Contacts of the helix formed by residues 112 - 145 (chain A) in PDB entry 5LLU
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 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 1.4 73.1 - - - +
113A ALA* 1.4 55.7 + - - +
114A LYS 3.6 0.9 - - - +
115A ALA* 3.6 23.5 - - + +
116A SER* 2.7 38.7 + - - -
118A ARG* 4.8 4.5 + - - +
481A GLU* 4.8 5.4 - - - +
484A LYS* 5.0 11.0 - - - +
485A GLN* 2.8 35.1 + - - +
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Residues in contact with ALA 113 (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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111A LEU 4.0 0.6 + - - -
112A ASP* 1.4 74.3 - - - +
114A LYS* 1.3 61.8 + - + +
116A SER* 3.5 13.6 - - - -
117A GLY* 3.6 4.0 + - - -
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Residues in contact with LYS 114 (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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112A ASP* 3.6 1.0 - - - +
113A ALA* 1.3 74.4 - - - +
115A ALA* 1.4 54.2 + - - +
116A SER 3.2 0.9 - - - -
117A GLY* 3.0 9.7 + - - +
118A ARG* 2.8 57.6 + - + +
121A MET* 5.7 7.4 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.7 4.3 - - + -
112A ASP* 3.2 35.4 + - + +
114A LYS* 1.4 76.6 - - - +
116A SER* 1.4 56.7 + - - +
118A ARG* 3.3 29.5 + - - +
119A LEU* 2.9 40.0 + - + +
481A GLU* 4.2 13.7 - - + -
485A GLN* 6.4 0.2 - - + -
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Residues in contact with SER 116 (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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108A LEU* 3.4 33.9 + - - +
111A LEU* 3.3 28.8 + - - +
112A ASP 2.7 26.0 + - - -
113A ALA* 3.5 7.7 - - - -
115A ALA* 1.4 72.6 - - - +
117A GLY* 1.3 57.0 + - - +
119A LEU* 3.7 2.3 + - - +
120A GLY* 3.2 22.7 + - - -
235A ILE* 5.7 5.2 - - - -
369A PHE* 5.6 2.8 - - - -
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Residues in contact with GLY 117 (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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113A ALA 3.6 3.9 + - - -
114A LYS* 3.0 18.8 + - - -
116A SER* 1.3 78.4 - - - +
118A ARG* 1.4 52.3 + - - +
120A GLY* 3.5 1.5 + - - -
121A MET* 2.8 37.5 + - - +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 4.8 4.9 + - - +
114A LYS* 2.8 32.4 + - + +
115A ALA* 3.5 35.9 - - - +
117A GLY* 1.4 74.1 - - - +
119A LEU* 1.4 59.5 + - - +
121A MET* 3.2 6.7 + - - +
122A ARG* 2.9 45.0 + - - +
480A LYS* 5.8 4.8 - - - +
481A GLU* 3.6 41.4 + - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.8 26.2 - - + -
115A ALA* 2.9 27.2 + - + +
116A SER 3.9 4.7 - - - +
118A ARG* 1.4 74.8 - - - +
120A GLY* 1.3 56.8 + - - +
122A ARG* 3.6 4.2 + - - +
123A ALA* 3.2 26.7 + - - +
365A ARG 5.6 0.2 - - - +
366A ILE* 3.7 31.9 - - + -
369A PHE* 4.3 12.6 - - + -
370A VAL* 5.8 1.3 - - + -
474A VAL* 3.8 20.9 - - + +
478A SER* 3.3 34.1 - - - +
481A GLU* 4.2 18.2 - - + -
482A LEU* 6.0 2.7 - - + -
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Residues in contact with GLY 120 (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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116A SER 3.2 13.1 + - - -
117A GLY* 3.8 3.6 - - - -
118A ARG 3.2 0.2 - - - -
119A LEU* 1.3 77.3 - - - +
121A MET* 1.4 53.2 + - - +
