Contacts of the helix formed by residues 114 - 137 (chain B) in PDB entry 3NO1
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 ASP 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 6.2 0.6 - - + +
113B ARG* 1.3 76.4 - - - +
115B ARG* 1.3 68.6 + - - +
116B ARG* 3.0 31.8 + - - +
117B LEU* 3.1 34.2 + - + +
118B GLY 4.2 0.5 + - - -
271B PHE* 5.0 3.6 - - - -
113D ARG 4.8 0.2 - - - -
114D ASP* 3.3 49.5 + - + +
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Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B THR* 2.7 44.8 + - - +
109B PHE* 4.3 9.5 + - - +
110B ASP 4.4 8.3 + - - +
111B ILE* 5.0 3.0 - - - +
113B ARG* 3.0 8.7 + - - +
114B ASP* 1.3 74.2 + - - +
116B ARG* 1.3 61.1 + - - +
117B LEU 3.1 0.9 + - - -
118B GLY* 3.2 4.8 + - - +
119B LEU* 3.1 27.4 + - + +
271B PHE* 5.0 14.8 - - + -
218D GLN* 3.3 22.4 + - - +
246D TRP* 3.4 64.8 - - - +
269D THR* 4.1 19.0 - - - +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 5.4 3.8 - - - +
114B ASP* 3.0 21.3 + - - +
115B ARG* 1.3 76.7 - - - +
117B LEU* 1.3 61.0 + - + +
119B LEU* 4.2 4.0 - - - +
120B VAL* 2.9 38.1 + - + +
268B GLN 3.4 9.3 + - - -
269B THR* 3.1 26.1 + - - +
270B GLU 3.0 26.9 + - - -
271B PHE* 3.1 33.9 - - + +
294B TRP* 2.9 64.2 + - + +
295B SER* 3.3 9.1 + - - -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 5.6 1.6 - - - +
73B THR* 3.4 40.8 - - + +
76B ASP* 4.6 17.0 - - + +
77B ILE* 3.9 20.8 - - + +
80B ILE* 4.9 10.8 - - + +
113B ARG* 4.2 28.5 - - + +
114B ASP* 3.1 29.1 + - + +
116B ARG* 1.3 80.0 - - + +
118B GLY* 1.3 62.3 + - - +
120B VAL* 3.8 2.3 - - - +
121B ALA* 3.1 23.6 + - - +
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 4.8 1.3 - - - -
107B VAL* 3.7 35.8 + - - +
108B THR* 4.3 2.2 - - - -
113B ARG* 4.7 7.4 - - - +
114B ASP 4.2 0.8 + - - -
115B ARG* 3.2 6.8 + - - +
117B LEU* 1.3 80.9 - - - +
119B LEU* 1.3 55.8 + - - +
121B ALA* 3.2 5.9 + - - +
122B LEU* 2.8 31.5 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 6.1 0.7 - - + -
105B TYR* 5.1 5.4 - - + -
108B THR* 3.7 22.2 - - + +
115B ARG* 3.1 23.0 + - + +
116B ARG* 3.9 3.6 - - - +
118B GLY* 1.3 75.2 - - - +
120B VAL* 1.3 58.0 + - - +
122B LEU* 3.5 4.0 + - + -
123B ALA* 3.0 23.9 + - - +
271B PHE* 3.6 53.6 - - + +
294B TRP 3.3 21.3 - - - +
295B SER* 3.7 15.7 - - - +
296B GLY* 3.1 16.4 + - - +
246D TRP* 4.3 12.3 - - + -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 6.1 0.9 - - + -
67B THR* 4.6 10.1 - - + +
68B GLY* 5.2 4.3 - - - -
70B GLU* 3.9 25.4 - - + +
77B ILE* 3.6 29.4 - - + -
116B ARG* 2.9 27.6 + - + +
117B LEU 3.8 2.7 - - - +
119B LEU* 1.3 76.7 - - - +
121B ALA* 1.3 58.7 + - - +
123B ALA* 3.3 2.8 + - - +
124B ALA* 3.0 27.1 + - + +
293B SER 3.8 20.9 - - - +
294B TRP* 4.0 21.5 - - + +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.0 12.1 - - + +
80B ILE* 3.7 32.5 - - + -
81B ILE* 3.8 12.1 - - + +
85B LEU* 3.2 19.1 - - + +
117B LEU 3.1 17.5 + - - +
118B GLY 3.6 4.5 - - - +
120B VAL* 1.3 78.3 - - - +
122B LEU* 1.3 61.9 + - - +
124B ALA* 3.3 4.0 + - - +
125B VAL* 3.3 17.0 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.7 12.3 - - + +
100B LEU 5.6 0.2 - - - +
101B TRP* 3.7 53.4 - - + +
104B GLY* 4.2 21.8 - - - +
