Contacts of the helix formed by residues 125 - 147 (chain D) in PDB entry 3FZ7
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 GLY 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D THR* 2.5 24.4 + - - -
124D ILE* 1.3 80.7 - - - +
126D SER* 1.3 65.4 + - - -
127D SER* 3.2 3.1 + - - -
128D GLU* 3.5 3.9 + - - +
129D ALA* 3.2 9.4 + - - +
275D HIS* 3.7 9.4 - - - -
285D GLY* 3.8 12.6 - - - -
467D PO4 3.4 14.8 - - - -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLY* 1.3 68.6 - - - -
127D SER* 1.3 63.9 + - - +
129D ALA* 4.1 7.6 - - - -
130D CYS* 2.8 38.9 + - - -
163D GLN* 6.0 0.2 - - - -
165D CYS* 4.8 2.0 - - - -
243D ASP* 4.8 1.0 + - - -
245D ALA* 3.6 17.4 - - - +
271D SER* 4.9 0.9 - - - -
272D ALA* 3.4 17.8 + - - -
273D SER* 2.7 22.6 + - - -
285D GLY* 4.4 0.8 - - - -
467D PO4 2.6 24.6 + - - -
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Residues in contact with SER 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLY* 3.2 1.3 - - - -
126D SER* 1.3 80.3 - - - +
128D GLU* 1.3 64.1 + - - +
130D CYS* 3.4 3.1 - - - +
131D MET* 3.0 33.9 + - - +
165D CYS* 3.9 21.1 - - - +
168D LYS* 4.2 6.2 + - - -
467D PO4 3.4 19.5 + - - -
315E ILE 2.7 25.0 + - - -
316E ASN* 3.9 4.4 + - - -
317E PHE* 3.8 16.4 - - - -
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Residues in contact with GLU 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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122D ASN 5.5 0.4 - - - -
123D THR* 3.2 20.6 - - + -
124D ILE 3.0 20.9 + - - +
125D GLY 3.5 4.4 + - - +
126D SER 3.3 0.2 - - - -
127D SER* 1.3 76.2 - - - +
129D ALA* 1.3 67.2 + - - +
131D MET* 3.1 12.1 + - - +
132D LEU* 2.9 29.8 + - + +
314D ALA* 3.7 6.8 - - - +
315D ILE* 2.7 40.0 + - + +
316D ASN* 2.8 33.3 + - - +
319D ARG* 4.8 2.6 + - - -
315E ILE* 4.5 4.5 + - + -
316E ASN* 4.0 14.1 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D THR* 3.6 17.7 - - + +
125D GLY 3.2 15.7 + - - +
126D SER* 3.7 6.5 - - - +
128D GLU* 1.3 77.8 - - - +
130D CYS* 1.3 56.3 + - - +
132D LEU* 3.2 5.2 + - - +
133D GLY* 2.9 24.8 + - - -
271D SER* 3.7 25.0 - - - -
286D TRP 3.8 8.1 - - - +
287D VAL* 3.8 21.4 - - + +
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Residues in contact with CYS 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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126D SER* 2.8 32.1 + - - +
127D SER 3.4 2.0 - - - +
129D ALA* 1.3 70.5 - - - +
131D MET* 1.3 57.7 + - - +
133D GLY* 3.1 1.8 + - - +
134D GLY* 2.8 33.4 + - - -
165D CYS* 3.2 33.9 - - + +
166D TRP* 3.5 39.5 - - + -
169D PHE* 4.8 0.4 - - - -
241D HIS* 4.8 1.1 - - - -
243D ASP* 3.7 10.1 - - - -
271D SER* 3.8 15.3 - - - -
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Residues in contact with MET 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D SER* 3.0 23.0 + - - +
128D GLU* 3.1 9.6 + - - +
130D CYS* 1.3 75.3 - - - +
132D LEU* 1.3 58.3 + - - +
135D MET* 2.9 35.6 + - - +
165D CYS 4.1 14.8 - - - +
168D LYS* 4.2 22.2 - - + -
169D PHE* 4.0 15.1 - - - -
172D TYR* 4.5 3.8 - - + -
173D TRP* 3.8 26.9 - - + -
315D ILE* 3.6 25.8 - - + -
315E ILE* 3.5 35.9 - - + +
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Residues in contact with LEU 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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121D THR* 3.8 10.3 - - + -
123D THR* 3.8 28.5 - - + -
128D GLU* 2.9 19.5 + - + +
129D ALA 3.5 5.4 - - - +
131D MET* 1.3 77.2 - - - +
133D GLY* 1.3 64.2 + - - +
135D MET* 3.4 10.7 + - + +
136D ALA* 3.0 20.1 + - - +
287D VAL* 4.0 3.1 - - + -
289D TRP* 4.0 8.1 - - + -
313D PHE* 3.4 74.0 - - + +
314D ALA* 4.3 2.0 - - - +
