Contacts of the helix formed by residues 109 - 136 (chain A) in PDB entry 1JT6
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 THR 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 3.2 27.4 + - - +
107A TYR 4.6 0.2 - - - -
108A LYS* 1.3 80.0 - - - +
110A ASN* 1.3 62.4 + - - +
111A SER* 3.5 24.7 - - - +
112A ILE* 3.9 15.0 - - + -
113A ASN* 2.9 31.1 + - - +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS 4.4 7.9 + - - -
109A THR* 1.3 75.1 - - - +
111A SER* 1.3 67.0 + - - +
113A ASN* 4.4 6.6 - - - +
114A GLU* 3.0 27.4 + - - +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 5.5 1.4 + - - -
109A THR* 3.5 9.5 - - - +
110A ASN* 1.3 82.2 - - - +
112A ILE* 1.3 79.1 + - - +
114A GLU* 3.6 3.1 - - - +
115A LYS* 3.4 37.3 + - - +
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 4.3 25.6 - - + +
48A ASN* 5.8 3.1 - - - +
51A LEU* 4.3 17.0 - - + -
102A PHE* 3.8 16.2 - - + -
106A TYR* 3.8 46.0 - - + +
109A THR* 3.7 15.3 + - + +
110A ASN 3.3 0.2 - - - -
111A SER* 1.3 90.2 - - - +
113A ASN* 1.3 65.2 + - - +
114A GLU 3.0 2.3 + - - -
115A LYS* 3.1 5.4 + - + +
116A MET* 2.9 38.8 + - + +
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Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.8 31.4 + - - -
106A TYR 4.2 0.6 + - - -
107A TYR* 3.5 24.4 - - - +
109A THR 2.9 24.8 + - - +
110A ASN* 4.5 6.3 - - - +
112A ILE* 1.3 73.8 - - - +
114A GLU* 1.3 59.8 + - - +
116A MET* 3.8 10.0 - - - +
117A ASN* 3.0 38.3 + - - +
201A DEQ 5.6 2.2 - - - +
164B HIS 4.7 1.7 - - - +
165B GLU* 3.6 26.4 - - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN 3.0 22.1 + - - +
111A SER* 3.6 4.3 - - - +
112A ILE 3.0 0.2 + - - -
113A ASN* 1.3 77.6 - - - +
115A LYS* 1.3 77.7 + - - +
117A ASN* 3.0 18.2 + - + +
118A LYS* 3.3 37.0 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 4.3 24.2 - - - +
51A LEU* 3.5 33.7 - - + -
111A SER* 3.5 26.7 - - - +
112A ILE* 3.1 6.8 + - - +
114A GLU* 1.3 91.7 - - - +
116A MET* 1.3 62.5 + - - +
118A LYS* 3.2 17.5 + - - +
119A LEU* 3.3 15.4 + - - +
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Residues in contact with MET 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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51A LEU* 4.0 9.6 - - + -
54A LEU* 4.7 7.2 - - + -
99A ILE* 5.9 0.9 - - + -
102A PHE* 4.0 21.1 - - + -
103A TYR* 3.5 36.3 - - + -
106A TYR* 5.6 2.2 - - - +
107A TYR* 5.7 0.4 - - - -
112A ILE* 2.9 35.4 + - + +
113A ASN* 3.9 14.4 - - - +
114A GLU 3.2 0.2 - - - -
115A LYS* 1.3 77.0 - - - +
117A ASN* 1.3 57.7 + - - +
119A LEU* 3.1 11.4 + - - +
120A GLU* 2.9 28.2 + - - +
201A DEQ 3.4 41.6 - - + +
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Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.0 24.1 + - - +
114A GLU* 3.0 12.8 + - - +
116A MET* 1.3 77.9 - - - +
118A LYS* 1.3 60.3 + - - +
120A GLU* 3.7 10.6 - - - +
121A ASN* 2.7 53.8 + - - +
201A DEQ 5.7 6.9 - - - +
165B GLU* 3.5 44.1 + - - +
166B GLN* 4.4 5.1 + - - -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.3 42.7 + - - +
115A LYS* 3.2 12.2 + - - +
116A MET 3.2 0.6 - - - -
117A ASN* 1.3 82.3 - - - +
119A LEU* 1.3 66.1 + - + +
121A ASN* 3.3 17.0 + - - +
122A LYS* 3.0 31.4 + - - +
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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
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51A LEU* 4.3 15.7 - - + +
54A LEU* 3.6 28.5 - - + +
55A ASN* 3.3 38.4 - - - +
58A GLU* 4.0 24.3 - - + +
115A LYS 3.3 12.2 + - - +
116A MET* 3.1 11.1 + - - +
118A LYS* 1.3 82.2 - - + +
