Contacts of the helix formed by residues 117 - 141 (chain A) in PDB entry 3NX4
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.2 1.6 - - - -
115A GLY 4.1 1.8 + - - -
116A LEU* 1.3 78.6 - - - +
118A SER* 1.3 64.2 + - - +
119A ARG* 3.5 8.1 + - - +
120A ASN* 2.9 36.7 + - - +
121A ALA* 2.9 22.3 + - - +
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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
----------------------------------------------------------
35A HIS* 4.7 3.6 + - - +
36A TRP* 3.5 18.5 - - - -
66A ALA* 3.4 31.5 - - - +
67A GLY* 4.1 2.9 + - - -
82A GLU* 3.9 20.3 + - - -
83A VAL 5.2 0.6 + - - -
112A LEU* 3.8 19.7 - - - +
117A SER* 1.3 72.8 - - - +
119A ARG* 1.3 62.7 + - - +
121A ALA* 3.3 14.8 + - - +
122A MSE 3.5 5.0 + - - +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 3.5 40.2 - - + +
117A SER* 3.2 7.3 + - - +
118A SER* 1.3 78.7 - - - +
120A ASN* 1.3 66.0 + - - +
122A MSE 3.2 5.9 + - - +
123A ILE* 3.1 38.9 + - + +
291A TYR* 5.3 3.0 + - - +
295A ALA* 5.1 5.5 - - - +
297A GLU* 2.9 37.2 + - - +
320A LEU* 3.5 23.4 - - + +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.9 11.4 - - + +
117A SER* 2.9 27.0 + - - +
119A ARG* 1.3 80.6 + - - +
121A ALA* 1.3 65.2 + - - +
123A ILE* 3.3 18.2 + - - +
124A ILE* 3.1 27.4 + - - +
288A GLU* 4.7 8.5 + - - -
291A TYR* 3.5 47.0 - - + +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 4.6 1.1 - - + -
84A LEU* 3.8 29.4 - - + -
112A LEU* 3.9 7.9 - - + -
116A LEU* 3.8 17.6 - - + +
117A SER 2.9 13.6 + - - +
118A SER 3.4 11.2 - - - +
119A ARG 3.2 0.2 - - - -
120A ASN* 1.3 75.8 - - - +
122A MSE 1.3 70.8 + - + +
124A ILE* 3.5 4.8 - - - +
125A GLY 2.9 19.9 + - - -
279A TRP* 3.6 6.6 - - - -
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Residues in contact with MSE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 3.6 26.7 - - + +
37A SER* 3.7 11.2 - - - +
38A SER* 3.4 7.8 - - - -
64A ASP* 3.5 28.0 - - + +
65A PHE* 3.4 34.1 - - - +
66A ALA* 3.7 15.5 - - + -
84A LEU* 4.3 10.3 - - + -
85A LEU 4.1 7.4 - - - +
86A THR* 4.4 9.0 - - + -
118A SER 3.5 0.4 + - - +
119A ARG 3.2 4.3 + - - +
120A ASN 3.1 0.4 - - - -
121A ALA* 1.3 98.4 - - + +
123A ILE* 1.3 66.4 + - - +
124A ILE 3.1 0.9 - - - -
125A GLY* 3.4 3.2 + - - +
279A TRP* 5.0 1.1 - - + -
318A ARG* 3.0 20.3 + - - -
319A THR 5.1 0.2 - - - +
320A LEU* 3.6 22.4 - - + -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.1 33.1 + - - +
120A ASN* 3.3 28.7 + - - +
122A MSE 1.3 75.1 - - - +
124A ILE* 1.3 53.9 + - - +
290A PHE* 4.3 12.1 - - + -
291A TYR* 3.8 30.3 - - + +
294A ALA* 4.9 0.4 - - + -
295A ALA* 3.6 36.1 - - + +
318A ARG* 2.7 43.0 + - + +
319A THR 6.3 0.2 - - - -
320A LEU* 3.9 16.8 - - + +
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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
----------------------------------------------------------
116A LEU* 4.0 12.8 - - + -
120A ASN 3.1 15.6 + - - +
121A ALA 3.5 5.6 - - - +
122A MSE 3.8 0.2 - - - -
123A ILE* 1.3 75.0 - - - +
125A GLY* 1.3 60.7 + - - +
128A GLY* 2.8 32.3 + - - -
129A PHE 3.5 23.6 - - - +
162A THR* 5.6 0.4 - - - -
279A TRP* 3.7 20.4 - - + -
282A LEU* 3.7 26.5 - - + -
286A LEU* 3.8 22.4 - - + -
290A PHE* 5.2 3.8 - - + -
291A TYR* 3.8 22.0 - - + +
318A ARG* 3.2 13.2 + - - -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.4 14.6 - - - -
86A THR* 4.0 11.9 - - - -
