Contacts of the helix formed by residues 116 - 141 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A NDS 3.8 3.1 - - - -
54C ASP* 2.6 29.2 + - - -
112C ARG* 3.2 16.1 + - - -
113C ALA 3.4 6.9 + - - +
115C THR* 1.3 82.4 - - - +
117C PRO* 1.3 61.9 - - - +
118C SER* 3.2 12.5 + - - -
119C LEU* 3.2 20.6 - - - +
120C ALA 2.9 23.6 + - - -
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Residues in contact with PRO 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A NDS 3.8 30.7 - - + -
54C ASP* 5.7 1.1 - - - +
115C THR 3.8 7.0 - - - +
116C SER* 1.3 84.9 - - - +
118C SER* 1.3 57.9 + - - +
120C ALA* 3.7 2.6 - - + +
121C GLU* 2.9 30.1 + - - +
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 2.6 29.4 + - - -
58C ALA* 3.9 19.4 - - - +
116C SER* 3.2 3.7 + - - -
117C PRO* 1.3 78.2 - - - +
119C LEU* 1.3 60.5 + - - +
121C GLU* 3.3 5.1 + - - +
122C ILE* 3.0 35.4 + - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 4.6 2.7 - - - +
57C PHE* 4.0 12.3 - - + +
58C ALA* 3.7 33.9 - - - +
61C LEU* 3.8 25.9 - - + +
109C PHE* 3.8 22.6 - - + +
112C ARG* 3.4 37.7 - - + -
113C ALA* 4.0 11.9 - - + +
116C SER* 3.2 22.5 + - - +
118C SER* 1.3 81.0 + - - +
120C ALA* 1.3 64.5 + - - +
122C ILE* 3.4 1.8 + - - +
123C ARG* 3.0 23.9 + - - +
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY* 3.3 28.5 - - - +
167A SER* 4.4 4.7 + - - +
601A NDS 3.8 11.0 - - + -
113C ALA* 3.6 21.4 - - + +
116C SER 2.9 16.9 + - - +
117C PRO 3.7 4.5 - - - +
119C LEU* 1.3 75.2 - - - +
121C GLU* 1.3 58.3 + - - +
123C ARG* 3.4 4.2 + - - +
124C ARG* 2.9 29.3 + - - +
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO 2.9 18.8 + - - +
118C SER* 3.7 5.6 - - - +
120C ALA* 1.3 74.1 - - - +
122C ILE* 1.3 68.1 + - + +
124C ARG* 2.7 40.5 + - - -
125C LYS* 2.5 57.4 + - + +
77D ARG* 3.2 32.8 + - - +
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Residues in contact with ILE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ALA* 3.4 43.7 - - + +
61C LEU* 3.6 31.4 - - + -
62C ARG* 3.5 27.4 - - + +
65C VAL* 4.4 7.6 - - + -
118C SER* 3.0 23.9 + - - +
121C GLU* 1.3 78.7 - - + +
123C ARG* 1.3 59.8 + - - +
125C LYS* 3.3 6.5 + - - +
126C THR* 2.9 37.0 + - - +
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 4.1 12.2 - - - +
163A ASP* 2.6 38.6 + - - +
166A GLY* 6.2 2.2 - - - -
61C LEU* 4.5 6.2 - - + +
65C VAL* 6.1 0.9 - - - -
106C MSE 4.1 26.5 + - - +
109C PHE 5.5 0.4 - - - -
110C ALA* 3.5 39.5 - - - +
113C ALA* 5.1 4.0 - - + -
119C LEU 3.0 16.9 + - - +
120C ALA* 3.7 7.0 - - - +
122C ILE* 1.3 77.0 - - - +
124C ARG* 1.3 57.9 + - - +
126C THR* 3.1 7.4 + - - -
127C LEU* 2.9 47.6 + - + +
158C ASP* 3.0 24.9 + - - -
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 4.2 13.0 - - - +
170A LEU* 3.4 28.7 - - + -
601A NDS 5.6 1.1 - - - -
120C ALA 2.9 18.2 + - - +
121C GLU* 2.7 43.3 + - - +
123C ARG* 1.3 77.8 - - - +
125C LYS* 1.3 66.7 + - - +
127C LEU* 3.4 9.5 + - - +
128C PHE* 2.9 22.9 + - - +
131C ARG* 5.1 0.7 + - - -
73D SER* 2.9 51.1 + - - -
74D GLU* 3.7 11.5 + - - -
76D GLU* 2.9 30.1 + - - +
77D ARG* 3.8 13.9 - - - +
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLU* 2.5 58.0 + - + +
122C ILE* 3.8 6.7 - - - +
