Contacts of the helix formed by residues 118 - 150 (chain M) in PDB entry 1NF6
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 ASP 118 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LYS* 5.9 0.9 - - - +
12M VAL* 3.5 26.9 - - + +
66M ARG* 3.1 18.4 + - - -
70M LEU* 3.9 10.3 - - - +
113M CYS* 2.7 21.2 + - - +
114M LYS* 4.7 0.4 - - - +
116M GLN 4.5 2.9 - - - +
117M GLY* 1.3 70.1 - - - +
119M ILE* 1.3 61.7 + - - +
120M VAL* 3.5 2.6 + - - +
121M THR* 2.6 39.5 + - - -
122M ALA* 3.1 22.3 + - - +
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Residues in contact with ILE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M LYS* 5.4 15.3 - - + +
117M GLY* 3.7 10.3 + - - +
118M ASP* 1.3 74.8 - - - +
120M VAL* 1.3 64.5 + - + +
122M ALA* 3.3 5.1 + - + +
123M ARG* 2.9 41.4 + - + +
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Residues in contact with VAL 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ARG* 3.5 37.9 - - - +
69M GLU* 5.0 2.2 - - - +
118M ASP* 3.3 0.8 + - - +
119M ILE* 1.3 79.2 - - + +
121M THR* 1.3 62.0 + - - +
123M ARG* 3.4 7.5 + - - +
124M LEU* 3.2 19.6 + - - +
127M ARG* 5.4 0.5 + - - -
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Residues in contact with THR 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M VAL* 3.6 19.8 - - + +
16M LEU* 3.6 31.0 - - + -
66M ARG* 3.1 21.8 + - + +
70M LEU* 4.3 0.3 - - - +
113M CYS* 3.6 12.6 - - - -
118M ASP* 2.6 35.1 + - - -
120M VAL* 1.3 73.7 - - - +
122M ALA* 1.3 68.3 + - - +
124M LEU* 3.2 8.4 + - + +
125M PHE* 3.1 22.7 + - + -
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Residues in contact with ALA 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M LEU* 3.8 24.1 - - + +
113M CYS* 3.8 17.8 - - + +
114M LYS* 4.2 11.4 - - + -
118M ASP 3.1 17.8 + - - +
119M ILE* 3.3 7.8 + - + +
121M THR* 1.3 77.6 - - - +
123M ARG* 1.3 64.3 + - + +
125M PHE* 3.2 4.3 + - - +
126M GLU* 2.9 30.7 + - - +
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Residues in contact with ARG 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M ILE* 2.9 33.5 + - + +
120M VAL* 3.8 7.2 - - - +
122M ALA* 1.3 76.2 - - + +
124M LEU* 1.3 57.7 + - - +
126M GLU* 2.5 55.7 + - - +
127M ARG* 2.9 81.2 + - - +
130M GLU* 5.9 0.8 + - - -
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Residues in contact with LEU 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LEU* 4.4 5.6 - - + -
62M ASN* 4.0 24.2 - - + +
63M PHE* 4.1 21.5 - - + -
66M ARG* 3.9 32.1 - - + -
120M VAL 3.2 10.6 + - - +
121M THR* 3.2 9.6 + - + +
123M ARG* 1.3 77.5 - - - +
125M PHE* 1.3 57.5 + - + +
127M ARG* 3.3 15.6 + - + +
128M ILE* 2.9 50.4 + - + +
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Residues in contact with PHE 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M VAL* 4.1 6.3 - - + -
16M LEU* 3.6 32.5 - - + -
19M ALA* 3.7 24.7 - - + -
63M PHE* 3.6 20.4 - + - -
106M TYR* 4.0 29.4 - + + +
109M PHE* 3.8 23.3 - + + -
110M LEU* 4.1 20.4 - - + -
113M CYS* 3.9 24.0 - - - -
121M THR* 3.1 22.2 + - + -
122M ALA 3.7 6.1 - - - +
124M LEU* 1.3 73.6 - - + +
126M GLU* 1.3 61.1 + - - +
128M ILE* 3.8 3.5 - - - +
129M ILE* 2.9 37.8 + - + +
