0.5 - - - +
944A GLN* 3.8 19.1 + - - +
945A GLY* 3.5 34.4 + - - -
948A GLU* 4.3 6.5 + - - +
992A THR* 2.8 42.3 + - - +
993A HIS* 3.9 5.8 - - - +
994A ILE 3.3 0.4 - - - -
995A LEU* 1.3 77.9 - - - +
997A PHE* 1.3 66.0 + - - +
998A ASP 3.6 1.3 - - - -
999A ARG* 3.1 15.0 + - + +
1000A TYR* 3.1 23.0 + - + +
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Residues in contact with PHE 997 (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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993A HIS* 2.9 41.5 + + - +
994A ILE* 3.3 19.5 + - - +
996A GLN* 1.3 77.6 - - - +
998A ASP* 1.3 77.7 + - - +
1000A TYR* 3.4 9.6 - - - -
1001A LEU* 3.1 48.2 + - + +
1033A LYS* 4.1 7.2 - - + -
1036A LEU* 3.5 35.9 - - + -
1037A LEU* 3.8 15.9 - - + -
1040A VAL* 3.6 13.7 - - + -
1085A MSE 3.8 25.4 - - + -
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Residues in contact with ASP 998 (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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994A ILE 4.8 0.4 + - - -
996A GLN 3.6 0.4 - - - -
997A PHE* 1.3 94.8 - - - +
999A ARG* 1.4 56.7 + - - +
1001A LEU* 4.7 2.9 - - - +
1002A GLY* 2.9 27.5 + - - -
1084A SER 3.6 8.5 + - - +
1085A MSE 3.4 13.0 - - - +
1086A GLU* 3.1 35.5 + - - +
1087A GLN* 5.1 3.3 + - - +
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Residues in contact with ARG 999 (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 GLU* 3.9 24.7 - - + +
995A LEU 5.8 0.2 - - - +
996A GLN* 3.1 20.2 + - + +
998A ASP* 1.4 76.3 - - - +
1000A TYR* 1.3 59.0 + - - +
1002A GLY* 4.0 0.2 - - - -
1003A LEU* 3.0 35.2 + - + +
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Residues in contact with TYR1000 (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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918A PHE* 4.6 3.8 - + - -
941A GLU 4.1 20.4 - - - +
942A LEU* 3.4 18.6 - - + +
945A GLY* 3.9 27.1 - - - -
946A LEU* 4.1 28.9 - - + -
949A LEU* 4.1 4.3 - - - +
993A HIS* 2.7 40.4 + + - -
996A GLN* 3.1 25.0 + - + +
997A PHE* 3.4 19.5 - - - -
999A ARG* 1.3 79.3 - - + +
1001A LEU* 1.3 80.1 + - + +
1003A LEU* 3.6 9.6 - - - +
1004A LEU* 3.1 27.1 + - + +
1036A LEU* 3.7 17.7 - - - +
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Residues in contact with LEU1001 (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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997A PHE* 3.1 58.6 + - + +
998A ASP* 4.4 3.4 - - - +
1000A TYR* 1.3 93.7 - - + +
1002A GLY* 1.3 63.6 + - - +
1004A LEU* 3.5 26.1 - - + +
1005A SER* 3.4 21.0 + - - -
1032A ALA* 4.6 0.4 - - + -
1033A LYS* 4.1 30.7 - - + +
1036A LEU* 3.5 33.4 - - + -
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Residues in contact with GLY1002 (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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998A ASP 2.9 19.2 + - - -
999A ARG 4.0 0.2 - - - -
1001A LEU* 1.3 72.6 - - - +
1003A LEU* 1.3 59.9 + - - +
1004A LEU 3.2 0.4 + - - -
1005A SER* 3.3 8.5 + - - -
1006A GLU* 3.0 31.9 + - - +
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Residues in contact with LEU1003 (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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938A ALA* 3.5 32.8 - - + +
941A GLU* 3.5 42.6 - - + +
942A LEU* 4.2 9.9 - - + +
999A ARG* 3.0 24.0 + - + +
1000A TYR* 3.6 9.6 - - - +
1002A GLY* 1.3 73.9 - - - +
1004A LEU* 1.3 55.3 + - - +
1006A GLU* 4.4 6.1 - - + -
1007A ASN* 3.0 38.0 + - - +
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Residues in contact with LEU1004 (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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918A PHE* 3.5 36.8 - - + -
922A VAL* 4.5 7.6 - - + -
942A LEU* 3.8 19.7 - - + +
946A LEU* 5.8 0.2 - - + -
1000A TYR* 3.1 20.0 + - + +
1001A LEU* 3.5 21.3 - - + +
1002A GLY 3.2 0.4 - - - -
1003A LEU* 1.3 72.6 - - - +
1005A SER* 1.3 66.3 + - - +
1007A ASN* 3.3 2.4 + - - -
1008A CYS* 3.0 28.0 + - - -
1014A LEU* 3.8 22.5 - - + +
1018A VAL* 3.7 28.9 - - + -
1032A ALA* 4.4 7.2 - - + -
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Residues in contact with SER1005 (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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1001A LEU 3.4 9.4 + - - -
1002A GLY* 3.3 11.1 + - - -
1004A LEU* 1.3 79.4 - - - +
1006A GLU* 1.4 63.2 + - - +
1008A CYS* 3.3 18.4 + - - +
1009A LEU* 3.5 16.5 - - - +
1018A VAL* 6.5 0.7 - - - -
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Residues in contact with GLU1006 (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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1002A GLY 3.0 19.8 + - - +
1003A LEU* 4.0 7.0 - - + +
1005A SER* 1.4 76.2 + - - +
1007A ASN* 1.3 63.9 + - - +
1008A CYS 3.2 0.2 - - - -
1009A LEU* 3.2 32.4 + - + +
1010A HIS* 3.9 11.3 - - - +
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Residues in contact with ASN1007 (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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929A MSE 6.3 1.4 - - - -
935A ASP* 4.7 7.3 + - - +
938A ALA* 3.5 32.8 - - - +
939A ARG* 5.1 4.4 - - - +
942A LEU* 4.8 6.7 - - + +
1003A LEU* 3.0 30.3 + - - +
1004A LEU 3.3 0.6 + - - -
1006A GLU* 1.3 76.1 - - - +
1008A CYS* 1.3 59.0 + - - +
1009A LEU 3.4 0.4 - - - -
1010A HIS* 3.8 24.1 + - - -
1011A SER* 2.8 34.4 + - - -
1014A LEU* 3.6 18.7 - - + +
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Residues in contact with CYS1008 (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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6A UNX 3.1 20.3 - - - -
1004A LEU 3.0 20.1 + - - -
1005A SER* 3.5 13.7 - - - +
1006A GLU 3.2 0.8 - - - -
1007A ASN* 1.3 75.6 - - - +
1009A LEU* 1.4 55.5 + - + +
1010A HIS 3.1 10.2 + - - -
1011A SER 3.5 2.9 + - - -
1014A LEU* 3.7 23.3 - - - -
1015A ALA* 3.6 19.5 - - + +
1018A VAL* 3.6 35.9 - - - -
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Residues in contact with LEU1009 (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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6A UNX 4.6 2.7 - - - -
1005A SER 3.5 16.6 - - - +
1006A GLU* 3.2 20.6 + - + +
1008A CYS* 1.4 75.4 - - + +
1010A HIS* 1.3 61.1 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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