Contacts of the helix formed by residues 133 - 158 (chain A) in PDB entry 4JR8
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 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY* 4.0 2.9 - - - -
131A VAL 4.3 0.2 + - - -
132A LEU* 1.3 80.8 - - - +
134A ALA* 1.3 63.9 + - - +
135A GLY* 3.9 3.0 + - - -
136A ALA* 3.4 22.6 + - - +
137A GLU* 3.0 19.6 + - - +
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Residues in contact with ALA 134 (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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69A ILE* 3.6 31.2 - - + -
70A ALA* 4.6 14.8 - - + +
127A ALA* 3.5 15.0 - - - -
128A GLY* 3.5 21.4 - - - +
133A SER* 1.3 72.4 - - - +
135A GLY* 1.3 59.6 + - - +
137A GLU* 3.1 3.6 + - - +
138A ARG* 2.8 36.1 + - - +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 3.4 3.9 + - - -
134A ALA* 1.3 79.4 - - - +
136A ALA* 1.3 60.1 + - - +
138A ARG* 3.4 9.5 + - - +
139A LEU* 3.0 32.4 + - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.3 23.4 - - + +
133A SER* 3.4 21.2 + - - +
134A ALA 3.3 0.4 - - - -
135A GLY* 1.3 74.9 - - - +
137A GLU* 1.3 63.3 + - - +
139A LEU* 3.3 8.5 + - - +
140A VAL* 3.0 24.5 + - - +
302A 22B 4.6 12.3 - - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 3.5 23.7 - - - +
127A ALA 2.4 28.5 - - - +
128A GLY* 4.2 3.5 - - - -
129A SER 4.3 9.8 - - - +
130A GLY* 5.4 1.0 - - - -
132A LEU* 3.8 23.7 + - + +
133A SER 3.0 15.7 + - - +
134A ALA 3.3 4.0 - - - +
136A ALA* 1.3 77.6 - - - +
138A ARG* 1.3 60.9 + - - +
140A VAL* 2.7 28.7 - - + +
141A TRP* 3.1 26.3 + - + +
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Residues in contact with ARG 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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69A ILE* 3.4 36.2 - - - +
74A ARG* 4.3 5.2 - - - +
76A ILE* 4.3 2.2 - - - +
123A ALA* 3.2 27.3 + - - +
124A THR* 3.1 31.1 + - - +
125A LEU 4.1 0.6 - - - -
126A SER* 2.8 42.3 + - - +
134A ALA 2.8 25.1 + - - +
135A GLY* 3.7 8.3 - - - +
137A GLU* 1.3 75.1 - - - +
139A LEU* 1.3 60.3 + - + +
142A TRP* 2.9 29.0 + - - +
193A TRP* 4.2 9.4 - - + -
198A GLU* 2.8 44.8 + - - +
199A GLY* 5.1 2.6 + - - -
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Residues in contact with LEU 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 GLY 3.0 22.0 + - - +
136A ALA* 3.7 6.5 - - - +
137A GLU 3.2 0.2 - - - -
138A ARG* 1.3 76.7 - - + +
140A VAL* 1.3 60.7 + - - +
142A TRP* 3.5 14.3 - - + +
143A GLY* 2.8 26.7 + - - -
193A TRP* 5.6 1.6 - - + -
194A LEU* 3.8 29.4 - - + -
200A ILE* 6.2 1.1 - - + -
302A 22B 3.8 29.0 - - + +
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Residues in contact with VAL 140 (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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132A LEU* 4.8 11.7 - - + -
136A ALA 3.0 14.0 + - - +
137A GLU* 2.7 32.1 - - + +
139A LEU* 1.3 76.2 - - - +
141A TRP* 1.3 78.2 + - + +
143A GLY* 3.2 2.4 + - - -
144A ILE* 3.0 24.7 + - + +
302A 22B 4.0 27.6 - - + +
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Residues in contact with TRP 141 (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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119A THR* 3.8 29.5 - - + +
122A VAL* 3.4 36.4 - - + +
123A ALA* 3.4 24.2 - - + +
126A SER* 4.0 4.9 - - - -
137A GLU* 3.1 44.9 + - + +
140A VAL* 1.3 88.8 - - + +
142A TRP* 1.3 58.8 + - - +
144A ILE* 2.8 42.1 - - + +
145A SER* 2.8 17.8 + - - -
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Residues in contact with TRP 142 (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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123A ALA* 3.8 3.3 - - - +
138A ARG 2.9 19.0 + - - +
139A LEU* 3.5 18.6 - - + +
141A TRP* 1.3 75.9 - - - +
143A GLY* 1.3 77.3 + - - +
145A SER* 3.3 6.5 + - - -
