Contacts of the helix formed by residues 116 - 141 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG* 3.1 32.2 + - - -
113D ALA 3.5 6.9 + - - +
115D THR* 1.3 80.1 - - - +
117D PRO* 1.4 61.7 - - - +
118D SER* 3.5 7.8 + - - -
119D LEU* 3.0 32.0 + - - +
120D ALA 2.9 24.6 + - - -
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Residues in contact with PRO 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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115D THR 3.7 7.0 - - - +
116D SER* 1.4 86.5 - - - +
118D SER* 1.3 57.3 + - - +
120D ALA* 3.6 8.9 - - + +
121D GLU* 3.0 26.5 + - - +
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Residues in contact with SER 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.3 10.6 + - - +
54D ASP* 5.5 7.2 - - - +
116D SER* 3.5 9.9 + - - -
117D PRO* 1.3 78.6 - - - +
119D LEU* 1.3 72.7 + - - +
121D GLU* 3.4 7.6 + - - +
122D ILE* 3.3 29.1 + - - +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 5.4 2.0 - - + -
54D ASP* 5.6 9.9 - - + -
57D PHE* 6.2 1.8 - - + -
109D PHE* 3.5 41.5 - - + -
112D ARG* 3.3 40.4 - - + +
113D ALA* 4.2 9.0 - - - -
116D SER* 3.0 27.9 + - - +
118D SER* 1.3 86.1 + - - +
120D ALA* 1.3 55.0 + - - +
122D ILE* 3.2 7.9 + - + -
123D ARG* 2.8 35.5 + - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY 3.4 24.5 - - - +
167B SER* 4.0 2.8 + - - -
113D ALA* 3.5 26.8 - - + +
116D SER 2.9 7.4 + - - +
117D PRO* 3.6 13.2 - - + +
119D LEU* 1.3 76.7 - - - +
121D GLU* 1.3 51.0 + - - +
123D ARG* 3.3 3.0 + - - +
124D ARG* 2.7 36.3 + - - +
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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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77C ARG* 3.9 23.1 - - - +
78C GLY* 3.7 17.5 + - - -
117D PRO 3.0 14.7 + - - +
118D SER* 3.7 10.3 - - - +
119D LEU 3.3 0.4 - - - -
120D ALA* 1.3 75.3 - - - +
122D ILE* 1.3 62.9 + - - +
124D ARG* 2.8 45.3 + - - +
125D LYS* 3.0 37.5 + - + +
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.7 33.4 - - - +
54D ASP* 3.9 30.3 - - + +
57D PHE* 5.5 0.7 - - + -
58D ALA* 4.0 23.6 - - + +
61D LEU* 3.8 24.5 - - + -
109D PHE* 3.8 10.8 - - + -
118D SER 3.3 14.7 + - - +
119D LEU* 3.2 13.3 + - + +
121D GLU* 1.3 76.0 - - - +
123D ARG* 1.3 56.7 + - - +
125D LYS* 3.4 5.7 + - - +
126D THR* 2.7 34.2 + - - +
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Residues in contact with ARG 123 (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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162B LEU* 4.4 8.3 + - - +
163B ASP* 2.8 38.2 + - - +
166B GLY* 5.6 3.4 - - - -
167B SER* 4.4 3.8 + - - +
61D LEU* 4.9 1.3 - - + -
106D MSE 4.2 25.7 + - - +
109D PHE* 3.8 19.7 - - + -
110D ALA* 3.2 43.9 + - - +
113D ALA* 4.5 7.0 - - + -
119D LEU 2.8 16.5 + - - +
120D ALA* 3.7 7.0 - - - +
122D ILE* 1.3 75.0 - - - +
124D ARG* 1.3 60.0 + - - +
126D THR* 3.1 10.3 + - - +
127D LEU* 2.8 53.1 + - + +
158D ASP* 3.7 11.3 + - - -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER* 3.5 23.9 + - - +
169B ALA* 5.3 8.3 - - - -
170B LEU* 3.9 32.9 - - + +
78C GLY* 5.4 2.2 - - - -
140C GLY* 6.3 1.2 - - - -
120D ALA 2.7 21.4 + - - +
121D GLU* 2.8 45.2 + - - +
123D ARG* 1.3 72.3 - - - +
125D LYS* 1.3 87.0 + - - +
127D LEU* 3.4 4.4 + - - +
128D PHE* 2.9 41.9 + - - +
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Residues in contact with LYS 125 (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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76C GLU 6.0 2.0 - - - +
77C ARG* 6.0 1.6 - - - +
78C GLY* 5.4 7.0 - - - +
136C ALA* 4.4 5.8 + - - -
137C VAL* 4.0 35.6 - - - +
140C GLY* 6.0 1.4 - - - -
121D GLU* 3.0 33.8 + - + +
122D ILE* 3.7 6.1 - - - +
