Contacts of the helix formed by residues 116 - 140 (chain A) in PDB entry 2NP5
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 SER 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.1 24.0 + - - -
112A ARG* 3.1 15.3 + - - -
113A ALA 3.4 7.9 + - - +
115A THR* 1.3 79.5 - - - +
117A PRO* 1.3 65.7 - - - +
118A SER* 3.3 8.0 + - - -
119A LEU* 3.4 22.3 + - - +
120A ALA* 3.0 18.0 + - - +
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Residues in contact with PRO 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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54A ASP* 5.5 2.0 - - - +
115A THR 3.8 7.6 - - - +
116A SER* 1.3 83.5 - - - +
118A SER* 1.3 58.0 + - - +
120A ALA* 3.4 6.9 + - + +
121A GLU* 3.0 29.6 + - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 2.7 41.5 + - - -
58A ALA* 4.2 16.7 - - - +
116A SER* 3.3 0.9 + - - -
117A PRO* 1.3 78.2 - - - +
119A LEU* 1.3 65.6 + - - +
121A GLU* 3.3 7.6 + - - +
122A ILE* 3.2 28.0 + - - +
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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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54A ASP* 5.2 0.4 - - - +
57A PHE* 3.9 20.2 - - + +
58A ALA* 3.6 36.3 - - + +
61A LEU* 3.7 25.5 - - + +
109A PHE* 4.0 15.9 - - + +
112A ARG* 3.7 29.8 - - + -
113A ALA* 4.0 12.8 - - + +
116A SER* 3.3 23.3 + - - +
118A SER* 1.3 79.8 + - - +
120A ALA* 1.3 60.7 + - - +
122A ILE* 3.2 3.4 + - + +
123A ARG* 2.8 29.8 + - - +
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Residues in contact with ALA 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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113A ALA* 3.6 16.2 - - - +
116A SER 3.0 17.0 + - - +
117A PRO* 3.6 9.4 - - + +
119A LEU* 1.3 75.9 - - - +
121A GLU* 1.3 57.0 + - - +
123A ARG* 4.4 0.4 - - - -
124A ARG* 2.7 33.4 + - - +
166C GLY 3.3 25.9 - - - +
168C PRO* 5.5 4.5 - - + -
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Residues in contact with GLU 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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117A PRO 3.0 17.2 + - - +
118A SER* 3.6 7.9 - - - +
119A LEU 3.2 0.2 - - - -
120A ALA* 1.3 77.2 - - - +
122A ILE* 1.3 62.1 + - + +
124A ARG* 3.4 33.9 + - - +
125A LYS* 3.0 44.9 + - - +
204A LMT 5.6 0.2 - - - +
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Residues in contact with ILE 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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58A ALA* 3.6 42.4 - - + +
61A LEU* 3.7 27.6 - - + -
62A ARG* 3.6 19.3 - - + -
65A VAL* 4.1 22.0 - - + -
118A SER* 3.2 17.2 + - - +
119A LEU 3.2 6.3 + - - +
121A GLU* 1.3 78.6 - - + +
123A ARG* 1.3 59.2 + - - +
125A LYS* 3.4 3.1 + - - +
126A THR* 2.8 32.7 + - - +
204A LMT 4.0 21.2 - - - +
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Residues in contact with ARG 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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61A LEU* 4.6 5.6 - - + +
65A VAL* 6.0 1.3 - - - -
106A MSE 4.3 23.4 - - - +
109A PHE 5.4 0.7 - - - -
110A ALA* 3.4 39.0 + - - +
113A ALA* 4.6 4.3 - - + -
119A LEU 2.8 17.8 + - - +
120A ALA* 3.7 4.9 - - - +
122A ILE* 1.3 74.1 - - - +
124A ARG* 1.3 64.7 + - - +
126A THR* 3.2 12.8 + - - +
127A LEU* 2.9 45.8 + - + +
158A ASP* 3.5 10.9 + - - -
162C LEU* 4.2 8.3 + - - +
163C ASP* 2.7 41.8 + - - +
166C GLY* 4.3 8.2 - - - +
167C SER* 3.5 13.0 - - - +
