Contacts of the helix formed by residues 114 - 138 (chain M) in PDB entry 1YST
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 LEU 114 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M ILE* 5.0 15.0 - - + -
73M TRP* 3.3 61.9 - - + +
94M LEU* 2.9 54.1 - - + +
95M GLU 4.2 6.5 - - - +
96M PRO* 5.7 0.2 - - + -
112M GLY 3.2 9.7 + - - +
113M GLY* 1.3 68.5 - - - +
115M TRP* 1.2 95.5 + - + +
117M ILE* 3.2 7.1 + - - +
118M ALA* 3.1 20.5 + - + +
177M TYR* 4.2 11.7 - - + -
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Residues in contact with TRP 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M PRO* 3.7 28.0 - - + +
97M PRO* 4.3 6.7 - - + -
113M GLY 2.7 5.0 + - - +
114M LEU* 1.2 92.0 - - + +
116M LEU* 1.3 70.8 + - + +
119M SER* 2.6 53.4 + - - +
161M GLY 3.1 26.9 - - - -
171M TRP* 3.9 30.1 - + + -
174M ALA* 3.1 39.5 - - + +
176M PRO* 3.6 20.2 - - + +
177M TYR* 3.5 29.5 - + - -
310M SPO 4.0 25.4 - - + -
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Residues in contact with LEU 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M PRO* 5.3 4.9 - - + -
104M SER 4.7 1.3 - - - +
105M PHE* 3.4 63.5 - - + +
107M ALA* 3.8 26.0 - - + +
113M GLY* 2.9 16.2 + - - +
115M TRP* 1.3 75.4 - - + +
117M ILE* 1.3 66.9 + - + +
119M SER* 4.0 3.3 - - - -
120M PHE* 2.9 26.9 + - - +
171M TRP* 3.8 27.4 - - + +
310M SPO 4.5 6.3 - - + +
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Residues in contact with ILE 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M MET* 4.7 6.3 - - + -
69M THR* 4.8 7.4 - - + -
73M TRP* 3.6 24.0 - - + -
113M GLY* 3.5 16.6 - - - +
114M LEU 3.2 12.8 + - - +
115M TRP 2.9 2.6 + - - -
116M LEU* 1.3 76.8 - - + +
118M ALA* 1.3 66.3 + - - +
120M PHE* 2.9 21.8 + - - +
121M PHE* 3.3 28.3 + - + -
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Residues in contact with ALA 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M MET* 4.5 11.4 - - - -
66M TRP* 3.3 18.4 - - + -
69M THR* 4.6 14.3 - - + +
70M ILE* 4.6 8.3 - - + -
73M TRP* 5.3 0.2 - - + -
114M LEU* 3.1 16.7 + - + +
115M TRP 3.0 4.6 + - - +
117M ILE* 1.3 76.1 - - - +
119M SER* 1.3 64.4 + - - +
120M PHE 2.9 1.4 + - - -
121M PHE* 2.9 13.5 + - - +
122M MET 3.1 9.9 + - - -
177M TYR* 3.9 20.9 - - + -
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Residues in contact with SER 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M TRP* 2.6 50.7 + - - -
118M ALA* 1.3 73.8 - - - +
120M PHE* 1.3 58.9 + - - -
122M MET* 3.9 3.1 - - - -
123M PHE* 3.0 24.8 + - - +
177M TYR* 2.5 27.5 + - - -
310M SPO 3.4 32.2 - - - +
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Residues in contact with PHE 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M LEU 2.9 16.7 + - - +
117M ILE* 2.9 10.9 + - - +
118M ALA 2.9 0.2 + - - -
119M SER* 1.3 77.0 - - - +
121M PHE* 1.3 101.9 + + - +
123M PHE* 3.1 24.4 + + - +
124M VAL* 3.2 24.9 + - + +
310M SPO 4.0 38.5 - - + +
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Residues in contact with PHE 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M PHE* 5.9 9.0 - + - -
62M SER* 3.9 24.9 - - - +
65M MET* 2.8 51.8 - - + -
66M TRP* 4.6 2.2 - - + -
117M ILE* 3.3 22.8 + - + -
118M ALA 2.9 5.3 + - - +
120M PHE* 1.3 104.1 - + - +
122M MET* 1.3 60.8 + - - +
124M VAL* 2.9 9.9 + - + +
125M ALA* 2.8 29.5 + - - +
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Residues in contact with MET 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M TRP* 3.3 63.7 - - + +
118M ALA 3.1 8.2 + - - +
119M SER* 4.1 4.9 - - - +
121M PHE* 1.3 77.3 - - - +
123M PHE* 1.3 63.7 + - - +
