Contacts of the helix formed by residues 113 - 138 (chain B) in PDB entry 3AXJ
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 PHE 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 3.8 38.1 - - + -
47B ARG* 3.5 33.0 - - + -
48B HIS* 3.9 15.9 - - + -
51B ILE* 3.9 24.9 - - + -
105B LEU* 3.8 21.3 - - + -
108B GLN* 3.8 12.3 - - + -
109B ASP 4.1 4.5 - - - -
110B VAL 3.5 1.8 + - - +
111B TYR 3.1 0.6 - - - -
112B GLN* 1.3 108.8 - - + +
114B ARG* 1.3 58.1 + - - +
115B SER* 3.2 4.3 - - - -
116B SER* 2.8 32.7 + - - +
117B TYR* 3.4 13.6 - - + -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 5.6 2.8 - - - +
86A TYR 3.2 24.2 + - - -
87A ARG* 3.9 15.2 + - - +
90A ASP* 5.0 11.7 + - - -
110B VAL 3.5 2.3 + - - +
111B TYR* 3.1 41.8 + - + +
112B GLN 3.5 0.6 - - - -
113B PHE* 1.3 77.1 - - - +
115B SER* 1.3 62.7 + - - +
116B SER 3.2 0.2 + - - -
117B TYR* 3.2 25.2 + - + +
118B SER* 2.8 35.8 + - - -
194B ASP* 5.7 3.4 + - - -
197B GLU* 5.1 14.4 - - + +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 4.7 8.2 - - - -
112B GLN 5.2 2.5 + - - -
113B PHE* 3.1 1.6 + - - -
114B ARG* 1.3 84.8 - - - +
116B SER* 1.3 65.6 + - - +
118B SER* 4.3 5.6 - - - -
119B PRO* 3.8 14.9 - - - +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 2.6 36.2 + - - -
51B ILE* 3.6 23.7 - - - +
52B VAL* 3.8 21.2 - - - +
55B SER* 3.2 19.6 + - - -
113B PHE* 2.8 23.7 + - - -
115B SER* 1.3 81.9 + - - +
117B TYR* 1.3 55.7 + - - -
118B SER 3.7 0.2 - - - -
119B PRO* 4.4 2.6 - - - +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.7 17.5 - - + -
55B SER* 3.7 9.7 + - - -
58B ILE* 6.6 0.2 - - + -
98B PHE* 6.2 1.3 - - + -
101B VAL* 4.4 10.8 - - + -
105B LEU* 3.6 28.9 - - + -
110B VAL* 2.7 39.6 + - - +
111B TYR* 4.7 0.5 - - - -
113B PHE* 3.4 26.2 - - + -
114B ARG* 3.2 16.6 + - + +
116B SER* 1.3 76.4 - - - +
118B SER* 1.3 71.4 + - - +
119B PRO* 3.4 3.6 - - - -
120B GLY* 3.2 4.3 + - - -
121B LEU* 3.0 32.5 + - + +
191B PHE* 3.7 28.9 - + + -
192B PHE* 5.1 7.1 + - - -
194B ASP* 6.0 2.3 - - + +
197B GLU* 5.4 5.4 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG 2.8 20.8 + - - -
115B SER* 4.5 4.0 - - - -
117B TYR* 1.3 81.9 - - - +
119B PRO* 1.4 69.5 - - - +
121B LEU* 3.3 1.5 + - - +
122B GLN* 3.0 36.7 + - - +
197B GLU* 2.4 36.1 + - - +
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Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 4.1 7.0 - - - +
59B THR* 3.6 13.0 + - + +
115B SER 3.8 14.4 - - - +
116B SER 4.4 1.6 - - - +
117B TYR* 3.5 4.5 - - - -
118B SER* 1.4 94.2 - - - +
120B GLY* 1.3 56.3 + - - +
122B GLN* 3.9 6.3 - - + +
123B GLU* 3.0 30.5 + - - +
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 3.1 23.1 + - - -
58B ILE* 3.5 19.1 - - - +
59B THR* 3.1 16.1 + - - -
98B PHE* 4.5 0.7 - - - -
117B TYR 3.2 1.0 + - - -
119B PRO* 1.3 76.1 - - - +
121B LEU* 1.3 66.5 + - - +
123B GLU* 3.3 1.0 + - - +
124B PHE* 2.9 25.5 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.9 21.3 - - + -
117B TYR* 3.0 26.6 + - + +
118B SER* 3.3 4.9 + - - +
120B GLY* 1.3 75.3 - - - +
122B GLN* 1.3 57.3 + - - +
124B PHE* 3.3 1.6 + - - +
125B ILE* 2.9 55.2 + - + +
154B ILE* 5.8 0.4 - - + -
158B MSE 4.9 5.6 - - + -
191B PHE* 3.6 34.1 - - + -
192B PHE 4.9 0.2 - - - +
193B VAL* 4.7 15.0 - - + -