146A THR* 2.8 53.5 + - + -
190A PRO* 2.9 34.5 + - + +
191A VAL* 5.0 7.2 - - + -
193A TRP* 3.4 26.6 - + + -
194A LEU* 4.0 28.8 - - + +
301A RET 3.3 27.3 - + - -
302A 22B 5.8 2.5 - - + -
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Residues in contact with GLY 143 (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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139A LEU 2.8 15.1 + - - -
140A VAL 3.6 4.3 - - - -
141A TRP 3.2 0.2 - - - -
142A TRP* 1.3 92.1 - - - +
144A ILE* 1.3 56.5 + - - +
146A THR* 3.3 3.8 + - - -
147A ALA* 2.9 26.9 + - - +
302A 22B 3.7 23.3 - - - +
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Residues in contact with ILE 144 (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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119A THR* 3.8 14.6 - - + -
140A VAL* 3.0 18.2 + - + +
141A TRP* 2.8 47.3 - - + +
143A GLY* 1.3 74.0 - - - +
145A SER* 1.3 61.7 + - - +
147A ALA* 3.2 5.8 + - - +
148A PHE* 3.1 47.6 + - + -
302A 22B 3.9 32.6 - - + +
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Residues in contact with SER 145 (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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116A MET* 2.8 33.3 + - - +
119A THR* 3.4 17.5 - - - -
120A GLY* 3.7 10.1 + - - -
141A TRP 2.8 17.8 + - - -
142A TRP* 4.3 0.7 - - - -
144A ILE* 1.3 78.6 - - - +
146A THR* 1.3 59.5 + - - +
148A PHE* 3.3 5.2 + - - +
149A LEU 3.2 14.6 + - - -
301A RET 3.2 31.4 - - - -
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Residues in contact with THR 146 (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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142A TRP* 2.8 52.6 + - + -
143A GLY* 3.7 6.7 - - - -
144A ILE 3.2 0.2 - - - -
145A SER* 1.3 73.8 - - - +
147A ALA* 1.3 66.1 + - - +
149A LEU* 3.1 4.9 + - + +
150A LEU* 2.9 43.3 + - + +
187A LEU* 5.9 0.9 - - + -
190A PRO* 4.1 6.2 - - + +
301A RET 3.6 20.6 - - + +
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Residues in contact with ALA 147 (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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143A GLY 2.9 14.1 + - - +
144A ILE 3.2 9.6 + - - +
146A THR* 1.3 76.5 - - - +
148A PHE* 1.3 62.5 + - - +
150A LEU* 3.1 14.0 + - - +
151A VAL* 3.0 30.5 + - + +
302A 22B 3.7 37.2 - - + -
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Residues in contact with PHE 148 (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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112A LEU* 3.7 32.0 - - + +
115A LEU* 3.6 57.4 - - + -
116A MET* 3.8 6.5 - - + -
119A THR* 3.9 9.9 - - + -
144A ILE* 3.1 41.8 + - + -
145A SER 3.5 6.3 - - - +
146A THR 3.2 0.2 - - - -
147A ALA* 1.3 79.7 - - - +
149A LEU* 1.3 60.4 + - - +
151A VAL* 3.5 5.2 + - - +
152A LEU* 3.0 25.0 + - - +
302A 22B 3.6 44.4 - - + -
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Residues in contact with LEU 149 (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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116A MET* 3.5 28.9 - - - -
145A SER 3.2 6.6 + - - +
146A THR* 3.1 10.6 + - + +
148A PHE* 1.3 76.8 - - - +
150A LEU* 1.3 55.4 + - + +
152A LEU* 3.2 8.9 + - + +
153A LEU* 2.7 63.4 + - + +
186A TRP* 4.0 35.2 - - + +
187A LEU* 3.8 24.2 - - + -
190A PRO* 4.1 5.6 - - + -
301A RET 4.0 21.1 - - + -
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Residues in contact with LEU 150 (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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146A THR* 2.9 37.2 + - + +
147A ALA* 3.4 14.8 - - - +
149A LEU* 1.3 79.0 - - + +
151A VAL* 1.3 58.5 + - + +
153A LEU* 3.3 7.5 + - + +
154A TYR* 2.8 30.0 + - - +
187A LEU* 4.4 20.4 - - + -
