Contacts of the helix formed by residues 126 - 150 (chain A) in PDB entry 3J41
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 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLY 4.0 1.6 + - - -
125A VAL* 1.3 77.2 - - - +
127A VAL* 1.3 59.8 + - - +
128A GLY* 3.2 6.3 + - - -
129A GLN* 3.0 40.6 + - - +
130A ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 5.1 2.9 - - - -
125A VAL 3.8 0.8 + - - -
126A SER* 1.3 74.1 - - - +
128A GLY* 1.3 56.1 + - - +
130A ALA* 3.7 8.0 - - - +
131A THR* 2.6 41.1 + - - +
200A ASN* 4.5 16.8 - - - +
202A TRP* 4.4 13.2 - - + +
203A VAL* 3.6 22.4 - - + +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 3.1 6.2 + - - -
127A VAL* 1.3 81.9 - - - +
129A GLN* 1.3 64.0 + - - +
131A THR* 3.3 6.8 + - - -
132A ILE* 3.2 30.6 + - - +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLY 3.9 5.5 - - - +
125A VAL* 3.9 10.3 - - + +
126A SER* 3.0 38.8 + - - +
128A GLY* 1.3 75.4 - - - +
130A ALA* 1.3 58.4 + - - +
132A ILE* 3.1 8.3 + - + +
133A VAL 2.9 17.3 + - - -
106B SER 2.6 31.5 + - - +
107B VAL* 2.8 48.3 - - + +
108B THR 4.1 6.3 + - - +
109B PRO* 5.2 2.1 - - - +
113B ARG* 5.0 4.2 - - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.0 38.8 - - + -
125A VAL* 3.6 8.7 - - + +
126A SER 2.9 17.5 + - - +
127A VAL* 3.7 6.3 - - - +
129A GLN* 1.3 78.7 - - - +
131A THR* 1.3 56.6 + - - +
133A VAL* 3.5 4.1 + - - +
134A GLU* 3.0 32.6 + - - +
179A THR* 3.5 9.8 - - + +
203A VAL* 3.9 4.7 - - + -
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 2.6 25.2 + - - +
128A GLY* 3.6 7.8 - - - -
129A GLN 3.2 0.2 - - - -
130A ALA* 1.3 74.7 - - - +
132A ILE* 1.3 62.5 + - + +
134A GLU* 4.4 1.6 - - - -
135A ILE* 2.9 41.3 + - + +
202A TRP* 4.4 6.0 + - - +
203A VAL* 3.6 22.8 - - - +
206A VAL* 3.6 30.3 - - + -
207A GLY* 3.7 9.9 - - - +
210A ILE* 5.3 0.7 - - + -
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY 3.2 18.3 + - - +
129A GLN* 3.1 9.7 + - + +
131A THR* 1.3 74.3 - - + +
133A VAL* 1.3 67.0 + - - +
135A ILE* 3.2 13.7 + - + +
136A PHE* 3.0 45.1 + - + -
25B PHE* 6.0 0.7 - - + -
103B VAL* 4.6 4.7 - - + -
106B SER* 5.5 1.6 - - - +
107B VAL* 3.6 26.9 - - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN 2.9 8.7 + - - +
130A ALA* 3.6 9.9 - - - +
132A ILE* 1.3 78.4 - - - +
134A GLU* 1.3 63.9 + - - +
136A PHE* 3.1 7.3 + - - +
137A LEU* 2.9 40.4 + - + +
174A PHE* 3.6 30.7 - - + -
175A GLY* 4.6 0.9 - - - -
178A TYR* 4.1 33.4 - - + -
179A THR* 4.5 5.4 - - + +
25B PHE* 5.1 3.4 - - + -
107B VAL* 3.1 31.2 - - + -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA 3.0 20.5 + - - +
131A THR 3.8 0.9 - - - +
132A ILE 3.3 0.2 - - - -
133A VAL* 1.3 75.8 - - - +
135A ILE* 1.3 57.7 + - - +
137A LEU* 3.6 8.1 - - - +
138A THR* 2.8 35.0 + - - -
179A THR* 2.6 27.1 + - - +
181A ALA* 3.4 2.8 - - - -
182A GLY* 2.7 23.4 + - - -
183A MET* 2.7 28.9 + - - -
203A VAL* 3.9 18.4 - - + +
204A TYR* 3.8 9.6 - - + -
207A GLY* 3.8 20.8 - - - -
208A PRO* 3.6 7.5 - - + +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 2.9 38.1 + - + +
132A ILE* 3.3 17.7 - - + +
133A VAL 3.1 0.2 - - - -
134A GLU* 1.3 73.9 - - - +
136A PHE* 1.3 70.8 + - + +
138A THR 3.4 0.2 + - - -
139A LEU* 2.8 35.6 + - + +
207A GLY* 3.4 23.8 - - - +
210A ILE* 3.7 25.8 - - + -
211A GLY* 3.3 15.8 - - - +
214A LEU* 3.9 20.0 - - + -
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Residues in contact with PHE 136 (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 ILE* 3.0 42.3 + - + +
133A VAL 3.1 6.5 + - - +
