Contacts of the helix formed by residues 120 - 142 (chain D) in PDB entry 3QBK
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 MET 120 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.8 23.6 - - + -
38D LEU* 3.6 43.3 - - + -
85D LEU* 4.0 21.3 - - + -
90D THR 4.2 5.2 - - - -
91D ILE* 4.1 16.8 - - + -
118D VAL* 3.7 14.6 + - + +
119D THR* 1.3 72.4 - - - +
121D TRP* 1.3 62.2 + - - +
122D GLY 3.0 8.1 + - - +
123D ARG* 3.3 33.1 + - - +
124D TYR* 3.7 14.6 - - - +
234D GLU* 4.2 3.8 + - - -
241D VAL* 4.2 12.8 - - + -
245D SER* 4.3 6.1 - - - +
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Residues in contact with TRP 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LEU* 3.9 8.3 - - + -
90D THR* 3.6 31.6 - - + -
91D ILE 3.7 5.2 - - - -
92D SER* 2.9 30.4 + - - -
119D THR* 3.2 25.9 + - + +
120D MET* 1.3 75.3 - - - +
122D GLY* 1.3 65.8 + - - +
123D ARG 3.0 1.7 + - - -
124D TYR* 3.1 24.2 + - + -
125D LEU* 3.1 36.8 + - + -
164D LEU* 3.6 27.6 - - + +
168D LEU* 3.9 22.6 - - + +
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Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D SER* 3.5 4.1 + - - -
85D LEU* 3.7 7.0 - - - -
90D THR* 2.9 44.1 + - - -
120D MET 3.0 1.6 - - - -
121D TRP* 1.3 81.7 - - - +
123D ARG* 1.3 58.2 + - - +
125D LEU* 3.8 2.7 - - - +
126D THR* 3.4 29.3 + - - +
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 3.4 17.2 - - - +
81D SER* 4.1 7.2 - - - +
82D TYR* 3.3 30.2 + - - -
85D LEU* 3.4 17.3 - - + -
120D MET* 3.3 29.3 + - - +
121D TRP 3.0 0.8 + - - -
122D GLY* 1.3 75.6 - - - +
124D TYR* 1.3 68.7 + - + +
125D LEU 3.3 0.2 + - - -
126D THR* 3.3 2.9 + - - -
127D TRP* 3.1 47.3 + - + +
245D SER* 2.7 39.1 + - - +
248D TYR* 3.4 45.8 - - - +
249D SER* 3.6 4.9 + - - -
252D ASP* 4.1 3.8 + - - -
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Residues in contact with TYR 124 (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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120D MET* 3.7 17.7 + - - +
121D TRP* 3.1 24.8 + - + +
123D ARG* 1.3 80.4 - - + +
125D LEU* 1.3 64.9 + - - +
127D TRP* 3.4 48.2 + + + +
128D ALA* 3.9 3.6 + - - +
160D CYS* 4.1 13.8 - - - +
163D GLY* 4.7 1.6 - - - -
164D LEU* 3.9 28.6 - - + +
167D ALA* 3.5 30.1 - - + -
229D TRP* 3.5 25.0 + + - -
234D GLU* 3.3 29.8 + - - +
248D TYR* 4.2 14.3 + + - -
292D RET 4.7 2.9 - - + -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D THR* 4.9 10.5 - - + -
121D TRP* 3.1 42.8 + - + +
122D GLY 3.8 4.5 - - - +
123D ARG 3.2 0.2 - - - -
124D TYR* 1.3 76.8 - - - +
126D THR* 1.3 69.9 + - + +
128D ALA* 3.3 23.5 + - + +
129D LEU* 4.3 7.9 + - + +
164D LEU* 4.2 21.7 - - + +
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Residues in contact with THR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL* 3.7 10.8 - - + +
80D ALA* 5.3 1.6 - - + -
81D SER* 2.7 46.6 + - - +
90D THR* 6.2 2.5 - - + -
122D GLY 3.4 7.6 + - - +
123D ARG 3.3 8.7 + - - -
125D LEU* 1.3 81.8 - - + +
127D TRP* 1.3 58.4 + - - +
128D ALA 3.1 0.2 - - - -
129D LEU* 2.9 18.9 + - + +
130D SER* 2.9 25.3 + - - -
401D BR 2.9 19.5 - - - +
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Residues in contact with TRP 127 (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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123D ARG* 3.1 37.4 + - + +
124D TYR* 3.4 43.5 - + + +
125D LEU 3.2 1.0 - - - -
126D THR* 1.3 71.5 + - - +
128D ALA* 1.3 54.0 + - - +
129D LEU 2.9 7.3 + - - -
130D SER* 3.4 5.2 - - - -
131D THR* 2.7 42.8 + - + -
160D CYS* 3.6 19.1 - - + -