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Residues in contact with GLU 126 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M LEU* 3.3 33.1 - - + +
114M LYS* 4.2 10.6 + - - -
122M ALA* 2.9 20.9 + - - +
123M ARG* 2.5 51.7 + - - +
125M PHE* 1.3 78.6 - - - +
127M ARG* 1.3 62.1 + - - +
129M ILE* 3.3 6.3 + - - +
130M GLU* 3.3 28.2 + - - +
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Residues in contact with ARG 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M VAL 5.4 0.4 + - - -
123M ARG* 2.9 66.7 + - - +
124M LEU* 3.6 14.8 - - + +
126M GLU* 1.3 78.0 - - - +
128M ILE* 1.3 63.6 + - + +
130M GLU* 3.3 21.0 + - - +
131M GLU* 3.4 19.4 + - - +
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Residues in contact with ILE 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M HIS* 3.7 48.2 - - + +
62M ASN* 4.6 6.7 - - + +
63M PHE* 3.5 34.1 - - + -
106M TYR* 3.6 31.0 - - + -
124M LEU* 2.9 34.7 + - + +
125M PHE* 4.2 3.1 - - - +
127M ARG* 1.3 76.7 - - + +
129M ILE* 1.3 60.9 + - - +
131M GLU* 3.4 6.1 + - - +
132M GLU* 2.9 26.4 + - + +
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Residues in contact with ILE 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M ILE* 4.4 23.0 - - + +
106M TYR* 3.8 38.6 - - + +
107M SER* 4.1 12.1 - - - +
110M LEU* 3.8 24.7 - - + -
125M PHE 2.9 26.2 + - - +
126M GLU* 3.5 7.0 - - - +
127M ARG 3.2 0.2 - - - -
128M ILE* 1.3 79.1 - - - +
130M GLU* 1.3 61.6 + - + +
132M GLU* 3.3 9.0 + - - +
133M GLN* 2.9 27.6 + - + +
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Residues in contact with GLU 130 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M ARG* 5.9 0.9 + - - -
126M GLU* 3.5 15.3 - - - +
127M ARG* 3.3 15.0 + - - +
128M ILE 3.3 0.4 - - - -
129M ILE* 1.3 82.6 - - + +
131M GLU* 1.3 61.4 + - + +
133M GLN* 3.3 10.1 + - - +
134M ALA* 3.1 19.6 + - - +
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Residues in contact with GLU 131 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M ASP* 4.8 1.2 - - - +
58M ARG* 2.7 24.6 + - - -
59M HIS* 2.7 36.9 + - + +
127M ARG* 3.6 15.6 - - - +
128M ILE* 3.4 6.7 + - - +
129M ILE 3.3 0.6 - - - -
130M GLU* 1.3 75.1 - - + +
132M GLU* 1.3 67.4 + - - +
134M ALA* 3.1 5.9 + - - +
135M HIS* 3.0 26.1 + - + -
172N VAL* 3.8 34.6 - - + +
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Residues in contact with GLU 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M GLU* 3.5 17.1 - - - +
56M GLU* 3.3 7.3 - - - +
59M HIS* 3.4 4.9 - - - -
99M GLU* 3.3 13.0 - - - +
102M THR* 3.1 26.3 - - + +
103M ILE* 3.7 19.6 - - + +
106M TYR* 4.1 17.9 - - + -
128M ILE* 2.9 22.8 + - + +
129M ILE* 3.5 6.1 - - - +
131M GLU* 1.3 76.0 - - - +
133M GLN* 1.3 56.9 + - - +
135M HIS* 3.1 7.1 + - - +
136M LEU* 2.9 28.9 + - - +
200M FE 1.9 33.4 - - - -
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Residues in contact with GLN 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M ILE* 4.0 19.3 - - + +
129M ILE* 2.9 15.6 + - + +
130M GLU* 3.3 13.7 - - - +
131M GLU 3.1 0.2 - - - -
132M GLU* 1.3 74.0 - - - +
134M ALA* 1.3 65.3 + - - +
136M LEU* 3.3 20.2 + - - +
137M THR* 3.0 38.2 + - - +