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Residues in contact with ARG 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 ALA 2.7 22.5 + - - +
121A GLU* 3.4 36.1 + - - +
123A ARG* 1.3 72.5 - - - +
125A LYS* 1.3 80.3 + - - +
128A PHE* 2.8 50.2 + - - +
167C SER* 3.3 19.7 + - - +
169C ALA* 4.9 15.0 - - + -
170C LEU* 3.5 26.6 - - + +
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Residues in contact with LYS 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 GLU* 3.0 35.9 + - - +
122A ILE 3.7 4.7 - - - +
123A ARG 3.3 0.2 - - - -
124A ARG* 1.3 96.1 - - - +
126A THR* 1.3 56.8 + - - +
128A PHE* 3.5 5.1 + - + +
129A THR* 3.0 35.2 + - - +
204A LMT 2.8 66.4 + - - +
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Residues in contact with THR 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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65A VAL* 3.5 41.4 - - + +
68A LEU* 6.1 4.3 - - + -
69A LEU* 4.6 10.8 - - + +
106A MSE 6.2 1.8 - - + -
122A ILE* 2.8 21.2 + - - +
123A ARG* 3.2 13.0 + - - +
125A LYS* 1.3 75.3 - - - +
127A LEU* 1.3 62.6 + - + +
129A THR* 3.3 3.3 + - - -
130A ILE* 3.0 47.4 + - + +
204A LMT 4.3 11.0 + - - -
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Residues in contact with LEU 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 ARG* 2.9 46.1 + - + +
126A THR* 1.3 74.2 - - + +
128A PHE* 1.3 66.0 + - - +
130A ILE* 4.1 3.3 - - + +
131A ARG* 2.9 30.7 + - - +
154A LEU* 3.6 26.9 - - + -
158A ASP* 4.1 2.7 - - - +
163C ASP* 3.9 31.6 - - + +
167C SER* 3.5 27.4 - - - +
170C LEU* 3.7 11.9 - - + -
171C TYR* 4.1 16.4 - - + +
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Residues in contact with PHE 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 ARG* 2.8 35.1 + - - +
125A LYS* 3.6 6.7 - - + +
127A LEU* 1.3 77.6 - - - +
129A THR* 1.3 65.6 + - - +
131A ARG* 3.8 4.6 - - - +
132A THR* 2.9 54.4 + - + -
170C LEU* 3.9 23.7 - - + +
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Residues in contact with THR 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 LEU* 4.4 5.4 - - + -
125A LYS* 3.0 13.0 + - - +
126A THR 3.6 4.0 - - - -
128A PHE* 1.3 81.6 - - - +
130A ILE* 1.3 67.6 + - - +
132A THR* 3.4 6.2 + - - -
133A GLY* 3.1 18.9 + - - -
204A LMT 2.7 76.6 + - + +
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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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68A LEU* 6.2 3.1 - - + -
69A LEU* 3.6 19.5 - - + -
72A LEU* 3.8 20.4 - - + -
89A MSE 4.4 11.0 - - + -
92A LEU* 4.3 15.0 - - + -
126A THR* 3.0 37.2 + - + +
127A LEU* 5.2 2.0 - - + -
129A THR* 1.3 76.6 - - - +
131A ARG* 1.3 63.4 + - - +
133A GLY* 3.1 3.3 + - - -
134A LEU* 3.0 36.1 + - + +
154A LEU* 3.8 30.3 - - + -
204A LMT 4.2 9.1 - - + +
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Residues in contact with ARG 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 LEU* 2.9 23.2 + - - +
128A PHE* 3.9 4.3 - - - +
130A ILE* 1.3 75.1 - - - +
132A THR* 1.3 52.5 - - - +
134A LEU* 3.3 6.4 + - - +
135A SER* 2.7 42.5 + - - +
147A GLU* 4.9 14.3 + - + +
150A ALA* 4.0 2.4 - - - +
151A ALA* 3.6 26.8 - - - +
154A LEU* 3.9 15.9 - - + -
170C LEU* 3.5 31.7 + - - +
171C TYR* 3.2 44.4 - - - -
175C TYR* 3.0 34.0 + - - -
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Residues in contact with THR 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 PHE* 2.9 49.7 + - + -
129A THR* 3.6 7.6 - - - -
130A ILE 3.2 0.2 - - - -
131A ARG* 1.3 78.1 - - - +
133A GLY* 1.3 62.0 + - - +
135A SER* 3.5 5.4 + - - -
