Contacts of the helix formed by residues 98 - 126 (chain D) in PDB entry 1ORZ
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 TRP 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D GLU 3.0 20.4 - - - +
93D ARG* 2.9 25.8 - - + -
94D VAL* 2.9 38.1 - - + +
96D GLY 3.2 13.5 - - - -
97D VAL* 1.3 76.0 - - + +
99D HIS* 1.3 87.2 + + + +
100D LYS 3.1 2.5 - - - -
101D TYR* 3.1 14.2 + - - +
102D ALA* 3.7 4.1 + - - +
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Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D VAL* 3.0 16.4 - - + +
98D TRP* 1.3 97.1 - + + +
100D LYS* 1.3 57.7 + - - +
102D ALA* 3.8 6.7 - - - +
103D MET* 2.7 54.8 + - + +
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Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ILE* 4.1 14.5 - - + +
92D GLU* 3.2 50.7 + - + +
97D VAL* 3.5 13.1 - - + +
98D TRP 3.1 1.0 + - - -
99D HIS* 1.3 80.4 - - - +
101D TYR* 1.3 61.5 + - - +
103D MET* 4.9 1.3 - - - -
104D TYR* 2.8 51.7 + - + +
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 3.0 27.4 + - - +
83D ASN* 3.3 11.3 + - - -
86D ILE* 3.0 40.5 - - + +
87D THR* 3.0 31.9 + - + +
90D ILE* 3.2 34.7 - - + +
92D GLU 3.5 8.3 - - - +
98D TRP 3.1 12.8 + - - +
100D LYS* 1.3 77.8 - - - +
102D ALA* 1.3 71.9 + - + +
104D TYR* 3.4 2.5 + - - +
105D MET* 3.1 34.9 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TRP 3.7 3.4 + - - +
99D HIS* 3.2 11.0 + - - +
101D TYR* 1.3 87.3 - - + +
103D MET* 1.3 67.2 + - + +
105D MET* 3.2 6.7 + - - +
106D LEU* 2.9 24.1 + - - +
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Residues in contact with MET 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 2.7 40.1 + - + +
100D LYS* 4.2 2.9 - - - +
102D ALA* 1.3 75.6 - - + +
104D TYR* 1.3 62.6 + - + +
106D LEU* 3.1 32.6 + - + +
107D GLY* 2.7 26.5 + - - -
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Residues in contact with TYR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TYR* 4.3 0.2 - - - -
86D ILE* 5.0 10.8 - - + -
90D ILE* 5.9 7.0 - - + -
100D LYS* 2.8 52.0 + - + +
101D TYR* 4.1 3.4 - - - +
103D MET* 1.3 79.5 - - + +
105D MET* 1.3 60.8 + - - +
107D GLY* 3.0 1.8 + - - +
108D LEU* 2.7 32.7 + - - +
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Residues in contact with MET 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP* 3.3 38.1 - - + +
79D TYR* 2.8 31.7 + - + +
83D ASN* 2.9 32.8 - - + +
86D ILE* 3.5 19.9 - - + +
101D TYR* 3.1 43.2 + - + +
102D ALA* 3.2 8.8 + - - +
104D TYR* 1.3 76.5 - - - +
106D LEU* 1.3 64.0 + - - +
109D GLY* 2.9 15.4 + - - -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA 2.9 13.5 + - - +
103D MET* 3.2 35.0 - - + +
105D MET* 1.3 78.0 - - - +
107D GLY* 1.3 65.9 + - - +
109D GLY* 3.9 0.7 - - - -
110D SER* 3.1 25.4 + - - -
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Residues in contact with GLY 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D MET* 2.7 18.5 + - - -