124M VAL 3.3 0.2 + - - -
125M ALA* 4.2 7.0 - - + -
126M VAL* 3.5 15.9 + - - +
157M TRP* 2.9 49.2 - - + -
177M TYR* 4.1 0.7 - - - -
307M BCL 4.7 9.9 - - + +
308M BCL 3.8 33.9 - - + -
310M SPO 3.9 15.3 - - + -
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Residues in contact with PHE 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M SER 3.0 16.5 + - - +
120M PHE* 3.2 18.2 - + - +
121M PHE 3.0 0.2 - - - -
122M MET* 1.3 79.2 - - - +
124M VAL* 1.3 67.2 + - + +
126M VAL* 4.8 0.5 - - - +
127M TRP* 3.3 54.9 + + + +
157M TRP* 4.2 9.8 - - - -
158M MET* 3.7 25.8 - - + -
162M PHE* 5.2 3.1 - + - -
310M SPO 3.6 59.5 - - + -
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Residues in contact with VAL 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M LEU* 5.1 14.4 - - + -
62M SER* 4.6 7.6 - - - +
120M PHE* 3.2 39.0 + - + +
121M PHE* 2.9 16.0 + - + +
123M PHE* 1.3 79.1 - - + +
125M ALA* 1.3 68.1 + - - +
127M TRP* 2.7 19.4 + - + -
128M SER* 2.6 26.2 + - - +
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Residues in contact with ALA 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M SER* 3.6 9.8 + - - +
62M SER* 3.9 7.2 + - - -
63M GLY* 4.0 29.4 - - - +
121M PHE 2.8 18.4 + - - +
122M MET* 3.9 9.4 - - + +
124M VAL* 1.3 71.3 - - - +
126M VAL* 1.3 61.7 + - + +
128M SER* 3.0 8.2 + - - -
129M TRP* 2.8 27.4 + - - +
308M BCL 5.2 4.5 - - + -
309M BPH 4.1 11.7 - - + -
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Residues in contact with VAL 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M MET 3.5 14.0 + - - +
123M PHE 4.8 0.2 - - - +
124M VAL 3.0 1.8 + - - -
125M ALA* 1.3 73.1 - - - +
127M TRP* 1.3 51.9 + - - +
129M TRP* 2.8 4.0 + - - +
130M TRP* 2.7 33.3 + - - +
150M PHE* 3.3 30.8 - - + -
154M ILE* 3.5 21.3 - - + -
157M TRP* 4.4 13.9 - - + +
308M BCL 3.6 49.6 - - + -
309M BPH 3.6 11.9 - - + +
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Residues in contact with TRP 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M PHE* 3.3 49.5 + + + +
124M VAL* 2.7 16.3 + - + +
126M VAL* 1.3 76.4 - - - +
128M SER* 1.3 55.6 + - - +
130M TRP* 3.2 40.7 + + + +
131M GLY* 3.1 19.8 + - - -
151M LEU* 4.5 18.2 - - + -
154M ILE* 3.1 35.7 - - + +
157M TRP* 5.0 2.0 - - - -
158M MET* 3.9 18.0 - - + +
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Residues in contact with SER 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LEU* 4.0 14.3 - - - +
58M LEU* 4.1 24.3 - - - +
59M SER* 3.2 20.5 + - - -
124M VAL* 2.6 39.3 + - - +
125M ALA* 3.0 9.5 + - - -
127M TRP* 1.3 72.9 - - - +
129M TRP* 1.3 57.1 + - - +
130M TRP 3.2 0.2 - - - -
131M GLY* 3.1 13.9 + - - +
132M ARG* 3.3 11.6 + - - +
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Residues in contact with TRP 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219L LEU* 4.2 16.7 - - + +
220L VAL* 5.6 2.9 - - + -
56M GLY* 5.0 2.9 - - - -
59M SER* 3.5 24.2 + - - -
60M LEU* 5.1 12.6 - - + -
125M ALA 2.8 6.0 + - - +
126M VAL 2.8 7.9 + - - +
128M SER* 1.3 74.1 - - - +
130M TRP* 1.3 61.8 + - - +
131M GLY 3.0 0.9 - - - -
132M ARG* 3.5 55.3 + - + +
133M THR* 2.8 18.4 + - - -
150M PHE* 5.0 4.3 - + + -
309M BPH 2.9 89.7 + + + +
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Residues in contact with TRP 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M VAL 2.7 11.3 + - - +
127M TRP* 3.2 43.3 - + + +
129M TRP* 1.3 76.4 - - - +
131M GLY* 1.3 75.6 + - - +
133M THR* 2.9 16.7 + - - -
134M TYR* 3.5 38.7 + + + +
147M ALA* 3.7 25.6 + - + +
148M TRP* 3.6 28.7 - + - -
150M PHE* 3.6 29.6 - + + -
151M LEU* 4.1 22.3 - - + +