124D ARG* 1.3 108.9 - - - +
126D THR* 1.3 59.1 + - - +
128D PHE* 3.3 9.2 + - - +
129D THR* 2.9 43.8 + - - +
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Residues in contact with THR 126 (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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61D LEU* 3.8 28.9 - - + +
64D LEU* 5.9 0.7 - - + -
65D VAL* 3.4 28.6 - - + +
106D MSE 4.7 14.1 - - + -
122D ILE* 2.7 21.3 + - - +
123D ARG* 3.3 13.7 - - + +
125D LYS* 1.3 77.2 - - - +
127D LEU* 1.3 67.2 + - + +
129D THR* 3.3 3.1 + - - -
130D ILE* 3.1 38.1 + - + +
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Residues in contact with LEU 127 (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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163B ASP* 3.9 28.7 - - + +
167B SER* 4.1 16.8 - - - +
170B LEU* 4.6 4.3 - - + -
171B TYR* 4.0 21.5 - - + +
123D ARG* 2.8 47.3 + - - +
124D ARG* 3.7 4.5 - - - +
126D THR* 1.3 77.7 - - + +
128D PHE* 1.3 56.7 + - - +
130D ILE* 3.3 3.0 + - + -
131D ARG* 2.9 34.6 + - - +
154D LEU* 3.7 18.9 - - + +
158D ASP* 3.7 22.9 - - - +
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Residues in contact with PHE 128 (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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170B LEU* 3.7 35.6 - - + +
136C ALA* 3.3 31.0 - - + -
139C ILE* 3.9 22.4 - - + -
140C GLY* 4.0 15.9 - - - -
124D ARG* 2.9 26.6 + - - +
125D LYS* 3.9 11.4 - - - +
127D LEU* 1.3 76.6 - - - +
129D THR* 1.3 58.1 + - - +
131D ARG* 3.4 23.6 + - + +
132D THR* 2.9 45.5 + - - -
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Residues in contact with THR 129 (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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132C THR* 3.8 8.2 - - + +
133C GLY* 4.3 20.8 + - - -
136C ALA* 3.8 17.1 - - - +
65D VAL* 3.8 23.1 - - + -
69D LEU* 4.1 15.6 - - + +
125D LYS* 2.9 26.1 + - - +
126D THR* 3.8 3.8 - - - -
128D PHE* 1.3 75.1 - - - +
130D ILE* 1.3 66.7 + - - +
132D THR* 3.3 3.1 + - - -
133D GLY* 3.2 17.2 + - - -
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Residues in contact with ILE 130 (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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64D LEU* 6.0 3.1 - - + -
65D VAL* 4.1 20.4 - - + -
68D LEU* 3.8 35.9 - - + -
69D LEU* 4.7 7.4 - - + -
72D LEU* 4.5 3.9 - - + +
89D MSE 4.1 3.1 - - + -
92D LEU* 5.0 5.2 - - + -
126D THR* 3.1 34.3 + - + +
127D LEU* 3.7 6.1 - - + +
129D THR* 1.3 75.6 - - - +
131D ARG* 1.3 57.6 + - - +
133D GLY* 3.2 3.5 + - - -
134D LEU* 2.9 41.1 + - + +
154D LEU* 3.6 30.3 - - + -
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Residues in contact with ARG 131 (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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170B LEU* 3.6 25.1 + - - +
171B TYR* 3.1 40.2 + - - -
175B TYR* 3.6 21.2 + - - -
127D LEU 2.9 23.7 + - - +
128D PHE* 3.7 26.1 - - + +
129D THR 3.3 0.2 - - - -
130D ILE* 1.3 74.7 - - - +
132D THR* 1.3 56.2 + - - +
134D LEU* 3.7 7.2 - - - +
135D SER* 2.8 38.6 + - - -
147D GLU* 5.1 4.6 + - - +
150D ALA* 4.0 5.4 - - + +
151D ALA* 3.6 32.9 - - - +
154D LEU* 3.8 15.0 - - + -
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Residues in contact with THR 132 (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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132C THR* 4.0 9.2 - - + +
135C SER* 4.0 19.5 - - - -
136C ALA* 3.4 22.0 - - - +
139C ILE* 3.7 26.0 - - + +
147C GLU* 4.7 6.8 - - - +
128D PHE* 2.9 34.1 + - - -
129D THR 3.6 5.4 - - - -
130D ILE 3.3 0.4 - - - -
131D ARG* 1.3 73.4 - - - +
133D GLY* 1.3 57.9 + - - +
135D SER* 3.2 9.5 + - - +