104D TYR* 3.0 3.1 + - - -
106D LEU* 1.3 78.8 - - - +
108D LEU* 1.3 60.9 + - - +
110D SER* 3.1 6.8 + - - -
111D ALA* 2.9 22.1 + - - +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLY 5.9 5.8 - - - +
79D TYR* 2.9 39.0 - - + +
82D PHE* 3.1 48.2 - - + -
86D ILE* 5.4 2.0 - - + -
104D TYR 2.7 15.7 + - - +
107D GLY* 1.3 72.9 - - - +
109D GLY* 1.3 61.7 + - - +
111D ALA* 3.1 13.8 + - + +
112D VAL* 2.9 33.2 + - + +
115D PHE* 6.0 1.8 - - + -
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 4.6 8.7 - - - -
79D TYR* 3.5 13.4 - - - -
105D MET 2.9 16.3 + - - -
106D LEU 3.9 1.1 - - - -
108D LEU* 1.3 76.2 - - - +
110D SER* 1.3 62.6 + - - +
112D VAL* 3.2 5.4 + - - +
113D SER* 2.9 22.9 + - - -
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Residues in contact with SER 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 3.1 19.7 + - - -
107D GLY* 3.4 10.5 - - - -
109D GLY* 1.3 76.4 - - - +
111D ALA* 1.3 63.8 + - - +
113D SER* 2.6 26.5 + - - -
114D LEU* 2.8 10.0 + - - +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLY 2.9 12.6 + - - +
108D LEU* 3.1 20.2 + - + +
110D SER* 1.3 75.8 - - - +
112D VAL* 1.3 62.6 + - - +
114D LEU* 3.1 12.1 + - - +
115D PHE* 2.8 44.7 + - + -
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 5.5 1.8 - - - +
72D VAL 5.3 2.3 - - - +
75D LEU* 4.6 9.9 - - + +
76D GLY* 3.0 39.5 - - - +
79D TYR* 3.8 22.7 - - + -
82D PHE* 5.8 3.6 - - + -
108D LEU* 2.9 26.4 + - + +
109D GLY* 3.4 8.3 - - - +
111D ALA* 1.3 76.4 - - - +
113D SER* 1.3 65.8 + - - +
115D PHE* 3.1 23.7 + - + +
116D GLY* 3.3 8.1 + - - -
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLY 2.9 13.6 + - - -
110D SER* 2.6 26.5 + - - -
112D VAL* 1.3 77.0 - - - +
114D LEU* 1.3 62.3 + - - +
116D GLY* 3.1 10.6 + - - -
117D ILE* 3.2 27.3 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR* 5.4 13.5 - - + -
110D SER* 2.8 12.8 + - - +
111D ALA* 3.3 14.6 - - - +
113D SER* 1.3 76.0 + - - +
115D PHE* 1.3 63.3 + - + +
117D ILE* 3.2 12.5 + - + +
118D TYR* 2.7 46.1 + - + +
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLY 4.9 8.7 - - - -
57C PHE* 3.9 21.0 - + + -
58C TYR* 2.9 65.1 - + + -
61C THR* 3.9 22.7 - - + +
62C ILE* 5.4 0.2 - - + -
72D VAL* 5.0 5.1 - - + +
75D LEU* 5.2 9.0 - - + -
108D LEU* 6.0 2.2 - - + -
111D ALA* 2.8 47.3 + - + -
112D VAL* 3.1 15.9 + - + +
114D LEU* 1.3 81.4 - - + +
116D GLY* 1.3 56.4 + - - +
118D TYR* 3.4 4.9 + - + +
119D LYS* 2.8 31.6 + - - +
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Residues in contact with GLY 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL* 4.1 23.9 + - - +
73D MET* 6.1 0.9 - - - -
112D VAL 3.3 5.6 + - - -
113D SER* 3.1 7.0 + - - -
115D PHE* 1.3 79.8 - - - +
117D ILE* 1.3 60.4 + - - +
119D LYS* 3.1 7.6 + - - +
120D LEU* 2.8 28.0 - - - +
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D SER* 3.2 25.8 + - - +
114D LEU* 3.9 12.8 - - + +