120A GLU* 1.3 62.4 + - - +
122A LYS* 2.9 24.9 + - + +
123A TYR 3.2 8.7 + - - -
201A DEQ 4.2 28.5 - - + -
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Residues in contact with GLU 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 MET 2.9 15.4 + - - +
117A ASN* 3.7 13.7 - - - +
119A LEU* 1.3 75.3 - - - +
121A ASN* 1.3 64.9 + - - +
123A TYR* 2.9 25.5 + - - +
124A ILE* 2.9 38.9 + - + +
153A ALA* 5.0 0.5 - - - +
154A ASN* 4.2 8.8 - - - +
157A ASN* 3.4 25.2 + - - -
201A DEQ 3.9 45.0 - - + +
162B PHE* 5.3 2.9 - - - +
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 2.7 41.5 + - - +
118A LYS* 3.5 19.2 + - - +
119A LEU 3.2 0.2 - - - -
120A GLU* 1.3 74.6 - - - +
122A LYS* 1.3 61.5 + - - +
124A ILE* 3.2 20.8 + - - +
125A ASP* 3.0 31.0 + - - +
150A LYS* 6.0 4.0 - - - +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 4.4 18.1 + - - +
58A GLU* 3.9 12.1 - - + +
59A SER* 5.3 7.0 + - - +
62A GLN* 3.4 36.9 + - - +
118A LYS* 3.0 21.3 + - - +
119A LEU* 2.9 18.9 + - + +
121A ASN* 1.3 75.4 - - - +
123A TYR* 1.3 63.5 + - - +
125A ASP* 3.3 28.2 + - - +
126A ALA* 3.9 3.5 + - - +
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Residues in contact with TYR 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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58A GLU* 3.8 21.2 + - - +
61A TRP* 4.2 14.6 - + - -
82A TYR* 3.1 52.9 + + - -
86A SER* 2.9 28.5 + - - -
119A LEU 3.2 6.2 + - - +
120A GLU* 2.9 32.1 + - - +
122A LYS* 1.3 76.7 - - - +
124A ILE* 1.3 62.9 + - - +
125A ASP 3.4 0.7 + - - -
126A ALA* 3.4 8.0 + - - +
127A TYR* 3.3 29.7 + + - -
153A ALA* 4.0 14.6 - - + -
156A VAL* 3.9 7.4 - - - +
157A ASN* 3.9 20.0 + - - -
201A DEQ 6.5 0.9 - + - -
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Residues in contact with ILE 124 (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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120A GLU* 2.9 31.4 + - + +
121A ASN* 3.6 25.8 - - - +
123A TYR* 1.3 75.4 - - - +
125A ASP* 1.3 67.6 + - - +
127A TYR* 2.9 22.9 + - - +
128A HIS* 3.3 8.4 + - + +
146A ASN 5.3 0.2 - - - +
149A SER* 3.9 27.8 - - - +
150A LYS* 4.3 24.2 - - + +
153A ALA* 3.6 22.4 - - + -
154A ASN* 4.9 8.1 - - - +
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Residues in contact with ASP 125 (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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121A ASN* 3.0 22.6 + - - +
122A LYS* 3.4 19.9 - - - +
123A TYR 3.2 0.4 - - - -
124A ILE* 1.3 78.9 - - - +
126A ALA* 1.3 63.6 + - - +
128A HIS* 2.8 25.2 + - + +
129A VAL* 2.9 20.0 + - + +
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Residues in contact with ALA 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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62A GLN* 6.4 2.2 - - + -
65A TRP* 4.0 16.6 + - + +
82A TYR* 3.2 43.3 - - + +
122A LYS 3.9 3.6 + - - +
123A TYR 3.4 3.2 + - - +
124A ILE 3.2 1.0 - - - -
125A ASP* 1.3 78.4 - - - +
127A TYR* 1.3 57.0 + - - +
129A VAL* 3.6 8.0 + - - +
130A ILE* 3.2 33.4 + - - +
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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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79A PHE* 3.7 29.8 - + - -
82A TYR* 3.5 28.8 - + + -
83A ASN* 2.6 33.7 + - - -
123A TYR* 3.3 29.7 + + - -
124A ILE 2.9 12.7 + - - +
126A ALA* 1.3 75.1 - - - +
128A HIS* 1.3 61.5 + - - +
130A ILE* 3.4 6.4 + - + +
131A PHE* 2.9 38.2 + + + -
149A SER* 3.6 20.6 - - - +
152A ALA* 3.8 9.6 - - + -
153A ALA* 3.7 33.9 - - + -