194B ASP 4.8 4.7 - - - +
197B GLU* 3.6 33.9 - - + +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 3.0 27.5 + - - +
119B PRO* 3.9 6.4 - - + +
121B LEU* 1.3 75.3 - - - +
123B GLU* 1.3 62.4 + - - +
125B ILE* 3.4 1.3 + - - -
126B GLN* 3.1 23.9 + - - +
197B GLU* 2.9 39.8 + - + +
200B LEU* 3.6 39.4 - - - +
201B GLY* 3.7 17.7 - - - +
204B ASP* 4.5 11.9 - - - +
249B GLU* 4.5 7.5 + - - +
253B LYS* 4.6 7.6 + - - -
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 3.8 22.4 - - + +
62B SER* 3.5 24.3 - - - -
63B LYS* 3.2 34.1 - - + +
66B ILE* 3.7 11.4 - - + +
119B PRO 3.0 18.5 + - - +
120B GLY 3.9 2.9 - - - +
122B GLN* 1.3 73.4 - - - +
124B PHE* 1.3 66.4 + - - +
126B GLN* 3.4 25.8 + - - +
127B ALA* 3.1 18.7 + - - +
204B ASP* 5.2 2.3 - - - +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.2 0.4 - - + -
62B SER* 3.3 11.3 + - - +
90B LEU* 3.5 38.8 - - + -
93B LEU* 4.1 13.7 - - + -
94B ILE* 3.5 31.0 - - + -
98B PHE* 3.5 23.8 - + + -
120B GLY 2.9 17.8 + - - +
121B LEU* 3.6 4.0 - - + +
123B GLU* 1.3 77.4 - - - +
125B ILE* 1.3 67.3 + - + +
127B ALA* 3.3 2.9 + - - +
128B TYR* 2.8 52.5 + + + +
154B ILE* 4.4 8.5 - - + -
158B MSE 3.3 25.8 - - + -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 2.9 45.1 + - + +
122B GLN 3.8 4.5 - - - +
123B GLU 3.3 0.2 - - - -
124B PHE* 1.3 82.8 - - + +
126B GLN* 1.3 57.8 + - - +
128B TYR* 4.4 2.9 - - - -
129B THR* 2.8 40.3 + - + +
154B ILE* 4.1 14.4 - - + -
193B VAL* 4.3 8.7 - - + -
197B GLU 4.3 2.9 - - - +
198B TYR* 3.7 51.8 - - + +
201B GLY* 4.4 1.3 - - - -
202B LEU* 3.9 21.8 - - - +
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.7 14.6 - - + +
122B GLN 3.1 11.4 + - - +
123B GLU* 3.4 29.7 + - - +
125B ILE* 1.3 77.8 - - - +
127B ALA* 1.3 56.7 + - - +
129B THR* 3.4 6.2 + - - -
130B TYR* 3.0 30.3 + - - +
201B GLY 3.8 13.4 + - - +
204B ASP* 3.3 38.9 + - + +
205B LEU* 4.0 3.9 - - - +
208B GLU* 2.8 42.8 + - + +
211B ARG* 5.0 0.8 - - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER* 3.9 15.3 - - - +
65B ILE* 4.4 8.1 - - + -
66B ILE* 3.7 26.7 - - + +
69B LEU* 3.8 6.9 - - - +
90B LEU* 4.0 18.9 - - + +
123B GLU 3.1 12.8 + - - +
124B PHE 3.7 6.1 - - - +
126B GLN* 1.3 73.4 - - - +
128B TYR* 1.3 65.0 + - - +
130B TYR* 3.4 1.5 + - - -
131B MSE 3.0 24.3 + - - +
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.5 27.6 + - - -
90B LEU* 3.9 21.7 - - + +
91B ASN* 5.5 2.7 - - - -
94B ILE* 4.5 16.8 - - + -
124B PHE* 2.8 46.9 + + + +
125B ILE* 3.8 5.4 - - - +
127B ALA* 1.3 72.7 - - - +
129B THR* 1.3 63.7 + - + +
131B MSE 3.3 7.8 + - + +
132B GLU* 3.2 52.5 + - + +
149B SER* 3.7 13.3 + - - -
154B ILE* 4.4 21.3 - - + -
157B VAL* 3.9 24.5 - - + +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.9 3.5 - - - -
125B ILE* 2.8 35.3 + - + +
126B GLN* 3.4 7.3 + - - -
128B TYR* 1.3 75.7 - - + +
130B TYR* 1.3 61.7 + - - +
132B GLU* 3.3 12.6 + - - +
133B TYR* 2.8 28.2 + - - +
148B VAL* 3.7 26.2 - - + -
149B SER 4.2 9.4 - - - +
154B ILE* 4.8 6.7 - - + -
198B TYR* 4.6 2.2 - - + -
202B LEU* 4.0 17.4 - - + +
205B LEU* 3.8 17.0 - - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 4.5 11.2 - - + -
69B LEU* 3.8 34.8 - - + -
70B HIS* 3.0 44.6 + + - -
126B GLN 3.0 20.3 + - - +
127B ALA* 3.8 5.6 - - - +