135A ILE* 1.3 85.2 - - + +
137A LEU* 1.3 62.9 + - - +
139A LEU* 3.6 12.4 - - + +
140A GLN* 3.1 27.4 + - - +
21B LEU* 3.6 29.2 - - + -
22B PHE* 4.0 21.6 - + - -
25B PHE* 3.9 35.4 - + + -
26B PHE* 3.4 5.2 - - + -
103B VAL* 3.5 26.5 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 2.9 33.6 + - + +
134A GLU* 3.6 29.8 - - - +
136A PHE* 1.3 76.3 - - - +
138A THR* 1.3 61.9 + - - +
140A GLN* 3.0 26.5 - - - +
141A PHE* 3.2 7.3 + - - +
171A GLY* 3.5 20.0 - - - +
174A PHE* 3.3 36.8 - - + -
175A GLY* 4.1 2.7 - - - -
179A THR* 4.3 0.2 - - - +
181A ALA* 4.1 9.9 - - - -
183A MET* 3.5 25.6 - - + +
26B PHE* 3.6 13.0 - - + -
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 5.6 0.4 - - - +
70A ALA* 4.3 5.4 - - + -
71A VAL* 5.8 0.4 - - + +
134A GLU 2.8 17.7 + - - -
135A ILE 4.0 1.8 - - - -
137A LEU* 1.3 74.9 - - - +
139A LEU* 1.3 56.2 + - - +
141A PHE* 3.9 9.0 - - + -
142A VAL* 2.7 44.9 + - + +
183A MET* 3.6 21.0 - - - +
208A PRO* 3.0 49.1 - - + +
211A GLY* 4.2 0.9 - - - -
212A ALA* 3.7 8.1 - - + +
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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 ILE* 2.8 22.0 + - + +
136A PHE* 3.6 13.9 - - + +
137A LEU 3.3 0.2 - - - -
138A THR* 1.3 74.3 - - - +
140A GLN* 1.3 61.5 + - - +
142A VAL* 4.1 0.3 - - - +
143A LEU* 2.9 33.6 + - + +
211A GLY* 3.5 11.6 + - - +
214A LEU* 3.8 23.6 - - + +
215A GLY* 3.2 31.4 - - - +
218A LEU* 4.2 16.8 - - + -
22B PHE* 3.7 29.8 - - + -
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Residues in contact with GLN 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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136A PHE 3.1 13.2 + - - +
137A LEU 3.0 17.4 - - - +
139A LEU* 1.3 77.8 - - - +
141A PHE* 1.3 69.1 + - - +
143A LEU* 3.6 11.3 - - - +
144A CYS* 3.0 22.2 + - - +
167A SER* 2.6 42.8 + - - +
170A LEU* 4.0 11.7 - - + +
171A GLY* 3.8 8.1 + - - -
183A MET* 3.7 7.8 - - - +
22B PHE* 4.9 12.8 - - + -
26B PHE* 3.3 27.6 - - + -
54B THR* 3.5 19.9 - - + +
55B LEU* 5.5 3.6 - - + -
58B ALA* 5.7 0.2 - - - +
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Residues in contact with PHE 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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23A TYR* 5.7 0.7 - - - -
52A LEU* 3.3 27.6 - - + -
68A ASN* 3.9 11.9 - - + -
71A VAL* 3.8 25.4 - - + -
137A LEU 3.2 15.9 + - - +
138A THR* 3.4 11.2 - - + +
139A LEU 3.1 0.2 - - - -
140A GLN* 1.3 82.2 - - - +
142A VAL* 1.3 63.1 + - - +
144A CYS* 3.1 6.8 + - - +
145A ILE* 3.0 36.1 + - + +
164A VAL* 3.5 27.8 - - + -
167A SER* 3.3 21.1 - - - +
168A LEU* 3.9 20.9 - - + -
183A MET* 3.7 22.2 - - + -
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Residues in contact with VAL 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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71A VAL* 4.6 17.0 - - + -
74A ALA* 3.8 12.3 - - + -
138A THR* 2.7 29.8 + - + +
139A LEU 4.1 2.0 - - - +
141A PHE* 1.3 71.0 - - + +
143A LEU* 1.3 60.6 + - - +
145A ILE* 3.0 9.4 + - + +
146A PHE* 2.8 49.5 + - + -
212A ALA* 3.5 44.9 - - + +
215A GLY* 4.1 1.6 - - - -
216A SER 3.9 10.5 - - - +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 2.9 22.5 + - + +
140A GLN* 3.6 7.6 - - - +
142A VAL* 1.3 78.3 - - - +
144A CYS* 1.3 56.7 + - - +
146A PHE* 4.0 3.5 - - - +
147A ALA* 3.0 24.4 + - - +
215A GLY* 4.6 7.4 - - - +
218A LEU* 4.2 16.4 - - + -
219A TYR* 3.7 31.9 - - + +
18B PHE* 5.9 1.1 - - + -
22B PHE* 3.9 30.5 - - + -
55B LEU* 5.4 2.7 - - + -