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Residues in contact with VAL 151 (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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112A LEU* 3.8 10.8 - - + -
147A ALA* 3.0 21.8 + - + +
148A PHE* 3.9 4.5 - - - +
150A LEU* 1.3 75.7 - - + +
152A LEU* 1.3 58.0 + - - +
154A TYR* 3.1 11.7 + - + +
155A PHE* 3.0 56.7 + - + -
302A 22B 4.2 34.3 - - + -
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Residues in contact with LEU 152 (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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92A LEU* 3.8 20.9 - - + -
109A LEU* 3.5 34.0 - - + +
112A LEU* 4.1 15.0 - - + +
113A ASP* 3.7 41.7 - - + +
116A MET* 4.8 9.0 - - - -
148A PHE 3.0 17.8 + - - +
149A LEU* 3.3 7.9 - - + +
151A VAL* 1.3 75.2 - - - +
153A LEU* 1.3 84.2 + - + +
154A TYR 3.2 0.3 + - - -
155A PHE 3.2 9.0 + - - -
156A LEU* 3.3 13.0 + - + +
186A TRP* 4.6 6.3 - - + -
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Residues in contact with LEU 153 (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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149A LEU* 2.7 38.9 + - + +
150A LEU* 3.8 8.1 - - + +
152A LEU* 1.3 87.0 - - + +
154A TYR* 1.3 62.3 + - - +
156A LEU* 3.3 19.4 - - + +
157A PHE* 3.2 23.8 - - + -
182A VAL* 4.5 9.0 - - + +
183A THR* 4.0 34.8 - - + +
186A TRP* 4.9 2.0 - - + -
187A LEU* 3.6 42.2 - - + +
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Residues in contact with TYR 154 (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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150A LEU 2.8 14.4 + - - +
151A VAL* 3.2 16.2 - - + +
152A LEU 3.1 0.2 - - - -
153A LEU* 1.3 79.1 - - - +
155A PHE* 1.3 76.4 + + - +
157A PHE* 3.1 8.9 + - + +
158A SER* 2.9 53.8 + - - -
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Residues in contact with PHE 155 (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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105A THR* 5.5 1.0 - - + +
108A SER* 4.9 9.2 - - - -
109A LEU* 4.1 14.4 - - + -
112A LEU* 3.4 22.4 - - + -
151A VAL* 3.0 42.3 + - + -
152A LEU* 3.2 6.2 + - - +
154A TYR* 1.3 90.7 - + - +
156A LEU* 1.3 66.8 + - - +
157A PHE 3.1 0.9 + - - -
158A SER* 5.5 0.7 - - - -
159A SER* 2.7 50.5 + - - +
160A LEU* 4.3 1.6 - - - +
302A 22B 3.5 53.2 - - + -
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Residues in contact with LEU 156 (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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92A LEU* 4.8 8.7 - - + -
95A LEU* 3.9 31.9 - - + -
109A LEU* 3.6 38.1 - - + -
152A LEU* 3.3 8.8 + - + +
153A LEU* 3.3 27.4 - - + +
155A PHE* 1.3 78.4 - - - +
157A PHE* 1.3 64.6 + - + +
160A LEU* 3.6 18.6 - - - +
175A PHE* 4.5 6.5 - - + -
179A ARG* 3.8 22.2 - - + -
182A VAL* 4.2 19.7 - - + -
183A THR* 4.5 7.4 - - - +
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Residues in contact with PHE 157 (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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153A LEU* 3.2 23.1 - - + -
154A TYR* 3.1 10.4 + - + +
155A PHE 3.0 0.4 - - - -
156A LEU* 1.3 82.3 - - + +
158A SER* 1.3 55.0 + - - +
160A LEU 4.4 0.2 - - - -
161A SER* 2.7 31.9 + - - -
179A ARG* 3.0 45.3 - - + +
180A ASN* 4.1 6.5 - - - -
183A THR* 3.4 35.2 - - + -
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Residues in contact with SER 158 (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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154A TYR* 2.9 50.3 + - - -
155A PHE* 4.8 1.6 - - - -
157A PHE* 1.3 74.2 - - - +
159A SER* 1.3 59.1 + - - +
160A LEU 2.8 12.4 + - - -
161A SER* 3.0 20.4 + - - -
162A GLY 5.0 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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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