Contacts of the helix formed by residues 116 - 143 (chain B) in PDB entry 4TLG
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 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 4.3 1.3 - - - -
115B ALA* 1.3 77.4 - - - +
117B LYS* 1.3 66.0 + - - +
118B GLN* 3.6 10.8 + - - +
119B ASP* 3.1 34.0 + - - +
120B MET* 3.1 22.5 + - - +
270B LEU* 5.4 0.8 - - - +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.8 19.2 - - + +
116B SER* 1.3 72.4 - - - +
118B GLN* 1.3 63.0 + - - +
120B MET* 3.3 4.2 + - - +
121B ILE* 2.9 25.1 + - + +
166B PRO 5.7 0.4 - - - +
169B GLU* 5.7 2.7 - - + -
170B VAL* 3.8 24.9 - - + +
173B GLN* 4.1 19.7 - - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLN* 4.6 16.2 + - - +
116B SER* 3.1 10.7 + - - +
117B LYS* 1.3 78.5 - - - +
119B ASP* 1.3 61.0 + - - +
121B ILE* 3.3 6.6 + - - +
122B ARG* 2.8 47.1 + - + +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.7 22.8 - - + -
77B PRO* 3.3 28.1 - - + +
80B ILE* 3.7 19.7 - - + +
116B SER* 3.1 28.4 + - - +
118B GLN* 1.3 81.1 - - - +
120B MET* 1.3 60.8 + - - +
122B ARG* 4.5 3.8 - - - -
123B LYS* 3.0 27.9 + - - +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 4.1 15.7 - - + -
84B ASP* 3.9 19.1 - - - +
106B LEU* 5.1 1.8 - - + -
108B PRO* 4.9 10.5 - - + -
111B LEU* 3.9 30.7 - - + -
112B LEU* 3.5 36.8 - - + -
115B ALA* 5.0 2.9 - - + -
116B SER 3.1 13.8 + - - +
117B LYS* 3.6 8.3 - - - +
119B ASP* 1.3 75.3 - - - +
121B ILE* 1.3 62.2 + - - +
123B LYS* 3.4 2.0 + - - +
124B ARG* 2.9 53.6 + - - +
170B VAL* 4.5 17.3 - - + -
171B TYR* 6.1 0.4 - - + -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 5.8 0.4 - - + -
117B LYS* 2.9 25.0 + - + +
118B GLN* 3.7 6.3 - - - +
120B MET* 1.3 75.0 - - - +
122B ARG* 1.3 59.6 + - + +
124B ARG* 3.1 8.6 + - + +
125B ILE* 2.9 36.3 + - + +
170B VAL* 3.4 36.1 - - + +
173B GLN* 3.8 23.6 - - + +
174B PHE* 3.9 21.3 - - + +
177B ILE* 3.5 26.5 - - + -
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLN* 3.0 56.8 + - - +
67B ASP* 5.7 1.6 - - - +
71B ILE* 3.5 24.5 - - - +
74B TRP* 3.6 57.1 - - + +
118B GLN* 2.8 43.1 + - + +
119B ASP* 4.5 6.5 - - - -
120B MET 3.4 0.2 - - - -
121B ILE* 1.3 70.8 - - + +
123B LYS* 1.3 60.1 + - - +
125B ILE* 4.2 9.6 - - + -
126B LYS* 2.9 29.5 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.6 11.3 - - + -
76B PRO* 4.8 3.8 - - + -
80B ILE* 3.8 23.6 - - + -
84B ASP* 3.0 32.7 + - - +
85B SER 2.7 27.7 + - - -
86B GLY 6.1 0.2 - - - -
99B TYR* 3.7 14.1 + - - -
119B ASP 3.0 14.6 + - - +
120B MET 3.6 7.9 - - - +
121B ILE 3.3 0.4 - - - -
122B ARG* 1.3 74.4 - - - +
124B ARG* 1.3 81.6 + - + +
126B LYS* 3.2 7.9 + - + +
127B VAL* 3.1 32.4 + - + +
504B EDO 4.3 16.8 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 2.8 44.1 + - - -
85B SER 5.5 0.2 + - - -
106B LEU* 4.0 10.1 - - - +
120B MET* 2.9 43.0 + - - +
121B ILE* 3.1 10.6 + - - +
123B LYS* 1.3 89.8 - - + +
125B ILE* 1.3 64.2 + - - +
127B VAL* 3.3 10.8 + - + +
128B CYS* 3.2 25.8 + - - -
170B VAL* 4.3 12.4 - - - +
171B TYR* 3.3 43.6 + - + +
174B PHE* 3.7 35.7 - - + -