128B TYR 3.3 0.2 - - - -
129B THR* 1.3 73.8 + - - +
131B MSE 1.3 65.6 + - - +
133B TYR* 3.2 17.4 + + - -
134B LEU* 3.0 38.6 + - + +
205B LEU* 3.6 22.9 - - + +
208B GLU* 4.3 18.2 - - + -
209B LEU* 4.4 4.5 - - + -
212B ARG* 3.3 25.0 + - - +
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Residues in contact with MSE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.9 21.0 - - + +
83B LEU* 3.9 23.1 - - + +
86B ALA* 4.1 1.3 - - + -
87B ARG* 3.1 71.6 - - - +
90B LEU* 3.6 24.2 - - + -
127B ALA 3.0 14.0 + - - +
128B TYR* 3.6 17.9 - - + +
129B THR 3.3 0.2 - - - -
130B TYR* 1.3 77.7 - - - +
132B GLU* 1.3 66.0 + - + +
134B LEU* 3.3 4.3 + - - +
135B CYS* 3.0 29.4 + - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.7 15.9 - - + -
87B ARG* 5.1 6.2 + - - +
128B TYR* 3.2 29.5 + - + +
129B THR* 3.6 10.7 - - - +
131B MSE 1.3 81.5 - - + +
133B TYR* 1.3 66.5 - - - +
135B CYS* 3.3 9.7 + - - +
136B HIS* 3.1 17.8 + - - +
147B SER 5.1 2.5 - - - +
148B VAL* 3.5 10.4 - - - +
149B SER* 2.6 52.3 + - - -
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.0 21.8 - - + -
4A PHE* 3.4 21.2 - + + -
129B THR 2.8 15.0 + - - +
130B TYR* 3.2 16.1 + + + +
132B GLU* 1.3 77.2 - - - +
134B LEU* 1.3 72.8 + - + +
136B HIS* 3.1 6.7 + - + +
137B GLU* 2.8 66.5 + - + +
205B LEU* 4.8 3.1 - - + -
209B LEU* 3.7 29.6 - - + -
212B ARG* 4.4 2.2 - - - -
227B ASP* 3.6 6.3 - - - +
228B THR* 3.4 25.9 + - + +
231B ALA* 3.7 20.4 - - + -
235B PHE* 5.7 0.2 - + - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.6 45.3 - - + +
72B ILE* 3.8 17.3 - - + -
83B LEU* 4.1 12.9 - - + +
130B TYR* 3.0 29.9 + - + +
131B MSE 3.8 4.7 - - - +
133B TYR* 1.3 82.3 - - + +
135B CYS* 1.3 64.9 + - - +
137B GLU* 3.5 6.1 + - - +
138B ASP* 3.4 24.4 + - - +
212B ARG* 3.4 46.4 - - - +
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.9 26.2 - - - -
87B ARG* 4.9 12.1 - - - -
131B MSE 3.0 23.2 + - - +
132B GLU* 3.5 11.4 - - - +
134B LEU* 1.3 77.5 - - - +
136B HIS* 1.3 58.5 + - - +
138B ASP* 3.0 19.8 - - - +
139B ALA* 3.8 9.4 + - - +
143B ASN* 4.6 14.5 + - + +
146B LYS* 5.7 8.3 - - + +
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A PRO* 3.0 43.1 + - + -
1A MSE 4.1 13.4 - - + -
4A PHE* 3.7 34.4 - + + +
132B GLU 3.1 12.2 + - - +
133B TYR* 3.1 12.3 + - + +
135B CYS* 1.3 74.3 - - - +
137B GLU* 1.3 67.4 + - - +
139B ALA* 3.2 17.9 + - - +
143B ASN* 3.6 25.4 - - - +
144B GLU* 3.1 21.4 + - + +
146B LYS* 3.9 9.6 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 5.7 0.2 - - - +
133B TYR* 2.8 50.0 + - + +
134B LEU* 3.8 8.2 - - - +
135B CYS 3.4 0.2 - - - -
136B HIS* 1.3 81.3 - - - +
138B ASP* 1.3 60.8 + - - +
139B ALA 3.2 5.2 + - - +
212B ARG* 2.8 45.3 + - - -
224B THR* 3.6 18.4 + - - +
227B ASP* 3.7 26.4 - - + +
228B THR* 3.9 0.9 - - - +
----------------------------------------------------------
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 6.5 0.2 - - + -
79B LYS* 4.2 39.9 + - + +
83B LEU* 5.1 8.8 - - - +
134B LEU 3.4 10.5 + - - +
135B CYS* 3.0 19.2 - - - +
137B GLU* 1.3 80.5 - - + +
139B ALA* 1.3 61.8 + - - +
140B GLU* 3.4 8.3 + - - +
----------------------------------------------------------
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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