123A ALA* 3.2 3.3 + - - +
124A VAL* 2.8 42.9 + - - +
369A PHE* 3.7 24.2 - - - -
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Residues in contact with MET 121 (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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114A LYS* 5.7 7.4 - - - +
117A GLY 2.8 25.5 + - - +
118A ARG* 3.5 9.4 - - - +
120A GLY* 1.4 71.5 - - - +
122A ARG* 1.4 57.7 + - + +
124A VAL* 3.4 9.4 + - - +
125A VAL* 2.9 50.1 + - + +
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Residues in contact with ARG 122 (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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118A ARG* 2.9 28.9 + - - +
119A LEU 3.7 5.8 - - - +
121A MET* 1.4 73.4 - - + +
123A ALA* 1.3 58.3 + - - +
125A VAL* 3.9 5.4 - - - +
126A TYR* 3.0 29.8 + - - +
474A VAL* 3.9 16.8 - - + +
477A LEU* 3.4 59.6 + - + +
478A SER* 2.8 26.8 + - - +
479A ARG* 6.0 0.2 - - - +
481A GLU* 2.9 25.4 + - - -
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Residues in contact with ALA 123 (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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119A LEU 3.2 12.2 + - - +
120A GLY 3.4 7.9 - - - +
122A ARG* 1.3 75.8 - - - +
124A VAL* 1.4 55.0 + - + +
126A TYR* 3.2 3.8 + - - +
127A TYR* 2.8 61.0 + - + +
369A PHE* 3.7 23.1 - - + -
370A VAL* 4.5 9.2 - - + -
474A VAL* 4.2 9.6 - - + +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY* 2.8 26.4 + - - +
121A MET* 4.0 9.9 - - - +
123A ALA* 1.4 69.8 - - + +
125A VAL* 1.4 58.3 - - + +
127A TYR* 3.3 14.3 + - + +
128A MET* 3.0 41.5 + - + +
369A PHE* 5.7 4.9 - - + -
373A VAL* 6.1 1.6 - - + -
377A ILE* 5.3 7.2 - - + -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 2.9 40.6 + - + +
122A ARG* 3.9 6.3 - - - +
124A VAL* 1.4 72.3 - - + +
126A TYR* 1.3 54.5 + - - +
128A MET* 4.2 2.7 - - - +
129A SER* 2.8 36.3 + - - +
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Residues in contact with TYR 126 (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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122A ARG 3.0 19.3 + - - +
123A ALA* 3.2 4.2 + - - +
125A VAL* 1.3 78.5 - - - +
127A TYR* 1.3 69.0 + + - +
129A SER* 3.0 17.1 + - - -
130A THR* 2.7 45.1 + - + +
313A LEU* 4.0 11.9 - - + +
316A ILE* 4.6 7.6 - - + -
320A ILE* 5.7 1.1 - - + -
378A ASN* 4.0 10.8 - - - -
466A GLY* 2.7 35.9 + - - -
469A LEU* 3.9 5.2 - - - +
470A GLY* 3.4 22.5 + - - -
473A ILE* 3.7 39.1 - - + +
474A VAL* 4.7 7.2 - - + -
477A LEU* 6.5 0.2 - - + -
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Residues in contact with TYR 127 (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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123A ALA* 2.8 43.1 + - + +
124A VAL* 3.6 10.3 - - + +
126A TYR* 1.3 87.2 - + - +
128A MET* 1.4 55.1 + - + +
130A THR* 2.9 17.7 + - - -
131A THR* 2.7 25.1 + - - -
369A PHE* 5.3 0.2 - + - -
370A VAL* 2.6 47.7 + - + +
373A VAL* 3.6 23.8 - - + +
374A GLY* 3.3 9.7 + - - -
377A ILE* 3.6 26.0 - - + -
378A ASN* 3.4 39.2 + - + +
467A ASP* 5.1 2.7 - - - -
474A VAL* 6.4 0.2 - - + -
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Residues in contact with MET 128 (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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124A VAL* 3.0 28.0 + - + +