136A ALA* 3.0 22.6 + - + +
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Residues in contact with GLY 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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77A ARG* 4.6 6.4 + - - -
129A THR 3.1 13.3 + - - -
130A ILE 3.7 2.5 - - - -
132A THR* 1.3 73.4 - - - +
134A LEU* 1.3 65.1 + - - +
136A ALA* 3.2 9.0 + - - +
137A VAL* 3.2 25.8 + - - +
204A LMT 4.1 23.8 - - - -
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Residues in contact with LEU 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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85A LEU* 3.6 28.7 - - + +
89A MSE 3.9 28.0 - - + -
130A ILE* 3.0 37.8 + - + +
131A ARG* 3.8 1.6 - - - +
133A GLY* 1.3 73.1 - - - +
135A SER* 1.3 63.6 + - - +
137A VAL* 3.2 7.0 + - - +
138A LEU* 3.0 27.8 + - + +
150A ALA* 3.7 34.3 - - + +
153A LEU* 4.3 8.7 - - + -
154A LEU* 4.1 10.5 - - + +
204A LMT 3.8 17.4 - - + +
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Residues in contact with SER 135 (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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131A ARG* 2.7 29.7 + - - +
132A THR* 3.7 7.0 - - - -
134A LEU* 1.3 72.0 - - - +
136A ALA* 1.4 52.5 + - - +
138A LEU* 3.2 4.6 + - - +
139A ILE* 2.8 53.0 + - - +
146A ALA 4.7 1.8 - - - -
147A GLU* 3.6 27.0 + - - +
150A ALA* 3.2 18.6 - - - +
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Residues in contact with ALA 136 (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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77A ARG* 5.1 7.6 - - - +
132A THR* 3.0 16.0 + - + +
133A GLY* 3.2 12.5 + - - +
135A SER* 1.4 74.9 - - - +
137A VAL* 1.3 58.3 + - - +
139A ILE* 3.9 7.0 - - - +
140A GLY* 2.9 27.4 + - - -
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Residues in contact with VAL 137 (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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77A ARG* 3.7 26.7 - - + +
81A PRO* 4.3 20.6 - - + -
84A ALA* 5.8 1.1 - - + -
85A LEU* 4.2 29.2 - - + -
133A GLY 3.2 12.9 + - - +
134A LEU 3.6 7.9 - - - +
136A ALA* 1.3 77.3 - - - +
138A LEU* 1.3 63.0 + - + +
140A GLY* 3.3 10.8 + - - -
141A ILE* 3.6 15.4 + - - +
204A LMT 3.9 22.9 - - + -
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Residues in contact with LEU 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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85A LEU* 4.0 16.8 - - + -
134A LEU* 3.0 20.2 + - + +
135A SER 3.8 2.9 - - - +
137A VAL* 1.3 76.1 - - + +
139A ILE* 1.3 63.1 + - - +
141A ILE* 3.3 7.5 + - + +
143A THR* 2.8 48.7 + - + +
146A ALA* 3.6 14.8 - - + +
149A ARG* 4.1 3.4 - - + -
150A ALA* 3.6 34.5 - - + +
153A LEU* 5.6 3.8 - - + -
187A ILE* 3.8 31.6 - - + -
188A LEU* 3.8 16.8 - - + -
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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 SER* 2.8 38.9 + - - +
136A ALA* 4.0 6.5 - - - +
138A LEU* 1.3 71.6 - - - +
140A GLY* 1.3 59.1 + - - +
141A ILE 3.0 5.9 + - - -
142A GLY* 3.1 13.5 + - - +
143A THR 4.8 1.1 - - - +
146A ALA* 3.6 19.1 - - + -
147A GLU* 5.3 8.7 - - + +
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Residues in contact with GLY 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 ALA 2.9 17.5 + - - -
137A VAL* 3.6 4.0 - - - -
138A LEU 3.2 1.0 - - - -
139A ILE* 1.3 77.0 - - - +
141A ILE* 1.3 65.1 + - - +
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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