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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
----------------------------------------------------------
62B PHE* 3.9 29.2 - - + -
66B GLN* 4.4 11.7 - - + +
68B LEU* 3.5 30.1 - - + -
71B ILE* 3.8 7.0 - - + -
121B ILE* 2.9 34.9 + - + +
122B ARG* 3.7 12.6 - - + +
124B ARG* 1.3 72.3 - - - +
126B LYS* 1.3 66.8 + - - +
128B CYS* 3.0 11.9 + - - +
129B GLU* 3.0 21.4 + - + +
174B PHE* 5.7 3.1 - - + -
177B ILE* 4.3 17.5 - - + -
182B TYR* 3.6 14.8 - - + +
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.4 35.0 - - + +
72B VAL* 3.6 23.3 + - - +
74B TRP* 2.6 36.1 + - + +
75B GLN* 4.3 10.7 + - - +
76B PRO* 4.2 9.9 - - + +
122B ARG 2.9 14.9 + - - +
123B LYS* 3.3 11.4 - - - +
125B ILE* 1.3 76.1 - - - +
127B VAL* 1.3 58.1 + - - +
129B GLU* 3.1 3.3 + - - +
130B LEU* 2.8 46.4 + - + +
504B EDO 4.0 21.0 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.7 1.3 - - + -
99B TYR* 3.5 59.7 - - + +
123B LYS* 3.1 20.6 + - - +
124B ARG* 3.4 13.2 - - + +
125B ILE 3.3 0.4 - - - -
126B LYS* 1.3 75.3 - - - +
128B CYS* 1.3 62.1 + - - +
130B LEU* 3.3 9.0 + - - +
131B LEU* 2.9 33.3 + - + +
151B MET* 4.6 7.0 - - + -
504B EDO 3.8 18.2 - - - +
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Residues in contact with CYS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG 3.2 16.2 + - - -
125B ILE* 3.0 9.9 + - - +
127B VAL* 1.3 77.1 - - - +
129B GLU* 1.3 57.7 + - - +
131B LEU* 3.3 1.4 + - - +
132B LEU* 3.0 26.8 + - - +
151B MET* 5.2 2.9 - - - -
174B PHE* 4.0 14.4 - - - -
178B LEU* 3.8 28.0 - - - -
182B TYR* 3.7 30.1 - - + -
505B EDO 3.2 28.4 + - - +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 3.1 37.7 + - - -
68B LEU* 4.1 9.5 - - + +
71B ILE* 3.6 29.4 - - + -
72B VAL* 4.0 9.4 - - + -
125B ILE* 3.0 10.7 + - + +
126B LYS 3.1 6.7 + - - +
128B CYS* 1.3 74.4 - - - +
130B LEU* 1.3 59.4 + - - +
132B LEU* 3.3 13.3 + - - +
133B HIS* 2.9 46.8 + - - -
182B TYR* 2.7 34.3 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.7 33.4 - - + +
88B LEU* 4.2 20.4 - - + +
126B LYS* 2.8 35.3 + - + +
127B VAL* 3.7 4.3 - - - +
129B GLU* 1.3 72.0 - - - +
131B LEU* 1.3 57.7 + - - +
133B HIS* 3.3 6.5 + - + +
134B GLU* 3.0 29.1 + - - +
504B EDO 3.5 37.5 - - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.7 25.8 - - + -
97B PRO* 3.9 18.3 - - + +
98B VAL 4.5 0.2 - - - -
99B TYR* 3.9 19.3 - - + -
127B VAL* 2.9 36.9 + - + +
128B CYS 3.6 4.3 - - - +
129B GLU 3.3 0.2 - - - -
130B LEU* 1.3 72.3 - - - +
132B LEU* 1.3 61.9 + - - +
134B GLU* 3.2 6.3 + - - +
135B CYS* 2.9 32.4 + - - -
149B ALA* 3.9 22.7 - - + -
151B MET* 4.1 7.6 - - + -
505B EDO 3.8 29.8 - - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 6.0 0.9 - - - +
63B ARG* 5.5 0.2 - - - +
128B CYS 3.0 10.1 + - - +
129B GLU* 3.3 19.7 + - - +
131B LEU* 1.3 77.9 - - - +
133B HIS* 1.3 62.8 + - + +
135B CYS* 3.2 12.3 + - + +
136B GLU* 3.0 21.8 + - - +
147B GLU 5.3 6.7 - - - +
182B TYR* 3.6 31.6 - - + -
185B THR* 4.1 17.3 - - + -
505B EDO 3.4 22.2 - - - +
508B EDO 3.9 19.5 - - - +
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 5.7 2.2 - - - -
69B ASP* 5.5 5.3 + - - -