125A VAL* 4.5 2.7 - - - +
127A TYR* 1.4 75.2 - - + +
129A SER* 1.3 59.8 + - - +
131A THR* 3.5 10.1 + - - -
132A ILE* 3.2 43.4 + - + +
414A THR* 4.3 16.2 - - + -
418A ILE* 3.7 29.6 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 2.8 26.9 + - - +
126A TYR* 3.0 16.5 + - - -
128A MET* 1.3 76.0 - - - +
130A THR* 1.4 53.1 + - - +
132A ILE* 3.1 11.2 + - - +
133A ILE* 2.9 42.8 + - - +
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Residues in contact with THR 130 (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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126A TYR* 2.7 49.5 + - + +
127A TYR* 2.9 11.8 + - - -
129A SER* 1.4 82.6 + - - +
131A THR* 1.4 53.6 + - - -
133A ILE* 3.4 6.9 + - + +
134A ALA* 3.1 28.1 + - - +
308A HIS* 3.8 5.2 - - - -
313A LEU* 4.0 17.9 - - + -
316A ILE* 4.6 12.8 - - + -
378A ASN* 3.2 8.7 + - - -
380A ASP* 3.1 24.1 + - - +
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Residues in contact with THR 131 (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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127A TYR* 2.7 24.7 + - + +
128A MET* 3.5 16.1 + - - -
130A THR* 1.4 74.5 - - - +
132A ILE* 1.4 55.9 + - - +
134A ALA* 4.3 2.5 - - - -
135A VAL* 3.5 15.4 + - - +
377A ILE 4.7 2.2 - - - +
378A ASN* 3.8 10.1 - - - +
379A MET 3.8 13.0 - - - +
380A ASP* 3.4 14.6 - - - +
383A ALA* 3.9 10.4 - - + +
414A THR* 3.4 31.8 + - - +
417A SER* 3.5 24.7 - - - +
418A ILE* 5.6 2.7 - - + +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.2 38.0 + - + +
129A SER* 3.1 11.5 + - - +
131A THR* 1.4 77.7 - - - +
133A ILE* 1.4 69.6 - - + +
134A ALA 3.4 0.2 - - - -
135A VAL* 3.2 9.1 - - + +
136A VAL* 3.1 34.9 + - + +
410A SER 5.6 0.7 - - - +
414A THR* 4.4 12.8 - - + +
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Residues in contact with ILE 133 (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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129A SER* 2.9 27.3 + - - +
130A THR* 3.4 8.9 + - - +
132A ILE* 1.4 84.7 - - + +
134A ALA* 1.3 50.6 + - - +
136A VAL* 3.3 7.4 + - + +
137A LEU* 2.8 39.6 + - + +
308A HIS* 4.3 3.1 - - + +
312A VAL* 3.6 34.1 - - + -
316A ILE* 5.4 7.0 - - + -
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Residues in contact with ALA 134 (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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130A THR 3.1 17.1 + - - +
131A THR 4.5 3.8 - - - +
133A ILE* 1.3 77.2 - - - +
135A VAL* 1.4 57.0 + - - +
137A LEU* 4.4 1.1 - - - -
138A GLY* 2.9 24.6 + - - -
308A HIS* 3.6 23.5 - - + +
380A ASP* 3.4 29.6 - - + +
383A ALA* 4.6 0.7 - - + -
384A LEU* 3.4 22.5 - - + +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR 3.5 12.1 + - - +
132A ILE* 3.2 22.0 + - + +
134A ALA* 1.4 75.0 - - - +
136A VAL* 1.4 62.6 + - + +
138A GLY* 4.0 0.3 - - - -
139A ILE* 3.1 35.8 + - + +
383A ALA* 3.9 12.7 + - + +
387A ALA* 3.8 13.8 - - + +
410A SER* 3.9 27.8 - - - +
413A ALA* 3.7 30.5 - - + -
414A THR* 3.3 20.9 - - - +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.1 28.9 + - + +
133A ILE* 3.8 7.4 - - + +
135A VAL* 1.4 78.6 - - + +
137A LEU* 1.4 64.6 + - - +
139A ILE* 3.4 6.7 + - + +
140A ILE* 3.2 42.3 + - + +