124C ARG* 1.3 83.5 - - - +
126C THR* 1.3 57.9 + - - +
128C PHE* 3.3 8.2 + - - +
129C THR* 2.9 34.5 + - - +
70D ALA* 3.7 33.8 - - + -
73D SER* 3.7 9.8 - - - +
74D GLU* 3.2 25.6 + - - -
77D ARG* 3.7 5.5 - - - +
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Residues in contact with THR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 3.1 46.9 - - + +
68C LEU* 4.8 5.8 - - + -
69C LEU* 4.8 5.4 - - + -
106C MSE 6.0 2.2 - - - -
122C ILE* 2.9 23.1 + - - +
123C ARG* 3.5 9.2 - - - -
125C LYS* 1.3 74.6 - - - +
127C LEU* 1.3 61.1 + - + +
129C THR* 3.3 8.0 + - - -
130C ILE* 3.0 47.9 + - + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 3.7 30.3 - - + +
171A TYR* 4.1 11.7 - - + +
123C ARG* 2.9 44.6 + - + +
124C ARG* 3.8 7.9 - - - +
126C THR* 1.3 77.4 - - + +
128C PHE* 1.3 57.8 + - - +
130C ILE* 3.3 4.0 + - + -
131C ARG* 2.8 46.3 + - - +
154C LEU* 3.8 26.2 - - + +
158C ASP* 3.6 23.8 - - - +
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Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG* 2.9 18.9 + - - +
125C LYS 3.5 4.5 - - - +
127C LEU* 1.3 76.9 - - - +
129C THR* 1.3 58.3 + - - +
131C ARG* 3.5 18.0 - - - +
132C THR* 2.8 55.3 + - - -
69D LEU* 3.4 36.8 - - + -
72D LEU* 4.2 13.0 - - + -
73D SER* 3.4 34.5 - - - -
76D GLU* 3.5 36.6 - - + +
133D GLY* 5.2 10.1 - - - -
136D ALA* 6.1 4.5 - - + -
137D VAL* 5.5 3.4 - - + -
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Residues in contact with THR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.3 18.8 - - + +
125C LYS 2.9 18.0 + - - -
126C THR* 3.5 7.2 - - - -
127C LEU 3.3 0.2 - - - -
128C PHE* 1.3 76.5 - - - +
130C ILE* 1.3 64.7 + - - +
132C THR* 3.4 3.3 + - - -
133C GLY* 3.1 19.1 + - - -
62D ARG* 5.1 3.2 + - - +
66D ASP* 3.3 41.1 + - + +
69D LEU* 4.1 28.0 - - + +
70D ALA* 4.7 4.2 + - - +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.1 19.5 - - + -
69C LEU* 3.9 17.7 - - + -
72C LEU* 4.0 14.4 - - + -
89C MSE 4.1 13.7 - - + -
92C LEU* 5.0 5.2 - - + -
126C THR* 3.0 38.4 + - + +
127C LEU* 5.0 3.8 - - + -
129C THR* 1.3 75.4 - - - +
131C ARG* 1.3 59.5 + - - +
133C GLY* 3.1 3.8 + - - -
134C LEU* 2.9 41.4 + - + +
154C LEU* 3.9 32.5 - - + -
62D ARG* 5.6 2.9 - - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 4.8 9.5 + - - -
175A TYR* 5.5 1.5 + - - -
124C ARG 5.1 0.4 + - - -
127C LEU* 2.8 41.4 + - - +
128C PHE* 3.5 23.0 + - - +
130C ILE* 1.3 78.7 - - - +
132C THR* 1.3 57.7 + - - +
134C LEU* 3.4 7.3 + - - +
135C SER* 2.8 35.6 + - - +
147C GLU 5.2 0.6 + - - +
150C ALA* 4.0 2.6 - - + +
151C ALA* 3.8 41.3 - - + +
154C LEU* 4.0 13.9 - - + +
76D GLU* 2.5 32.9 + - - -
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PHE* 2.8 44.9 + - - -
129C THR 3.8 4.0 - - - -
130C ILE 3.3 0.2 - - - -
131C ARG* 1.3 75.4 + - - +
133C GLY* 1.3 57.6 + - - +
135C SER* 3.3 7.4 + - - -
136C ALA* 2.9 28.2 + - - +
69D LEU* 4.0 18.2 - - + -
129D THR* 3.8 13.0 - - + +
132D THR* 4.0 6.4 - - + +
133D GLY* 3.7 31.8 - - - +
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Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 5.2 6.3 - - - -
129C THR 3.1 14.1 + - - -
130C ILE* 3.1 4.0 + - - -
132C THR* 1.3 76.9 - - - +
134C LEU* 1.3 60.5 + - - +