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Residues in contact with ALA 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M GLU 3.1 11.0 + - - +
131M GLU* 3.1 9.7 + - - +
133M GLN* 1.3 76.0 - - - +
135M HIS* 1.3 64.1 + - + +
137M THR* 3.4 7.2 + - - -
138M TYR* 3.1 22.9 + - - +
171N PHE* 4.3 10.2 - - + -
172N VAL* 4.1 19.3 - - + -
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Residues in contact with HIS 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M ILE* 3.7 29.1 - - + +
55M ASP* 2.6 40.3 + - + +
56M GLU* 3.2 18.0 + - - -
59M HIS* 4.2 4.9 - + - -
99M GLU* 3.1 20.2 - - + +
131M GLU 3.0 14.9 + - - -
132M GLU* 3.1 7.7 + - - +
134M ALA* 1.3 76.0 - - - +
136M LEU* 1.3 54.3 + - - +
138M TYR* 3.3 7.6 + - - +
139M TYR* 3.1 36.2 + - + -
200M FE 2.1 28.9 - - - -
171N PHE* 3.9 11.2 - + - -
172N VAL* 3.8 6.8 - - + +
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Residues in contact with LEU 136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ALA* 3.3 28.9 - - + +
99M GLU* 3.8 15.1 - - + +
100M ASP* 4.5 18.2 - - + +
103M ILE* 3.8 20.6 - - + -
132M GLU 2.9 15.9 + - - +
133M GLN* 3.6 20.6 - - - +
135M HIS* 1.3 72.2 - - - +
137M THR* 1.3 60.8 + - - +
139M TYR* 3.5 3.0 + - - +
140M GLU* 3.0 53.9 + - + +
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Residues in contact with THR 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M GLN* 3.0 31.7 + - - +
134M ALA* 3.7 7.4 - - - -
135M HIS 3.3 0.2 - - - -
136M LEU* 1.3 75.2 - - - +
138M TYR* 1.3 65.6 + - - +
140M GLU* 3.3 10.2 + - - +
141M ASN* 2.9 45.0 + - - +
----------------------------------------------------------
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Residues in contact with TYR 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M LEU* 3.8 21.0 + - - +
48M ASN* 3.3 40.2 + - + +
49M MET* 5.2 1.6 - - - -
52M ILE* 3.6 24.7 - - + -
92M TYR* 4.2 5.6 + + - -
134M ALA 3.1 13.4 + - - +
135M HIS* 3.5 7.6 - - - +
137M THR* 1.3 77.1 - - - +
139M TYR* 1.3 76.0 + + - +
141M ASN* 3.0 25.8 + - + +
142M ILE* 3.1 46.8 + - + +
171N PHE* 3.7 28.0 - + + -
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Residues in contact with TYR 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M TYR* 3.6 14.3 - + - -
49M MET* 3.2 31.9 - - + -
52M ILE* 3.3 38.8 - - + +
92M TYR* 3.7 31.6 - + - +
95M ASP* 3.6 34.5 - - + -
96M ALA* 4.0 16.4 - - + +
99M GLU* 3.6 28.5 - - + -
135M HIS* 3.1 19.0 + - + +
136M LEU 3.8 4.0 - - - +
138M TYR* 1.3 87.7 - + - +
140M GLU* 1.3 61.8 + - - +
142M ILE 3.6 0.5 + - - -
143M GLY* 3.1 19.1 + - - -
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Residues in contact with GLU 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ALA* 4.2 11.8 - - + +
136M LEU* 3.0 47.0 + - + +
137M THR* 3.6 9.7 + - - +
139M TYR* 1.3 72.8 - - - +
141M ASN* 1.3 70.7 + - - +
143M GLY* 3.6 1.1 + - - -
144M SER* 3.0 24.9 + - - -
147M LYS* 5.6 0.7 + - - -
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Residues in contact with ASN 141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M THR* 2.9 37.9 + - - +
138M TYR* 3.0 12.1 + - + +
140M GLU* 1.3 81.1 - - - +
142M ILE* 1.3 65.7 + - + +
144M SER* 3.1 8.1 + - - -