410A SER* 5.6 5.8 - - - -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 2.8 21.7 + - + +
134A ALA 3.9 3.8 - - - +
136A VAL* 1.4 75.4 - - - +
138A GLY* 1.3 61.3 + - - +
140A ILE* 3.7 8.1 + - + +
141A LEU* 3.3 37.7 + - + +
304A GLY 3.9 8.1 - - - +
307A ILE* 3.8 32.3 - - + -
308A HIS* 3.8 30.7 - - + +
312A VAL* 4.1 15.0 - - + -
384A LEU* 4.2 3.8 - - + -
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Residues in contact with GLY 138 (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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134A ALA 2.9 18.4 + - - -
135A VAL 3.6 1.8 + - - -
136A VAL 3.3 0.2 - - - -
137A LEU* 1.3 75.0 - - - +
139A ILE* 1.4 61.6 + - - +
141A LEU* 3.6 5.5 + - - +
142A VAL* 3.3 19.5 + - - +
384A LEU* 4.1 19.5 - - - +
387A ALA* 4.6 2.7 - - - -
388A VAL* 3.4 23.2 - - - +
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Residues in contact with ILE 139 (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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135A VAL* 3.1 26.9 + - + +
136A VAL* 3.4 6.5 + - + +
138A GLY* 1.4 71.9 - - - +
140A ILE* 1.3 68.6 + - + +
142A VAL* 3.2 8.8 - - - +
143A LEU* 3.1 44.6 + - + +
387A ALA* 3.8 9.2 - - + -
391A ILE* 3.7 19.1 - - + -
406A ILE* 3.7 30.5 - - + +
409A ILE* 4.5 2.0 - - + -
410A SER* 3.8 34.1 - - - +
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Residues in contact with ILE 140 (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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136A VAL* 3.2 37.2 + - + +
137A LEU* 4.1 8.3 - - + +
138A GLY 3.5 0.4 - - - -
139A ILE* 1.3 78.5 - - + +
141A LEU* 1.4 61.9 + - + +
143A LEU* 3.3 13.4 + - + +
144A ILE* 3.1 43.9 + - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.3 33.8 + - + +
138A GLY* 3.8 7.2 - - - +
140A ILE* 1.4 78.4 - - + +
142A VAL* 1.4 49.7 + - - +
144A ILE* 3.3 12.2 + - + +
145A ILE* 2.9 47.8 + - + +
300A THR* 4.0 14.1 - - + +
303A VAL* 5.1 6.5 - - + -
304A GLY* 3.7 30.3 - - - +
307A ILE* 3.8 24.9 - - + -
384A LEU* 5.7 0.2 - - + -
388A VAL* 5.5 1.3 - - + -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY 3.3 12.2 + - - +
139A ILE* 3.2 16.6 - - - +
141A LEU* 1.4 75.0 - - - +
143A LEU* 1.4 62.4 + - - +
145A ILE 3.4 7.4 - - - +
300A THR* 4.0 9.1 - - + +
388A VAL* 3.7 41.5 - - + +
391A ILE* 3.7 41.8 - - + +
392A PHE* 4.2 8.1 - - + +
395A GLN* 3.0 36.8 + - - +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.1 39.7 + - + +
140A ILE* 3.5 12.8 - - + +
141A LEU 3.3 0.2 - - - -
142A VAL* 1.4 77.2 - - + +
144A ILE* 1.3 62.6 + - + +
145A ILE 4.2 2.6 - - - +
391A ILE* 4.9 15.5 - - + -
395A GLN* 5.5 0.2 + - - -
406A ILE* 5.6 12.6 - - + -
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 3.1 35.9 + - + +
141A LEU* 3.6 14.1 - - + +
143A LEU* 1.3 78.8 - - + +
145A ILE* 1.3 77.8 + - + +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 2.9 31.4 + - + +
142A VAL* 3.4 13.1 - - - +
143A LEU 4.2 2.8 - - - +
144A ILE* 1.3 93.5 - - + +
296A MET* 4.0 37.7 - - + +
299A VAL* 5.9 4.0 - - + -
300A THR* 3.4 31.0 - - + +
395A GLN* 3.1 22.6 + - - -
----------------------------------------------------------
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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