225D TYR* 3.6 28.3 - + - -
248D TYR* 3.8 19.5 - + + -
252D ASP* 4.5 5.9 + - - -
256D LYS* 4.3 2.0 - - - +
292D RET 3.6 71.5 - - + +
401D BR 3.8 13.8 - - + +
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Residues in contact with ALA 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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124D TYR 3.9 1.5 + - - +
125D LEU* 3.3 14.9 + - + +
126D THR 3.1 0.6 - - - -
127D TRP* 1.3 77.5 - - - +
129D LEU* 1.3 65.0 + - + +
132D PRO* 3.0 21.0 - - - +
157D ILE* 3.8 17.5 - - + +
160D CYS* 3.6 24.2 - - + +
161D VAL* 4.4 17.7 - - + -
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Residues in contact with LEU 129 (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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161B VAL* 6.0 6.5 - - + -
77D VAL* 3.9 21.9 - - + +
125D LEU* 4.5 9.4 - - + +
126D THR* 2.9 20.6 + - + +
127D TRP 2.9 0.4 - - - -
128D ALA* 1.3 86.9 - - + +
130D SER* 1.3 63.0 + - - +
132D PRO* 3.5 7.4 - - - +
133D MET* 3.3 21.8 + - - +
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D VAL* 4.3 10.6 - - - +
77D VAL* 4.1 15.7 - - - +
126D THR 2.9 15.4 + - - -
127D TRP* 3.4 7.1 - - - -
129D LEU* 1.3 74.9 - - - +
131D THR* 1.3 62.4 + - - +
132D PRO 3.1 1.6 - - - -
133D MET* 2.7 30.6 + - - +
134D ILE* 3.1 12.9 + - - +
256D LYS* 3.7 19.5 + - - -
292D RET 3.9 2.0 - - - +
401D BR 3.3 22.6 - - - +
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D TRP* 2.7 32.7 + - + +
130D SER* 1.3 79.5 + - - +
132D PRO* 1.3 63.3 - - - +
134D ILE* 3.2 6.6 + - - +
135D LEU* 3.1 28.1 + - - +
156D ASP* 2.4 37.2 + - - +
160D CYS* 3.6 7.1 - - - -
222D TRP* 3.4 18.4 - - + -
292D RET 3.8 38.4 - - + -
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Residues in contact with PRO 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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127D TRP 3.2 9.0 - - - +
128D ALA 3.0 23.3 - - - +
129D LEU* 3.5 7.2 - - - +
130D SER 3.4 3.4 - - - -
131D THR* 1.3 97.6 - - - +
133D MET* 1.3 67.9 + - + +
135D LEU* 3.6 6.7 + - + +
136D LEU* 3.0 26.3 + - - +
153D ILE* 4.2 23.5 - - + +
156D ASP* 3.2 14.4 - - - +
157D ILE* 3.6 15.9 - - + -
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Residues in contact with MET 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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150B PHE* 3.9 26.9 - - + -
154B THR* 5.3 3.6 - - + -
70D SER* 3.5 25.0 - - - +
73D LEU* 4.1 25.1 - - + +
74D VAL* 4.0 7.4 - - + -
77D VAL* 5.4 2.9 - - + -
129D LEU 3.3 16.4 - - - +
130D SER* 2.7 18.6 + - - +
132D PRO* 1.3 87.4 - - + +
134D ILE* 1.3 63.0 + - - +
136D LEU* 3.3 17.1 + - + +
137D ALA* 3.1 21.7 + - - +
153D ILE* 5.9 1.8 - - + -
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Residues in contact with ILE 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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74D VAL* 3.7 30.9 - - + +
130D SER 3.1 5.9 + - - +
131D THR* 3.6 11.9 - - - +
133D MET* 1.3 76.2 - - - +
135D LEU* 1.3 68.9 + - + +
137D ALA* 3.2 7.4 + - - +
138D LEU* 3.0 35.7 + - + +
218D THR* 4.7 4.7 - - + +
222D TRP* 3.9 22.0 - - + +
255D ALA 3.6 22.0 - - - +
256D LYS* 4.6 2.0 - - + -
259D PHE* 3.5 31.0 - - + -
292D RET 4.1 15.3 - - + -
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Residues in contact with LEU 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 THR 3.1 14.1 + - - +
132D PRO* 3.8 4.5 - - + +
134D ILE* 1.3 78.2 - - + +
136D LEU* 1.3 60.4 + - - +
138D LEU* 4.5 9.6 - - + -
