Contacts of the helix formed by residues 1022 - 1042 (chain A) in PDB entry 5LUQ
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 ASP1022 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A PRO* 3.1 40.3 - - + +
723A ASP* 4.5 24.1 - - - +
724A GLU* 4.7 15.4 + - - +
971A ARG* 3.4 20.3 + - - -
1017A ILE* 4.9 0.6 - - - +
1020A PRO 4.2 5.8 - - - +
1021A VAL* 1.3 80.1 - - - +
1023A SER* 1.3 82.6 + - - +
1024A THR 3.4 1.1 - - - -
1025A LEU* 3.3 20.7 + - - +
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Residues in contact with SER1023 (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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595A ASP* 4.6 10.2 + - - -
598A PRO* 4.6 5.2 - - - +
723A ASP* 5.4 1.6 + - - -
971A ARG* 4.5 9.9 - - - -
1022A ASP* 1.3 95.0 + - - +
1024A THR* 1.3 66.5 + - - +
1025A LEU 2.9 2.5 + - - -
1026A ARG* 3.1 7.7 + - - +
1027A ASP* 2.8 32.1 + - - +
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Residues in contact with THR1024 (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 ARG* 5.3 0.4 - - - +
967A PRO* 4.7 4.4 - - + +
968A VAL* 3.8 25.7 - - + +
971A ARG* 2.4 47.4 + - + +
1013A ILE* 3.3 25.9 - - + +
1021A VAL* 2.8 24.6 - - + +
1023A SER* 1.3 76.4 - - - +
1025A LEU* 1.3 58.0 + - - +
1027A ASP* 3.4 7.2 - - - +
1028A PHE* 2.9 28.4 + - - +
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Residues in contact with LEU1025 (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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594A GLY 4.2 15.3 - - - +
597A ALA* 4.5 0.7 - - + -
598A PRO* 4.8 0.7 - - + -
1013A ILE* 3.8 4.2 - - - +
1014A LEU* 3.4 29.8 - - + +
1017A ILE* 3.4 46.0 - - + +
1021A VAL* 5.2 0.6 - - - +
1022A ASP 3.3 15.7 + - - +
1023A SER 2.9 0.8 - - - -
1024A THR* 1.3 77.5 - - - +
1026A ARG* 1.3 66.4 + - - +
1028A PHE* 3.0 31.5 + - + +
1029A CYS* 2.9 24.6 + - - -
1077A GLY 4.3 0.2 - - - +
1081A ALA* 4.1 20.9 - - + -
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Residues in contact with ARG1026 (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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591A GLN* 3.2 70.6 + - - +
594A GLY 4.7 4.4 + - - -
595A ASP* 2.7 47.1 + - - +
598A PRO* 5.0 0.4 - - + +
974A CYS* 5.9 4.8 - - - -
985A GLU* 5.8 1.4 + - - -
1022A ASP 4.0 0.8 + - - -
1023A SER* 3.1 11.1 + - - +
1025A LEU* 1.3 81.3 - - - +
1027A ASP* 1.3 73.7 + - - +
1028A PHE 3.1 0.3 + - - -
1029A CYS* 3.2 6.9 + - - +
1030A GLY 3.0 18.4 + - - -
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Residues in contact with ASP1027 (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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591A GLN* 4.8 2.2 - - - -
967A PRO* 3.9 5.9 - - + +
970A LEU* 3.1 32.8 - - + +
971A ARG* 2.8 38.4 + - - +
1023A SER* 2.8 20.2 + - - +
1024A THR* 3.4 7.6 - - - +
1026A ARG* 1.3 89.6 + - - +
1028A PHE* 1.3 63.8 + - - +
1030A GLY* 3.1 3.5 + - - -
1031A ARG* 3.0 34.5 + - - +
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Residues in contact with PHE1028 (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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967A PRO* 5.7 3.6 - - + -
1010A LEU* 3.0 60.1 - - + -
1011A GLU* 4.4 1.8 - - - -
1013A ILE* 3.4 14.4 - - + -
1014A LEU* 3.2 43.1 - - + -
1024A THR 2.9 14.8 + - - +
1025A LEU* 3.0 26.2 + - + +
1027A ASP* 1.3 73.5 - - - +
1029A CYS* 1.3 78.3 + - - +
1031A ARG* 2.5 33.4 + - - +
1032A CYS* 3.0 29.6 + - + -
1082A PHE* 5.8 4.3 - + - -