58B ALA* 3.7 28.3 - - + +
59B VAL* 5.0 10.5 - - + -
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Residues in contact with CYS 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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140A GLN 3.0 13.9 + - - +
141A PHE 3.1 9.4 + - - +
143A LEU* 1.3 74.8 - - - +
145A ILE* 1.3 55.5 + - + +
147A ALA* 4.1 0.8 - - - +
148A THR* 2.6 55.4 + - - +
163A ALA* 3.9 29.6 - - - -
164A VAL* 4.3 2.5 - - - -
167A SER* 3.8 14.8 - - - +
54B THR* 3.9 25.1 - - + +
57B GLN* 4.4 2.2 - - - -
58B ALA* 4.6 8.3 - - - -
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Residues in contact with ILE 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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71A VAL* 3.7 34.1 - - + -
75A PHE* 3.5 33.0 - - + -
141A PHE* 3.0 33.8 + - + +
142A VAL* 3.0 12.7 + - + +
144A CYS* 1.3 74.4 - - + +
146A PHE* 1.3 62.8 + - + +
148A THR* 3.2 6.1 + - - -
149A TYR* 2.8 51.0 + - + +
164A VAL* 3.9 23.3 - - + -
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Residues in contact with PHE 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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71A VAL* 6.1 0.2 - - + -
74A ALA* 3.3 33.4 - - + -
75A PHE* 3.7 36.1 - + - -
78A GLY* 4.6 4.9 - - - -
80A GLN* 4.2 14.6 - - - -
142A VAL* 2.8 40.6 + - + +
143A LEU* 4.0 2.5 - - - +
145A ILE* 1.3 75.4 - - + +
147A ALA* 1.3 62.6 + - - +
149A TYR* 3.9 3.3 - - - +
150A ASP* 2.9 26.2 + - - +
216A SER* 3.3 24.5 - - - -
219A TYR* 3.8 23.9 - + + -
220A ASP* 3.1 28.7 - - - -
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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
----------------------------------------------------------
143A LEU 3.0 19.3 + - - +
144A CYS 4.1 2.0 - - - +
146A PHE* 1.3 76.9 - - - +
148A THR* 1.3 58.4 + - - +
150A ASP* 3.3 17.5 - - - +
153A ARG* 3.0 22.3 + - - +
219A TYR* 3.5 19.4 - - + -
57B GLN 3.6 5.4 - - - +
58B ALA* 3.4 36.6 - - - +
61B HIS* 4.0 0.4 - - - +
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Residues in contact with THR 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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144A CYS* 2.6 29.8 + - - +
145A ILE 3.2 6.2 + - - -
147A ALA* 1.3 75.0 - - + +
149A TYR* 1.3 71.2 + - - +
150A ASP 3.3 1.3 - - - +
157A LEU* 3.9 11.1 - - + +
160A VAL* 3.6 32.8 - - - +
163A ALA* 4.1 12.1 - - + -
164A VAL* 3.6 10.7 - - - +
57B GLN* 3.8 34.8 - - + +
156D ARG* 3.8 11.3 + - - -
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Residues in contact with TYR 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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56A VAL* 4.0 18.2 - - + +
60A GLY* 6.1 0.2 - - - -
64A GLY* 2.7 38.6 + - - -
65A ALA 3.5 9.4 + - - -
66A HIS* 5.0 0.9 - + - -
75A PHE* 3.5 32.3 - + + -
80A GLN* 6.0 1.8 - - - +
145A ILE* 2.8 35.5 + - + +
146A PHE* 4.0 4.0 - - - +
148A THR* 1.3 83.3 - - - +
150A ASP* 1.3 65.8 + - - +
151A GLU* 3.0 9.6 + - - +
160A VAL* 4.2 16.2 - - + -
164A VAL* 4.1 19.0 - - + +
156D ARG* 4.8 5.4 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE 2.9 18.9 + - - +
147A ALA 3.3 10.8 - - - +
148A THR 3.3 0.6 - - - +
149A TYR* 1.3 73.7 - - - +
151A GLU* 1.3 69.4 + - - +
152A ARG* 3.0 55.0 + - - +
153A ARG* 3.4 17.6 + - + +
219A TYR* 2.4 25.6 + - + +
61B HIS* 4.6 1.9 - - - -
156D ARG* 3.3 13.0 + - - -
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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