139D GLY* 2.8 26.3 + - - -
149D LEU* 4.1 1.7 - - - +
152D ALA* 3.7 16.2 - - + +
153D ILE* 4.5 7.4 - - + +
156D ASP* 3.5 38.8 - - + +
190D VAL* 4.0 17.9 - - + -
194D LEU* 5.5 3.4 - - + -
198D TRP* 3.4 22.8 - - + -
218D THR* 5.5 1.8 - - + -
222D TRP* 3.1 30.3 - - + -
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Residues in contact with LEU 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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150B PHE* 3.7 37.5 - - + -
66D LEU* 4.5 6.3 - - + -
70D SER* 3.7 12.1 - - - +
132D PRO 3.0 18.8 + - - +
133D MET* 3.6 13.9 - - + +
134D ILE 3.3 0.2 - - - -
135D LEU* 1.3 76.4 - - - +
137D ALA* 1.3 64.8 + - - +
139D GLY* 3.9 0.2 - - - -
140D LEU* 3.0 55.4 + - + +
149D LEU* 4.5 17.3 - - + -
153D ILE* 4.5 13.7 - - + +
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Residues in contact with ALA 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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67D ILE* 4.3 7.3 - - + +
70D SER* 3.8 11.8 + - - +
71D THR* 3.5 26.7 - - - +
133D MET 3.1 9.6 + - - +
134D ILE* 3.2 11.9 - - - +
136D LEU* 1.3 80.0 - - - +
138D LEU* 1.3 63.2 + - - +
140D LEU* 3.2 6.5 + - - +
141D LEU* 2.9 23.3 + - - +
259D PHE* 4.9 1.6 - - + -
263D LEU* 3.6 16.6 - - + -
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Residues in contact with LEU 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 ILE* 3.0 26.4 + - + +
135D LEU* 3.9 5.8 - - + +
137D ALA* 1.3 78.0 - - - +
139D GLY* 1.3 64.9 + - - +
141D LEU* 3.1 8.7 + - + +
142D ALA* 3.0 23.9 + - - +
194D LEU* 3.8 23.1 - - + -
198D TRP* 4.0 11.9 - - + -
211D PHE* 4.0 20.2 - - + -
214D LEU* 3.8 37.7 - - + +
215D LYS* 5.3 0.7 - - - -
218D THR* 3.6 24.2 - - + +
259D PHE* 4.0 11.2 - - + -
263D LEU* 5.1 1.6 - - + -
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Residues in contact with GLY 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 LEU 2.8 20.9 + - - -
138D LEU* 1.3 73.6 - - - +
140D LEU* 1.3 60.7 + - - +
142D ALA 3.5 1.0 + - - -
143D GLY 3.4 2.1 + - - -
144D SER* 2.9 32.8 + - - -
149D LEU* 3.8 8.1 - - - -
198D TRP* 3.6 31.3 - - - -
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Residues in contact with LEU 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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63D ARG* 2.6 43.7 + - + +
66D LEU* 4.0 35.9 - - + -
67D ILE* 3.9 30.7 - - + -
70D SER* 4.4 2.2 - - - +
136D LEU* 3.0 50.9 + - + +
137D ALA* 3.6 3.4 - - - +
139D GLY* 1.3 73.5 - - - +
141D LEU* 1.3 66.1 + - - +
143D GLY 3.1 4.0 + - - -
144D SER 4.9 1.1 - - - +
149D LEU* 4.9 10.3 - - + -
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 5.5 0.5 + - - -
67D ILE* 4.4 9.6 - - + +
137D ALA 2.9 13.3 + - - +
138D LEU* 3.3 11.7 - - + +
140D LEU* 1.3 79.4 - - - +
142D ALA* 1.3 57.4 + - - +
143D GLY 3.2 4.0 + - - -
205D ALA* 3.8 6.8 - - - +
207D THR* 2.8 44.1 + - + +
210D ILE* 3.9 13.2 - - + -
211D PHE* 4.3 17.3 - - + -
214D LEU* 3.8 29.2 - - + -
263D LEU* 3.9 15.0 - - + -
266D TYR* 4.1 13.9 - - + -
267D LEU* 5.5 0.4 - - + -
274D VAL* 3.9 19.3 - - + +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU 3.0 13.4 + - - +
139D GLY 3.5 4.0 + - - +
140D LEU 3.3 0.2 - - - -
141D LEU* 1.3 75.7 - - - +
143D GLY* 1.3 64.6 + - - +
144D SER 3.2 0.4 - - - +
198D TRP* 3.5 42.6 - - + +
201D ASP* 3.0 25.6 - - + +
202D ALA* 3.8 15.9 - - + +
205D ALA* 3.8 4.3 - - - -
211D PHE* 3.9 6.3 - - + -
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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