136C ALA* 3.3 5.0 + - - +
137C VAL* 3.2 27.7 + - - +
62D ARG* 6.1 3.4 - - - -
129D THR* 4.3 16.6 + - - +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 4.2 12.9 + - - +
85C LEU* 3.6 28.0 - - + +
88C ALA* 5.4 0.4 - - + -
89C MSE 4.0 25.8 - - + -
130C ILE* 2.9 39.4 + - + +
131C ARG* 3.7 4.5 - - - +
133C GLY* 1.3 71.6 - - - +
135C SER* 1.3 64.0 + - - +
137C VAL* 3.2 7.6 + - - +
138C LEU* 3.0 28.1 + - + +
150C ALA* 3.8 30.5 - - + +
153C LEU* 4.2 10.8 - - + -
154C LEU* 4.1 15.5 - - + +
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Residues in contact with SER 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ARG* 2.8 28.0 + - - +
132C THR* 3.5 7.4 - - - -
134C LEU* 1.3 71.7 - - - +
136C ALA* 1.3 58.8 + - - +
138C LEU* 3.2 4.3 + - - +
139C ILE* 2.8 37.4 + - - +
146C ALA 4.7 1.8 - - - -
147C GLU* 3.5 32.2 + - - +
150C ALA* 3.3 18.3 - - - +
132D THR* 4.0 10.1 - - - -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C THR 2.9 16.4 + - - +
133C GLY 3.6 5.2 - - - +
134C LEU 3.2 0.2 - - - -
135C SER* 1.3 76.1 - - - +
137C VAL* 1.3 64.2 + - - +
139C ILE* 4.6 0.2 - - - -
140C GLY* 3.0 20.1 + - - -
125D LYS* 4.4 6.4 + - - +
128D PHE* 3.3 21.8 - - + -
129D THR* 3.8 24.5 - - - +
132D THR* 3.4 25.3 - - - +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 4.1 24.9 - - + +
81C PRO* 4.6 16.8 - - + +
84C ALA* 6.0 3.8 - - + -
85C LEU* 4.1 31.0 - - + -
133C GLY 3.2 12.9 + - - +
134C LEU* 3.2 8.5 + - - +
136C ALA* 1.3 77.9 - - + +
138C LEU* 1.3 62.4 + - + +
140C GLY* 3.3 10.1 + - - -
141C ILE* 3.5 16.4 + - + +
125D LYS* 4.0 22.9 - - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.9 18.2 - - + -
134C LEU* 3.0 17.6 + - + +
135C SER 3.2 1.1 + - - +
137C VAL* 1.3 73.3 - - + +
139C ILE* 1.3 65.3 + - - +
141C ILE* 3.3 8.3 + - + -
143C THR* 2.9 48.0 + - + +
146C ALA* 3.6 29.2 - - + +
149C ARG* 4.3 2.9 - - + -
150C ALA* 3.7 24.0 - - + +
153C LEU* 5.6 3.8 - - + -
187C ILE* 3.8 24.2 - - + -
188C LEU* 3.8 23.3 - - + -
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C SER 2.8 25.2 + - - +
136C ALA 3.9 2.9 - - - +
138C LEU* 1.3 72.1 - - - +
140C GLY* 1.3 63.7 + - - +
142C GLY* 3.0 16.3 + - - +
143C THR 4.8 1.8 - - - +
146C ALA* 3.5 18.6 - - + -
147C GLU* 4.4 21.5 - - + +
128D PHE* 3.9 20.0 - - + -
132D THR* 3.7 28.0 - - + +
135D SER* 5.9 1.1 - - - +
147D GLU* 5.1 12.1 - - - +
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Residues in contact with GLY 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ALA 3.0 17.3 + - - -
137C VAL 3.3 2.9 + - - -
138C LEU 3.2 0.6 - - - -
139C ILE* 1.3 77.2 - - - +
141C ILE* 1.3 63.7 + - - +
142C GLY 3.5 0.4 + - - -
124D ARG* 6.3 1.1 - - - -
125D LYS* 6.0 1.8 - - - -
128D PHE* 4.2 14.4 - - - -
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.8 35.2 - - + -
137C VAL* 3.6 14.4 - - + +
138C LEU* 3.4 8.1 - - + +
140C GLY* 1.3 82.8 - - - +
142C GLY* 1.3 54.3 + - - +
143C THR* 3.4 16.3 + - - +
188C LEU* 3.6 31.6 - - + -
191C ALA* 4.1 6.3 - - + -
192C ASP* 2.7 55.6 + - - +
193C VAL 4.7 3.8 - - - +
----------------------------------------------------------
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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