156A VAL* 3.7 8.3 - - - +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.3 4.1 + - + +
125A ASP* 2.8 24.2 + - - +
127A TYR* 1.3 80.3 - - - +
129A VAL* 1.3 61.4 + - + +
131A PHE* 3.2 1.7 + - - +
132A LYS* 2.9 35.5 + - + +
145A VAL* 3.4 26.6 - - + +
146A ASN* 3.7 34.3 + - - -
149A SER* 3.2 16.5 + - - +
801A SO4 3.8 36.2 + - - -
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Residues in contact with VAL 129 (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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69A GLN* 5.4 7.6 - - - +
125A ASP* 2.9 20.0 + - + +
126A ALA* 3.8 9.4 - - - +
128A HIS* 1.3 79.5 - - + +
130A ILE* 1.3 66.8 + - + +
132A LYS* 4.7 4.5 - - - -
133A GLU* 2.9 41.4 + - + +
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Residues in contact with ILE 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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65A TRP* 4.1 15.7 - - + +
69A GLN* 6.0 0.7 - - - +
75A ASN* 3.5 38.1 - - + +
78A LYS* 3.9 22.7 - - + +
79A PHE* 3.9 33.7 - - + +
82A TYR* 4.4 8.7 - - + -
126A ALA 3.2 22.5 + - - +
127A TYR* 3.7 9.2 - - + +
128A HIS 3.3 0.2 - - - -
129A VAL* 1.3 80.3 - - + +
131A PHE* 1.3 63.5 + - + +
134A GLY 3.0 21.5 + - - -
140A TRP* 3.4 14.3 - - + -
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.7 32.5 - + - -
127A TYR* 2.9 28.7 + - + +
128A HIS 3.8 2.7 - - - +
130A ILE* 1.3 77.0 - - + +
132A LYS* 1.3 64.7 + - - +
135A ASN* 3.2 22.7 + - - -
140A TRP* 3.2 27.4 + + - -
142A ILE* 3.5 20.1 - - + +
145A VAL* 3.9 16.3 - - + +
148A VAL* 3.4 38.1 - - + -
149A SER* 3.5 16.8 - - - -
152A ALA* 4.2 7.0 - - + -
182A PHE* 4.0 6.7 - + - -
183A LEU* 4.5 2.9 - - + -
186A LEU* 3.9 18.2 - - + -
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Residues in contact with LYS 132 (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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128A HIS* 2.9 26.7 + - + +
129A VAL* 4.0 4.5 - - - +
131A PHE* 1.3 75.5 - - - +
133A GLU* 1.3 73.8 + - - +
135A ASN* 2.8 24.7 + - - +
136A LEU* 3.0 33.9 - - + +
145A VAL* 4.4 6.9 - - + +
801A SO4 2.7 50.5 + - - +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 3.5 21.3 - - - +
129A VAL* 2.9 36.4 + - + +
132A LYS* 1.3 89.5 - - - +
134A GLY* 1.3 60.4 + - - +
136A LEU* 3.6 23.7 + - - +
137A ASN* 2.9 33.7 + - - +
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Residues in contact with GLY 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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75A ASN* 3.7 12.1 - - - +
130A ILE 3.0 15.9 + - - -
132A LYS 3.1 0.6 - - - -
133A GLU* 1.3 74.0 - - - +
135A ASN* 1.3 61.4 + - - +
137A ASN 3.8 0.6 - - - -
138A GLY 3.2 1.6 + - - -
139A GLU* 2.7 37.2 + - - +
140A TRP* 3.5 27.7 + - - -
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Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE 3.2 9.4 + - - -
132A LYS* 2.8 13.9 + - - +
134A GLY* 1.3 74.0 - - - +
136A LEU* 1.3 60.2 + - + +
137A ASN 2.7 14.1 + - - -
138A GLY* 2.8 14.7 + - - -
140A TRP* 3.1 23.7 + - - +
141A SER* 3.3 3.4 + - - +
142A ILE* 2.9 46.2 - - - +
145A VAL* 3.8 14.7 - - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 3.0 34.0 + - + +
133A GLU* 3.7 30.5 - - - +
135A ASN* 1.3 79.4 - - + +
137A ASN* 1.3 61.9 + - - +
138A GLY 3.6 0.4 - - - -
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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
------------------------------------------------------------
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