315D ILE* 4.2 16.8 - - + +
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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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129D ALA 2.9 14.1 + - - -
130D CYS 3.1 3.8 + - - -
132D LEU* 1.3 77.3 - - - +
134D GLY* 1.3 56.1 + - - +
136D ALA* 3.3 3.6 + - - +
137D MET* 2.9 34.8 + - - +
140D ARG* 5.1 0.3 + - - -
241D HIS* 3.9 22.0 - - - -
269D SER* 4.4 6.2 + - - -
287D VAL* 4.6 0.2 - - - -
289D TRP* 4.2 12.9 - - - -
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Residues in contact with GLY 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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130D CYS 2.8 16.6 + - - -
133D GLY* 1.3 73.2 - - - +
135D MET* 1.3 59.7 + - - +
137D MET* 3.2 20.4 + - - +
138D LYS* 2.9 25.5 + - - +
166D TRP* 4.2 2.5 - - - -
169D PHE* 3.2 31.6 - - - -
203D ILE* 4.2 0.5 - - - +
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Residues in contact with MET 135 (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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131D MET 2.9 22.7 + - - +
132D LEU* 3.7 15.5 - - + +
134D GLY* 1.3 75.7 - - - +
136D ALA* 1.3 63.3 + - - +
138D LYS* 3.0 4.7 + - - +
139D TRP* 2.9 36.3 + - + -
169D PHE* 3.5 2.8 - - - -
173D TRP* 3.4 44.2 - - + +
299D LEU* 4.1 7.4 - - + -
313D PHE* 4.0 21.1 - - + -
315D ILE* 4.1 7.6 - - + -
172E TYR* 3.5 52.3 - - + +
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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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132D LEU 3.0 12.7 + - - +
133D GLY 3.7 4.7 - - - +
135D MET* 1.3 76.2 - - - +
137D MET* 1.3 59.0 + - - +
139D TRP* 3.2 1.9 + - - +
140D ARG* 2.8 41.2 + - - +
289D TRP* 3.5 30.5 - - + +
295D LEU* 4.2 7.0 - - + -
296D PRO* 3.9 18.3 - - + +
299D LEU* 3.9 11.1 - - + +
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Residues in contact with MET 137 (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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133D GLY 2.9 10.3 + - - +
134D GLY* 3.4 24.7 - - - +
135D MET 3.2 0.2 - - - -
136D ALA* 1.3 75.0 - - - +
138D LYS* 1.3 56.7 + - - +
140D ARG* 3.0 30.1 + - - +
141D TRP* 2.9 31.0 + - - +
157D LEU* 3.9 15.3 - - + -
166D TRP* 4.2 4.3 - - + -
203D ILE* 4.0 16.6 - - + +
204D GLY* 3.8 28.3 - - - -
206D VAL* 3.7 17.0 - - + -
239D ASP* 5.1 0.7 - - + +
240D MET 4.8 1.1 - - - -
241D HIS* 3.4 37.9 - - + -
269D SER* 5.5 0.4 - - - +
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Residues in contact with LYS 138 (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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134D GLY 2.9 17.0 + - - +
135D MET* 3.5 5.4 - - - +
137D MET* 1.3 75.7 - - - +
139D TRP* 1.3 70.1 + - + +
141D TRP* 3.4 2.9 + - + +
142D ARG* 2.9 66.6 + - + +
152D THR 6.0 0.7 - - - -
155D PRO* 4.4 12.6 - - - -
169D PHE* 4.9 0.9 - - + -
173D TRP* 2.7 41.8 + - + +
174D ASP* 4.5 4.2 + - - +
175D VAL* 4.0 18.4 - - + -
203D ILE* 4.1 24.5 - - + -
174E ASP* 4.4 6.1 + - - -
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Residues in contact with TRP 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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135D MET* 2.9 48.3 + - + +
138D LYS* 1.3 89.1 - - + +
140D ARG* 1.3 67.1 + - - +
142D ARG* 3.3 39.7 + - + +
143D LYS* 3.0 30.3 + - + +
173D TRP* 4.8 2.2 - + - -
296D PRO* 3.6 19.7 - - + -
298D GLU* 4.0 27.9 - - + +
299D LEU* 3.6 32.5 - - + +
171E ARG* 3.4 31.8 - - + +
172E TYR 3.8 15.9 - - - -
174E ASP* 3.6 8.5 - - - -