121A ALA 2.9 20.3 + - - -
122A MSE 3.4 7.9 + - - -
124A ILE* 1.3 81.1 - - - +
126A THR* 1.3 62.7 + - - -
129A PHE* 3.0 19.4 + - - +
279A TRP* 4.3 1.1 - - - -
318A ARG* 3.6 8.3 - - - -
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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
----------------------------------------------------------
40A ASN* 3.5 10.3 + - - +
42A LYS* 6.3 0.2 - - - -
63A ILE* 3.5 24.1 - - + +
64A ASP* 2.5 33.5 + - - -
86A THR* 3.5 12.1 - - - -
87A GLY* 4.3 4.0 + - - -
125A GLY* 1.3 71.5 - - - -
127A ALA* 1.3 54.5 - - - +
129A PHE* 3.8 5.9 - - - +
130A THR* 2.7 37.4 + - - -
267A SER* 3.6 24.5 - - - +
330A NAP 3.6 19.1 - - + -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN* 3.0 16.9 + - - +
125A GLY 3.2 0.8 - - - -
126A THR* 1.3 77.9 - - - +
128A GLY* 1.3 58.7 + - - +
130A THR 3.4 0.3 + - - -
131A ALA* 3.0 22.0 + - - +
158A GLY* 3.6 28.0 - - - -
159A VAL* 3.4 28.4 - - + +
162A THR* 4.6 0.2 - - - -
318A ARG* 3.6 20.0 - - - +
330A NAP 4.3 6.7 - - - +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 2.8 34.5 + - - -
127A ALA* 1.3 71.5 - - - +
129A PHE* 1.3 66.2 + - - +
131A ALA* 3.2 2.8 + - - +
132A MSE 3.0 22.9 + - - +
162A THR* 3.6 26.1 + - - -
282A LEU* 3.7 5.5 - - - +
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 4.1 11.2 - - - +
124A ILE* 3.5 2.4 - - - +
125A GLY 3.0 18.7 + - - +
126A THR* 3.8 4.9 - - - +
128A GLY* 1.3 74.8 - - - +
130A THR* 1.3 58.8 + - - +
132A MSE 3.2 5.0 + - - +
133A LEU* 3.0 51.8 + - + +
267A SER* 3.7 29.2 - - - -
270A THR* 3.7 7.2 - - + -
275A ARG* 3.7 38.6 - - + -
278A ALA* 3.7 24.7 - - + -
279A TRP* 3.5 39.7 - + + -
282A LEU* 4.0 8.3 - - + -
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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 THR 2.7 22.5 + - - -
127A ALA 3.4 4.9 - - - -
129A PHE* 1.3 73.7 - - - +
131A ALA* 1.3 66.1 + - - +
133A LEU* 3.2 12.0 + - - +
134A CYS* 2.9 21.3 + - - -
159A VAL* 4.2 2.5 - - + -
240A CYS* 3.7 37.7 - - + -
265A VAL* 4.3 9.2 - - + -
267A SER* 3.2 11.5 - - - -
330A NAP 3.1 33.2 - - + -
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Residues in contact with ALA 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 ALA 3.0 11.1 + - - +
128A GLY 3.2 8.2 + - - +
130A THR* 1.3 75.0 - - - +
132A MSE 1.3 57.8 + - - +
134A CYS* 3.1 7.3 + - - +
135A VAL* 2.9 32.4 + - - +
159A VAL* 3.5 32.3 - - + +
162A THR* 3.7 12.1 - - + -
163A ALA* 3.7 19.7 - - + +
166A LEU* 4.2 2.2 - - + -
216A ILE* 4.5 0.3 - - - +
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Residues in contact with MSE 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 GLY 3.0 13.1 + - - +
129A PHE 3.4 8.5 - - - +
130A THR 3.1 0.2 - - - -
131A ALA* 1.3 74.0 - - - +
133A LEU* 1.3 65.2 + - - +
135A VAL* 3.3 16.2 + - + -
136A MSE 2.9 38.7 + - + +
166A LEU* 3.9 29.1 - - + +
170A LEU* 5.2 0.2 - - + -
278A ALA* 3.6 31.2 - - + +
281A ARG* 3.6 50.7 - - + +
282A LEU* 3.8 21.5 - - + -
285A ASP* 4.3 1.8 - - - +
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Residues in contact with LEU 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 PHE* 3.0 44.4 + - + +
130A THR* 3.2 6.9 + - - +
132A MSE 1.3 75.9 - - - +
134A CYS* 1.3 58.6 - - - +
136A MSE 3.4 8.4 + - - +
137A ALA* 3.0 26.0 + - - +
265A VAL* 3.7 18.6 - - + +
266A ASP 3.9 11.7 - - - +
267A SER* 4.1 6.3 - - - -
270A THR* 3.6 22.0 - - + +