116D GLY* 1.3 71.3 - - - +
118D TYR* 1.3 68.6 + - - +
120D LEU* 3.0 19.7 + - + +
121D GLU* 3.1 12.9 + - + +
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR* 3.6 25.6 - - + -
62C ILE* 5.8 4.9 - - + -
65C GLY* 3.7 30.4 + - - -
114D LEU* 2.7 36.8 + - + +
115D PHE* 3.9 4.9 - - + +
117D ILE* 1.3 73.7 - - - +
119D LYS* 1.3 63.8 + - - +
121D GLU* 3.1 30.3 + - + +
122D THR* 2.9 39.7 + - + +
125D ASP* 5.5 0.9 + - - -
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 5.5 2.7 - - + -
61C THR* 5.3 4.9 - - + -
68D SER* 4.5 8.3 - - - +
69D PHE* 2.9 48.7 + - + +
72D VAL* 2.9 48.0 - - + +
115D PHE 2.8 19.5 + - - +
116D GLY 3.2 1.8 - - - +
117D ILE 3.0 0.2 - - - -
118D TYR* 1.3 77.4 - - - +
120D LEU* 1.3 99.2 + - - +
122D THR* 2.7 28.6 - - + +
123D GLU* 2.9 6.0 + - + +
127D VAL* 5.6 2.0 - - + -
128D VAL* 5.4 0.4 - - + -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D PHE* 3.8 10.5 - - + -
116D GLY* 2.8 29.8 - - - +
117D ILE* 3.0 10.4 + - + +
119D LYS* 1.3 111.8 - - - +
121D GLU* 1.3 64.1 + - - +
123D GLU* 2.9 36.7 + - - +
124D ASN* 3.1 8.5 + - - +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ILE* 3.1 11.7 + - + +
118D TYR* 3.1 39.2 + - + +
120D LEU* 1.3 75.4 - - - +
122D THR* 1.3 60.2 + - - +
124D ASN* 2.5 34.4 + - - +
125D ASP* 3.3 18.8 + - - +
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR* 5.4 1.8 - - + -
64C PHE* 2.8 41.8 + - + -
65C GLY* 4.1 7.1 + - - -
68C GLY* 5.5 0.3 - - - -
118D TYR* 2.9 35.0 + - + +
119D LYS* 2.7 33.9 - - + +
121D GLU* 1.3 79.0 - - - +
123D GLU* 1.3 60.6 + - - +
125D ASP* 2.6 41.0 + - - +
126D GLY 3.3 1.0 + - - -
127D VAL* 3.4 5.0 + - + -
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PHE* 2.9 30.9 - - + -
119D LYS 2.9 13.6 + - - +
120D LEU* 2.9 26.5 + - - +
122D THR* 1.3 76.6 - - - +
124D ASN* 1.3 69.4 + - - +
126D GLY 3.2 1.6 + - - -
127D VAL* 2.7 29.2 + - + -
128D VAL* 2.6 44.5 + - + +
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU 3.1 4.2 + - - +
121D GLU* 2.5 37.8 + - - +
123D GLU* 1.3 85.4 - - + +
125D ASP* 1.3 87.2 + - - +
126D GLY* 3.2 0.9 + - - -
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Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY 5.5 2.4 - - - +
68C GLY* 4.4 11.5 - - - -
70C LEU* 4.2 24.6 + - - +
71C GLY* 5.1 6.0 - - - -
118D TYR* 5.5 0.7 + - - -
121D GLU* 3.3 10.7 - - - +
122D THR* 2.6 42.5 + - - +
124D ASN* 1.3 94.3 - - - +
126D GLY* 1.3 74.5 + - - +
127D VAL 3.8 1.6 + - - -
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Residues in contact with GLY 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 2.6 39.8 - - - +
70C LEU 4.9 0.2 - - - -
123D GLU 3.7 2.0 - - - -
124D ASN 3.2 3.1 - - - -
125D ASP* 1.3 89.8 + - - +
127D VAL* 1.4 51.7 + - - +
128D VAL 3.5 3.2 + - - +
130D LEU* 4.4 1.6 - - - +
131D VAL* 2.6 25.3 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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