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Residues in contact with CYS1029 (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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591A GLN* 5.6 2.7 - - - -
594A GLY* 4.6 5.6 - - - -
1025A LEU* 2.9 24.2 + - - -
1026A ARG* 3.6 8.5 - - - +
1028A PHE* 1.3 90.3 - - - +
1030A GLY* 1.3 56.8 + - - +
1032A CYS* 4.5 3.6 - - - +
1033A ILE* 3.0 19.8 + - - +
1081A ALA* 3.7 24.2 - - - -
1082A PHE* 4.9 0.9 - - - -
1085A ILE* 3.0 59.7 - - + +
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Residues in contact with GLY1030 (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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591A GLN* 3.6 26.9 + - - +
989A MSE 3.1 21.8 - - - +
1026A ARG 3.0 11.3 + - - -
1027A ASP 3.4 5.4 - - - -
1029A CYS* 1.3 76.9 - - - +
1031A ARG* 1.3 69.3 + - - +
1033A ILE* 3.2 18.7 - - - +
1034A ARG* 3.8 0.7 - - - -
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Residues in contact with ARG1031 (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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591A GLN* 5.5 1.0 + - - +
967A PRO* 4.6 10.0 - - + +
970A LEU* 2.8 37.8 - - - +
985A GLU* 3.2 23.0 + - - +
988A VAL* 3.2 28.6 - - - +
989A MSE 3.2 42.9 - - - +
992A ILE* 3.2 24.3 - - + +
1010A LEU* 3.4 21.5 - - + -
1027A ASP* 3.1 28.5 + - - +
1028A PHE* 2.5 21.1 + - - +
1030A GLY* 1.3 75.1 - - - +
1032A CYS* 1.3 66.7 + - - +
1034A ARG* 3.0 5.0 + - - +
1035A GLU 3.0 16.1 + - - -
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Residues in contact with CYS1032 (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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1007A VAL* 6.0 2.2 - - - -
1010A LEU* 3.7 15.5 - - - +
1028A PHE* 3.0 40.6 + - + +
1029A CYS* 3.8 9.6 - - - +
1031A ARG* 1.3 73.3 - - - +
1033A ILE* 1.3 57.7 + - - +
1035A GLU* 2.4 34.9 + - - +
1036A PHE* 3.0 42.2 + - + -
1059A LEU* 6.1 0.2 - - - -
1082A PHE* 4.7 9.2 - - + -
1085A ILE* 5.1 2.5 - - + -
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Residues in contact with ILE1033 (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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587A THR 4.7 1.1 - - - +
590A GLU* 3.3 35.7 - - + +
591A GLN* 5.6 3.8 - - + +
1029A CYS 3.0 21.0 + - - +
1030A GLY* 3.2 19.7 - - - +
1032A CYS* 1.3 76.2 - - - +
1034A ARG* 1.3 83.5 + - - +
1036A PHE* 3.4 13.1 - - - -
1037A LEU* 3.5 18.0 + - - +
1085A ILE* 3.1 24.4 - - + +
1089A PHE* 3.1 36.4 - - + -
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Residues in contact with ARG1034 (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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587A THR* 4.7 24.8 + - - +
591A GLN* 4.9 11.4 - - - +
989A MSE 3.7 40.5 - - + +
992A ILE* 3.9 6.9 - - + +
993A HIS* 5.2 1.8 - - + +
1030A GLY 3.8 3.4 - - - -
1031A ARG 3.0 8.9 + - - +
1032A CYS 2.7 1.2 + - - -
1033A ILE* 1.3 105.5 - - - +
1035A GLU* 1.3 58.0 + - - +
1036A PHE 3.5 0.2 - - - -
1037A LEU* 3.4 23.6 - - + +
1038A LYS* 2.9 24.8 + - - +
1089A PHE* 6.1 1.9 - - - -
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Residues in contact with GLU1035 (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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992A ILE* 3.3 23.7 - - + +
995A PHE* 3.8 11.5 - - - -
996A THR* 3.8 19.1 - - + +
1006A THR* 4.1 15.1 - - - +
1007A VAL* 2.7 38.5 + - - +
1010A LEU* 4.7 6.2 - - - +
1031A ARG 3.0 4.7 + - - +
1032A CYS* 2.4 29.7 + - - +