145M HIS* 3.0 37.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE 142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M LEU* 3.8 16.8 - - + -
92M TYR* 3.7 30.5 - - + -
138M TYR* 3.1 53.9 + - + +
141M ASN* 1.3 79.6 - - + +
143M GLY* 1.3 65.5 + - - +
145M HIS* 2.8 22.6 + - + +
146M ILE* 2.9 24.4 + - + +
153M TYR* 3.7 24.0 - - + +
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Residues in contact with GLY 143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M PRO* 5.7 2.7 - - - -
92M TYR* 3.8 20.6 - - - +
93M GLU 5.5 0.2 - - - -
139M TYR 3.1 12.7 + - - -
140M GLU* 3.9 1.6 - - - -
142M ILE* 1.3 79.8 - - - +
144M SER* 1.3 55.2 + - - +
146M ILE* 4.0 8.0 - - - +
147M LYS* 3.0 43.1 + - - +
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Residues in contact with SER 144 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M GLU 3.0 18.3 + - - -
141M ASN* 3.3 8.3 - - - -
142M ILE 3.0 0.8 - - - -
143M GLY* 1.3 76.1 - - - +
145M HIS* 1.3 62.8 + - - +
147M LYS* 4.3 2.6 - - - +
148M ASN* 2.6 43.9 + - - +
2303M SO4 2.6 34.0 + - - -
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Residues in contact with HIS 145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M ASN* 3.0 30.1 + - + +
142M ILE* 2.8 16.5 + - + +
144M SER* 1.3 74.3 + - - +
146M ILE* 1.3 62.4 + - - +
148M ASN* 4.5 1.6 + - - +
149M LEU* 2.7 50.9 + - + +
150M GLY 3.4 0.3 + - - -
153M TYR* 3.8 41.8 - + + +
----------------------------------------------------------
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Residues in contact with ILE 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M LEU* 5.2 0.9 - - + -
88M VAL* 3.4 33.2 - - + +
89M PRO* 4.0 30.3 - - + -
92M TYR* 3.8 22.9 - - + -
142M ILE* 2.9 25.5 + - + +
143M GLY* 4.1 6.5 - - - +
145M HIS* 1.3 78.5 - - - +
147M LYS* 1.3 59.2 + - + +
150M GLY* 2.8 36.6 + - - +
153M TYR* 4.3 16.8 - - + -
154M LEU* 4.9 11.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M PRO* 6.1 4.0 - - + -
93M GLU* 5.6 6.7 - - - +
140M GLU 5.6 1.2 + - - -
143M GLY* 3.0 37.7 + - - +
144M SER* 3.8 5.3 - - - +
146M ILE* 1.3 81.7 - - + +
148M ASN* 1.3 61.2 + - - +
150M GLY 4.8 0.5 + - - -
2303M SO4 3.2 27.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M SER* 2.6 38.9 + - - +
145M HIS* 4.9 1.5 + - - +
147M LYS* 1.3 79.4 - - - +
149M LEU* 1.3 75.5 + - + +
2303M SO4 3.1 30.5 + - - -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145M HIS* 2.7 38.8 + - + +
148M ASN* 1.3 87.4 - - + +
150M GLY* 1.3 63.4 + - - +
151M ASP 3.3 0.3 + - - -
152M THR* 2.9 30.9 + - + -
153M TYR* 3.8 26.7 - - + +
----------------------------------------------------------
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Residues in contact with GLY 150 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145M HIS 3.4 1.2 + - - -
146M ILE* 2.8 29.1 + - - -
147M LYS 4.6 0.4 + - - -
148M ASN 3.8 0.6 - - - -
149M LEU* 1.3 75.4 - - - +
151M ASP* 1.3 60.8 + - - -
153M TYR* 3.0 21.7 + - - +
154M LEU* 3.3 14.7 + - - +
----------------------------------------------------------
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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).
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