274A ARG* 4.1 35.3 + - + +
278A ALA* 4.1 17.9 - - + -
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Residues in contact with CYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR 2.9 18.3 + - - -
131A ALA* 3.1 8.7 + - - +
133A LEU* 1.3 72.7 - - - +
135A VAL* 1.3 67.8 + - - +
137A ALA* 3.2 4.7 + - - +
138A LEU* 3.1 24.1 + - - +
159A VAL* 5.2 0.2 - - - -
216A ILE* 3.8 31.0 - - + -
238A ALA* 3.7 21.2 - - + +
240A CYS* 4.0 25.1 - - - -
265A VAL* 3.9 20.6 - - - -
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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 ALA 2.9 18.3 + - - +
132A MSE 3.3 20.6 + - + +
134A CYS* 1.3 76.4 - - - +
136A MSE 1.3 63.1 + - - +
138A LEU* 3.2 9.8 + - + +
139A GLU* 3.0 31.0 + - + +
163A ALA* 4.8 1.6 - - - +
166A LEU* 4.1 22.0 - - + -
167A LEU* 4.1 18.2 - - + -
170A LEU* 3.7 27.6 - - + -
172A TYR* 5.6 2.0 - - + -
216A ILE* 3.8 18.6 - - + -
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Residues in contact with MSE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MSE 2.9 37.6 + - + +
133A LEU* 3.7 7.0 - - - +
134A CYS 3.2 0.2 - - - -
135A VAL* 1.3 75.7 - - - +
137A ALA* 1.3 57.7 + - - +
139A GLU* 3.3 16.8 + - - +
140A ASP* 2.8 34.1 + - - +
274A ARG* 3.6 42.6 - - + +
277A GLU* 3.5 40.6 - - + +
278A ALA* 3.9 30.1 - - - -
281A ARG* 4.2 7.4 - - - +
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Residues in contact with ALA 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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133A LEU 3.0 14.0 + - - +
134A CYS* 3.2 9.8 + - - +
136A MSE 1.3 73.6 - - - +
138A LEU* 1.3 66.3 + - - +
140A ASP* 3.2 13.9 + - - +
141A ALA* 3.0 21.8 + - - +
236A CYS* 4.3 4.1 - - - -
238A ALA* 4.1 12.8 - - + -
261A ARG* 4.8 1.4 + - - -
263A GLN* 3.9 29.1 - - + +
265A VAL* 4.5 3.6 - - + -
274A ARG* 4.1 2.8 - - - +
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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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134A CYS 3.1 12.8 + - - +
135A VAL* 3.5 8.1 - - + +
137A ALA* 1.3 75.0 - - - +
139A GLU* 1.3 63.6 + - + +
141A ALA* 3.0 11.0 + - - +
143A ILE* 3.0 36.3 + - + +
150A VAL* 3.9 34.3 - - + -
167A LEU* 4.4 10.8 - - + -
172A TYR* 5.3 3.6 - - + +
214A GLY* 4.2 4.0 - - - -
215A ALA 3.8 14.1 - - - +
216A ILE* 4.0 18.2 - - + -
236A CYS* 3.3 38.8 - - + +
238A ALA* 4.3 4.5 - - + +
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Residues in contact with GLU 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* 3.0 26.6 + - + +
136A MSE 3.4 15.1 - - - +
138A LEU* 1.3 73.5 - - + +
140A ASP* 1.3 61.7 + - - +
142A GLY* 2.9 21.0 + - - +
143A ILE 4.6 5.6 - - - +
170A LEU* 4.2 7.1 - - - +
172A TYR* 4.3 16.4 + - - +
281A ARG* 2.8 45.6 + - - -
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MSE 2.8 20.1 + - - +
137A ALA* 3.4 12.4 - - - +
139A GLU* 1.3 73.3 - - - +
141A ALA* 1.3 60.6 + - - +
142A GLY* 3.2 1.1 + - - -
261A ARG* 3.9 14.5 + - - +
274A ARG* 2.9 31.6 + - - -
261B ARG* 4.8 10.6 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.0 10.9 + - - +
138A LEU 3.0 10.2 + - - +
140A ASP* 1.3 76.2 - - - +
142A GLY* 1.3 60.4 + - - +
143A ILE* 3.6 8.9 + - + +
234A GLY 5.2 3.5 - - - +
236A CYS* 3.5 31.9 - - + -
261A ARG* 3.5 23.6 - - + +
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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