1034A ARG* 1.3 66.3 - - - +
1036A PHE* 1.3 65.3 + - + +
1037A LEU 3.2 0.7 - - - -
1038A LYS* 3.1 4.4 + - - +
1039A TRP* 2.9 25.5 + - - +
1054A VAL* 4.6 8.0 - - - +
1055A ASN* 4.2 7.4 + - - +
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Residues in contact with PHE1036 (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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1007A VAL* 6.5 0.7 - - + -
1032A CYS* 3.0 54.7 + - + -
1033A ILE* 3.4 9.9 - - + -
1035A GLU* 1.3 81.4 - - + +
1037A LEU* 1.3 57.1 + - - +
1039A TRP* 3.5 1.6 + - - +
1040A SER* 2.9 31.0 + - - -
1055A ASN* 3.8 14.3 + - - +
1059A LEU* 3.2 39.0 - - + -
1082A PHE* 3.0 28.7 - + - -
1085A ILE* 5.4 1.6 - - + -
1086A TYR* 3.1 50.1 + + + +
1089A PHE* 5.9 0.4 - - - -
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Residues in contact with LEU1037 (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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1033A ILE 3.5 16.8 + - - +
1034A ARG* 3.4 28.0 + - + +
1035A GLU 3.2 0.4 - - - -
1036A PHE* 1.3 79.5 - - - +
1038A LYS* 1.3 56.8 + - + +
1040A SER* 3.8 7.6 - - - +
1041A ILE* 2.9 51.9 + - + +
1089A PHE* 4.2 26.6 - - + -
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Residues in contact with LYS1038 (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* 3.2 55.5 + - + +
996A THR* 2.9 27.6 + - + +
997A ASN* 4.3 18.3 - - + +
1034A ARG 2.9 15.4 + - - +
1035A GLU* 3.1 5.3 + - - +
1037A LEU* 1.3 76.4 - - + +
1039A TRP* 1.3 60.4 + - - +
1041A ILE* 3.8 29.6 - - + +
1042A LYS* 2.9 29.1 + - - +
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Residues in contact with TRP1039 (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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996A THR* 4.0 10.2 + - - -
1035A GLU 2.9 7.0 + - - +
1036A PHE 3.8 3.6 - - - +
1037A LEU 3.4 0.2 - - - -
1038A LYS* 1.3 74.6 - - - +
1040A SER* 1.3 65.8 + - - +
1042A LYS* 2.7 53.0 + - + +
1043A GLN 6.0 0.2 - - - -
1048A GLN* 3.5 29.4 - - + -
1049A GLN* 3.3 36.9 - - + +
1052A SER* 3.9 17.5 - - - -
1054A VAL* 3.6 24.7 - - + -
1055A ASN* 3.2 47.3 - - + +
1056A THR* 3.1 28.9 - - + +
1093A GLU* 5.3 4.5 - - - -
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Residues in contact with SER1040 (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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1036A PHE 2.9 21.3 + - - -
1037A LEU* 4.1 9.4 - - - +
1039A TRP* 1.3 80.2 - - - +
1041A ILE* 1.3 60.2 + - - +
1042A LYS 4.7 0.4 - - - -
1043A GLN* 4.6 6.1 + - - +
1086A TYR* 5.6 1.3 - - - -
1089A PHE* 6.3 2.2 - - - -
1093A GLU* 3.6 31.2 + - - +
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Residues in contact with ILE1041 (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 ASN* 4.5 5.3 - - - +
1037A LEU* 2.9 53.9 + - + +
1038A LYS* 4.0 36.1 - - + +
1040A SER* 1.3 75.7 - - - +
1042A LYS* 1.3 53.3 + - - +
1043A GLN* 2.7 31.4 + - - +
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Residues in contact with LYS1042 (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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996A THR 3.1 18.8 - - - +
997A ASN* 3.2 52.4 + - - +
998A ASN* 3.9 9.2 + - - +
1038A LYS 2.9 20.1 + - - +
1039A TRP* 2.7 41.6 + - + +
1041A ILE* 1.3 65.7 - - - +
1043A GLN* 1.3 65.9 + - - +
1044A ILE* 3.1 50.6 - - + +
1048A GLN* 5.2 4.4 - - + +
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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