72B VAL* 3.7 32.8 - - + +
129B GLU* 2.9 38.1 + - - +
130B LEU* 3.6 11.0 - - + +
131B LEU 3.3 0.2 - - - -
132B LEU* 1.3 76.3 - - + +
134B GLU* 1.3 58.1 + - - +
136B GLU* 3.2 7.9 + - + +
137B LEU* 2.9 43.5 + - + +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.6 12.4 - - + +
91B TYR* 2.6 42.8 + - + +
97B PRO* 3.8 17.3 - - + -
130B LEU 3.0 14.8 + - - +
131B LEU* 3.2 9.8 + - - +
133B HIS* 1.3 77.1 - - - +
135B CYS* 1.3 55.3 + - - +
137B LEU* 3.3 15.4 + - - +
138B GLN* 3.0 36.2 + - - +
141B LYS* 5.4 4.2 + - - -
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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
----------------------------------------------------------
97B PRO* 3.7 12.8 - - - -
131B LEU 2.9 19.2 + - - -
132B LEU* 3.5 16.4 - - + +
134B GLU* 1.3 76.6 - - - +
136B GLU* 1.3 56.9 + - - +
138B GLN* 3.5 2.5 + - - +
139B THR* 2.9 32.8 + - - -
146B ILE* 3.3 23.0 - - - +
147B GLU* 4.1 4.9 - - - -
148B MET* 3.5 40.6 - - - -
149B ALA* 4.3 1.3 - - - -
505B EDO 6.1 0.9 - - - -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU 3.0 12.9 + - - +
133B HIS* 3.2 11.6 + - + +
135B CYS* 1.3 77.8 - - - +
137B LEU* 1.3 63.7 + - + +
139B THR* 3.3 17.7 + - - +
140B GLN* 3.0 50.8 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B HIS* 2.9 41.5 + - + +
134B GLU* 3.3 18.4 + - - +
136B GLU* 1.3 81.5 - - + +
138B GLN* 1.3 63.8 + - + +
140B GLN* 3.3 21.0 + - - +
141B LYS* 3.0 51.5 + - + +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.6 34.4 + - + +
95B GLY* 2.9 41.5 + - - +
97B PRO* 5.1 0.9 - - + -
134B GLU* 3.0 23.1 + - - +
135B CYS* 3.8 4.3 - - - +
137B LEU* 1.3 76.4 - - - +
139B THR* 1.3 57.1 + - - +
141B LYS* 4.4 18.7 + - - +
142B LEU* 2.8 47.9 + - + +
146B ILE* 4.1 14.4 - - + -
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B CYS 2.9 23.7 + - - -
136B GLU* 3.5 22.8 + - - +
137B LEU 3.3 0.2 - - - -
138B GLN* 1.3 74.7 - - - +
140B GLN* 1.3 58.9 + - - +
143B GLY* 2.9 30.2 + - - -
144B ARG 3.4 19.5 + - - +
145B LYS* 3.8 14.0 - - + -
146B ILE* 2.9 25.2 + - - +
147B GLU* 5.4 0.3 - - - +
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU* 3.0 48.2 + - - +
137B LEU* 3.3 23.7 + - - +
139B THR* 1.3 77.7 - - - +
141B LYS* 1.3 65.5 + - + +
143B GLY* 3.8 6.2 + - - -
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 5.9 0.6 + - - -
134B GLU* 5.4 4.4 + - - -
137B LEU* 3.0 44.2 + - + +
138B GLN* 3.9 19.0 + - - +
139B THR 3.3 0.2 - - - -
140B GLN* 1.3 81.3 - - + +
142B LEU* 1.3 66.3 + - + +
143B GLY 3.8 0.2 + - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU 4.5 6.3 - - - +
95B GLY* 4.8 2.2 - - - -
138B GLN* 2.8 39.5 + - - +
141B LYS* 1.3 82.9 - - + +
143B GLY* 1.3 62.3 - - - +
144B ARG* 3.5 45.5 + - - +
146B ILE* 4.3 19.1 - - + -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B THR* 2.9 12.9 + - - -
140B GLN 3.8 4.4 + - - -
141B LYS 3.4 2.8 + - - -
142B LEU* 1.3 78.0 - - - +
144B ARG* 1.3 62.0 + - - +
----------------------------------------------------------
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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