136D ALA* 3.0 28.9 + - + +
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Residues in contact with GLY 133 (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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128C PHE* 5.2 6.5 - - - -
132C THR* 3.7 19.1 - - - +
69D LEU* 4.4 3.8 - - - -
72D LEU* 3.7 14.9 - - - +
129D THR 3.2 11.8 + - - -
130D ILE 3.2 2.9 + - - -
132D THR* 1.3 75.7 - - - +
134D LEU* 1.3 62.4 + - - +
136D ALA* 3.4 6.8 + - - +
137D VAL* 3.3 24.9 + - - +
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Residues in contact with LEU 134 (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 LEU* 3.7 21.0 - - + +
85D LEU* 3.7 26.1 - - + +
89D MSE 4.1 21.3 - - + -
130D ILE* 2.9 40.2 + - + +
131D ARG* 3.7 5.2 - - - +
133D GLY* 1.3 74.9 - - - +
135D SER* 1.3 64.0 + - - +
137D VAL* 3.1 9.1 + - - +
138D LEU* 3.1 24.7 + - + +
150D ALA* 3.8 32.1 - - + +
153D LEU* 4.2 10.5 - - + -
154D LEU* 4.1 13.5 - - + +
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Residues in contact with SER 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ILE* 5.9 1.6 - - - +
131D ARG 2.8 26.1 + - - -
132D THR* 3.2 12.1 + - - +
134D LEU* 1.3 73.4 - - - +
136D ALA* 1.3 56.8 + - - +
138D LEU* 3.2 5.4 + - - +
139D ILE* 2.7 42.1 + - - +
146D ALA 4.2 1.1 - - - -
147D GLU* 4.1 29.8 + - - +
150D ALA* 3.6 18.8 - - - +
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Residues in contact with ALA 136 (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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128C PHE* 6.1 5.2 - - + -
147C GLU* 3.6 21.3 - - - +
132D THR* 3.0 17.8 + - + +
133D GLY* 3.7 7.4 - - - +
134D LEU 3.2 0.2 - - - -
135D SER* 1.3 77.1 + - - +
137D VAL* 1.3 63.3 + - + +
139D ILE* 3.9 7.9 - - - +
140D GLY* 3.1 20.4 + - - -
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PHE* 5.5 4.7 - - + -
72D LEU* 4.2 33.0 - - + +
75D VAL* 4.1 31.0 - - + +
81D PRO* 4.3 18.6 - - + -
85D LEU* 4.4 20.4 - - + -
133D GLY 3.3 13.7 + - - +
134D LEU 3.1 7.7 + - - +
136D ALA* 1.3 75.8 - - + +
138D LEU* 1.3 66.6 + - + +
140D GLY* 3.2 11.3 + - - -
141D ILE* 3.4 15.9 + - + +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LEU* 4.1 15.3 - - + -
134D LEU* 3.1 11.1 + - + +
135D SER 3.7 6.7 - - - +
137D VAL* 1.3 75.8 - - + +
139D ILE* 1.3 62.1 + - - +
141D ILE* 3.4 4.3 - - + +
142D GLY 3.3 3.1 + - - -
143D THR* 2.7 46.2 + - + +
146D ALA* 3.6 26.0 - - + +
149D ARG* 4.1 4.9 - - + -
150D ALA* 3.8 19.5 - - + +
153D LEU* 5.9 2.7 - - + -
187D ILE* 3.6 26.9 - - + -
188D LEU* 3.7 30.3 - - + -
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Residues in contact with ILE 139 (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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147C GLU* 5.0 11.4 - - - +
135D SER* 2.7 39.1 + - - +
136D ALA* 3.9 7.6 - - - +
138D LEU* 1.3 72.3 - - - +
140D GLY* 1.3 58.9 + - - +
142D GLY* 2.9 20.2 + - - +
143D THR 4.8 1.6 - - - +
146D ALA* 3.6 20.2 - - + -
147D GLU* 4.7 14.4 - - + +
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Residues in contact with GLY 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA 3.1 14.8 + - - -
137D VAL* 3.2 5.3 + - - -
139D ILE* 1.3 77.5 - - - +
141D ILE* 1.3 63.2 + - - +
142D GLY 3.5 0.2 - - - -
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D VAL* 5.7 3.8 - - + -
81D PRO* 4.0 33.9 - - + -
137D VAL* 3.4 12.8 + - + +
138D LEU* 3.4 7.0 - - + +
140D GLY* 1.3 80.8 - - - +
142D GLY* 1.3 61.6 + - - +
143D THR* 3.3 16.4 - - - +
188D LEU* 3.6 32.1 - - + -
191D ALA* 3.8 8.1 - - + -
192D ASP* 2.9 48.6 + - + +
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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