154M ILE* 4.9 4.0 - - + -
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Residues in contact with GLY 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LEU* 3.7 17.0 - - - -
127M TRP 3.1 12.3 + - - -
128M SER* 3.1 7.8 + - - -
129M TRP 3.0 1.0 - - - -
130M TRP* 1.3 89.8 - - - +
132M ARG* 1.3 67.9 + - - +
134M TYR* 3.0 14.9 + - - +
135M LEU* 3.5 7.3 + - - +
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Residues in contact with ARG 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L ASP 4.3 4.6 + - - -
219L LEU* 2.9 55.4 + - + +
50M ILE* 5.8 2.4 - - - +
51M TYR 3.8 25.2 + - - +
52M LEU* 4.8 11.5 - - - +
53M GLY 5.0 1.0 - - - +
55M LEU* 3.7 16.7 - - + +
56M GLY* 3.9 26.7 - - - -
128M SER 3.3 8.8 + - - +
129M TRP* 3.5 54.2 - - - +
131M GLY* 1.3 73.1 - - - +
133M THR* 1.3 54.1 + - - +
134M TYR 2.6 14.0 + - - -
135M LEU* 2.9 2.9 + - - +
136M ARG* 2.8 35.7 + - + +
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Residues in contact with THR 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L PHE* 4.3 4.1 - - + -
219L LEU* 4.2 23.1 - - + +
129M TRP* 2.8 21.5 + - - -
130M TRP* 2.9 13.7 + - - -
132M ARG* 1.3 72.2 - - - +
134M TYR* 1.3 55.1 + - - +
136M ARG* 4.7 2.0 - - - -
137M ALA* 3.1 24.2 + - - +
146M THR* 3.9 36.7 - - - +
147M ALA* 3.9 17.4 - - - +
150M PHE* 5.4 3.8 - - + -
309M BPH 4.2 13.5 - - + +
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Residues in contact with TYR 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L GLU* 5.1 3.8 - - - -
130M TRP* 3.5 39.3 - + + +
131M GLY 3.0 9.3 + - - +
132M ARG 2.6 7.3 + - - -
133M THR* 1.3 73.2 - - - +
135M LEU* 1.3 74.0 + - + +
136M ARG 3.2 0.7 - - - -
137M ALA* 3.0 5.3 + - + +
138M GLN* 2.8 37.8 + - + +
143M GLY 5.5 0.9 - - - -
144M LYS* 3.4 45.2 - - + +
147M ALA* 4.5 9.0 - - + -
148M TRP* 4.9 11.1 - + - -
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Residues in contact with LEU 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LEU* 3.5 44.0 - - + -
131M GLY* 3.5 11.6 + - - +
132M ARG* 2.9 3.4 + - - +
134M TYR* 1.3 87.0 - - + +
136M ARG* 1.3 72.1 + - - +
138M GLN* 3.1 23.0 + - - +
139M ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L PHE* 3.9 23.8 - - + -
218L ASP* 3.5 50.5 + - + +
219L LEU* 4.6 8.7 - - + -
24M VAL* 4.8 2.6 - - - +
25M ASN 5.5 0.2 - - - +
51M TYR* 3.3 44.7 + - - -
53M GLY* 6.1 0.4 - - - -
55M LEU* 5.8 5.7 - - - +
132M ARG* 2.8 25.8 + - + +
135M LEU* 1.3 93.3 + - - +
137M ALA* 1.3 59.6 + - - +
139M ALA* 3.8 30.6 - - - +
140M MET* 4.2 10.4 - - + +
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Residues in contact with ALA 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L PHE* 4.2 7.2 - - + -
133M THR 3.1 21.4 + - - +
134M TYR* 3.0 9.4 + - + +
136M ARG* 1.3 78.6 - - - +
138M GLN* 1.3 58.7 + - - +
139M ALA 3.4 0.4 + - - -
140M MET 3.7 0.7 + - - -
141M GLY 2.5 35.6 + - - +
142M MET* 3.5 31.5 - - + +
143M GLY 4.4 5.6 - - - +
144M LYS* 4.8 5.2 - - - +
146M THR* 4.6 5.6 - - + -
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Residues in contact with GLN 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L GLU* 4.9 19.0 + - + +
23M ASP* 5.0 4.2 - - - +
134M TYR* 2.8 28.7 + - + +
135M LEU* 3.4 25.3 - - - +
137M ALA* 1.3 74.1 - - - +
139M ALA* 1.3 55.9 + - - +
140M MET* 2.9 16.5 + - - -
141M GLY* 4.2 4.1 + - - -
143M GLY 5.6 1.1 - - - -
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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
------------------------------------------------------------
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