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Residues in contact with ARG 140 (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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136D ALA* 2.8 33.4 + - - +
137D MET* 3.3 34.9 + - - +
139D TRP* 1.3 72.7 - - - +
141D TRP* 1.3 63.9 + - - +
143D LYS* 3.3 7.9 + - + +
144D ARG* 3.1 22.5 + - - +
203D ILE 5.3 0.8 + - - -
239D ASP* 4.2 18.2 + - - +
240D MET 4.9 2.0 + - - -
268D LYS* 3.6 38.3 - - - +
269D SER* 4.7 4.8 + - - -
289D TRP* 4.2 6.5 - - - +
293D GLU 4.2 5.8 - - - +
294D ALA* 2.9 36.4 + - - +
296D PRO* 4.1 15.5 - - + -
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Residues in contact with TRP 141 (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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137D MET 2.9 16.0 + - - +
138D LYS* 3.7 5.2 - - + +
140D ARG* 1.3 76.8 - - - +
142D ARG* 1.3 93.0 + - + +
144D ARG* 3.0 28.9 + - - +
145D MET* 3.0 40.5 + - + +
152D THR* 3.4 39.3 - - - -
154D LYS 4.6 0.4 - - - -
155D PRO* 3.5 25.4 - - + -
200D GLU 3.0 19.3 + - - -
201D ASN* 3.6 35.2 - - - -
202D THR 3.5 17.7 - - - -
203D ILE* 3.7 28.7 - - + +
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Residues in contact with ARG 142 (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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138D LYS* 2.9 49.3 + - + +
139D TRP* 3.3 41.3 + - + +
141D TRP* 1.3 97.0 - - + +
143D LYS* 1.3 62.3 + - + +
145D MET* 3.2 1.9 + - - +
146D GLU* 3.0 42.5 + - - +
152D THR* 4.0 26.4 - - + +
174E ASP* 2.9 41.8 + - - -
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Residues in contact with LYS 143 (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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139D TRP* 3.0 24.1 + - + +
140D ARG* 3.7 7.2 - - + +
142D ARG* 1.3 76.2 - - + +
144D ARG* 1.3 58.7 + - - +
146D GLU* 3.5 15.4 + - - +
147D ALA* 3.1 30.1 + - - +
296D PRO* 4.1 17.5 - - + +
297D GLN 4.9 0.4 - - - +
298D GLU* 3.1 40.2 + - - -
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Residues in contact with ARG 144 (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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140D ARG 3.1 11.9 + - - +
141D TRP* 3.0 29.9 + - - +
143D LYS* 1.3 74.5 - - - +
145D MET* 1.3 84.9 + - - +
147D ALA* 4.0 5.4 + - - +
148D ALA* 3.5 22.3 + - - +
200D GLU* 3.9 12.3 + - - +
202D THR 4.4 7.3 + - - -
203D ILE 5.9 0.8 + - - -
236D ILE* 4.6 14.3 - - - +
237D ASP* 2.9 40.1 + - - +
238D ILE* 4.7 2.0 - - - +
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TRP* 3.0 32.9 + - + +
142D ARG 3.8 1.3 - - - +
144D ARG* 1.3 100.1 - - - +
146D GLU* 1.3 66.0 + - - +
148D ALA* 3.0 6.8 + - - +
149D GLY 3.0 5.0 + - - -
150D LYS* 2.9 53.7 + - + +
151D PRO* 3.8 17.0 - - + +
152D THR* 3.7 19.5 - - + -
200D GLU* 3.2 31.4 - - + +
201D ASN* 4.0 11.4 - - - +
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Residues in contact with GLU 146 (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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142D ARG* 3.0 39.6 + - - +
143D LYS* 3.8 16.4 - - - +
145D MET* 1.3 73.5 - - - +
147D ALA* 1.3 58.5 + - - +
149D GLY* 2.9 21.9 + - - +
150D LYS 4.5 4.5 + - - +
152D THR* 4.5 13.8 + - + +
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Residues in contact with ALA 147 (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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143D LYS 3.1 18.1 + - - +
144D ARG* 4.1 5.8 - - - +
145D MET 3.4 0.2 - - - -
146D GLU* 1.3 74.0 - - - +
148D ALA* 1.3 56.6 + - - +
149D GLY 3.5 0.2 - - - -
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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