105B TYR* 4.1 25.4 - - + +
107B VAL* 4.4 5.4 - - + -
108B THR* 4.5 9.0 - - + -
118B GLY 2.8 16.1 + - - +
119B LEU* 3.8 5.6 - - + +
121B ALA* 1.3 75.8 - - - +
123B ALA* 1.3 57.2 - - - +
125B VAL* 3.5 5.5 + - + +
126B ASN* 2.9 32.8 + - + +
296B GLY* 3.9 8.1 - - - -
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 4.7 2.7 - - - +
119B LEU 3.0 17.7 + - - +
120B VAL 3.6 4.9 - - - +
121B ALA 3.2 0.2 - - - -
122B LEU* 1.3 75.6 - - - +
124B ALA* 1.3 62.6 + - - +
126B ASN* 3.9 0.2 - - - +
127B THR* 2.7 34.0 + - - +
292B SER 3.5 12.8 - - - +
293B SER* 3.6 16.8 - - - +
296B GLY 3.5 0.9 - - - +
297B GLY* 3.3 29.8 - - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 5.9 2.5 - - + -
53B THR* 3.6 22.4 - - - +
65B ALA* 5.5 1.2 - - - +
67B THR* 3.4 30.5 - - + +
77B ILE* 5.8 0.7 - - + -
81B ILE* 4.0 15.7 - - + -
120B VAL* 3.0 11.0 + - + +
121B ALA 3.5 9.6 - - - +
122B LEU 3.3 0.2 - - - -
123B ALA* 1.3 78.2 - - - +
125B VAL* 1.3 62.5 + - - +
127B THR* 3.9 2.4 - - - -
128B ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 5.0 5.2 - - + -
53B THR* 4.6 11.2 - - + -
55B VAL* 5.3 1.6 - - + -
81B ILE* 3.9 27.8 - - + -
85B LEU* 4.0 20.9 - - + -
89B LEU* 3.2 40.8 - - + -
121B ALA 3.3 6.5 + - - +
122B LEU* 3.9 7.6 - - + +
124B ALA* 1.3 81.7 - - - +
126B ASN* 1.3 60.0 + - - +
128B ALA* 3.4 2.3 + - - +
129B ILE* 2.8 39.9 + - + +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.9 10.0 - - - +
101B TRP* 3.5 16.2 + - + +
122B LEU* 2.9 20.4 + - + +
123B ALA* 3.9 2.2 - - - +
125B VAL* 1.3 79.3 - - - +
127B THR* 1.3 61.1 + - - +
129B ILE* 3.7 7.3 - - - +
130B TRP* 3.0 39.1 + - - -
296B GLY 3.6 12.0 + - - +
297B GLY 3.6 2.6 - - - -
298B PRO* 3.1 19.2 - - - +
299B THR* 3.1 45.2 + - - +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 3.8 22.2 - - + -
66B TYR 5.5 2.5 - - - +
67B THR* 4.6 10.4 + - - +
123B ALA* 2.7 24.0 + - - +
124B ALA* 3.9 4.0 - - - -
126B ASN* 1.3 75.3 - - - +
128B ALA* 1.3 64.1 + - - +
130B TRP* 3.4 4.1 + - + +
131B ASP* 3.2 20.6 + - - +
145B TRP* 6.0 0.2 - - + -
292B SER* 4.8 1.9 + - - -
293B SER* 5.3 1.9 + - - -
297B GLY* 4.4 1.4 - - - -
298B PRO* 3.5 21.0 - - + +
323B VAL* 4.0 29.1 - - + +
371B LEU* 4.2 9.1 - - + +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR* 3.9 25.8 - - + +
55B VAL* 3.5 23.1 - - + -
63B GLY* 3.3 13.5 - - - +
64B GLU* 4.3 9.4 - - - +
65B ALA* 4.5 2.2 - - - +
124B ALA 3.2 15.3 + - - +
125B VAL 3.8 1.3 - - - +
127B THR* 1.3 77.3 - - - +
129B ILE* 1.3 64.9 + - - +
131B ASP* 3.1 7.8 + - - +
132B ALA 3.0 17.2 + - - -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 4.8 9.2 - - + -
55B VAL* 4.0 21.1 - - + -
89B LEU* 5.2 0.9 - - + -
94B ALA* 3.2 35.2 - - + +
97B ILE* 3.4 29.4 - - + -
100B LEU* 4.6 11.7 - - + -
125B VAL* 2.8 34.7 + - + +
126B ASN* 3.7 16.8 - - - +
128B ALA* 1.3 76.0 - - - +
130B TRP* 1.3 61.1 + - - +
132B ALA* 3.1 9.9 + - - +
133B VAL* 2.8 28.2 + - + +
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Residues in contact with TRP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU 6.0 1.8 - - - -
97B ILE* 3.5 34.9 - - + +
98B GLU* 6.2 0.2 - - - -
126B ASN* 3.0 37.9 + - - +
127B THR* 3.6 7.0 - - + +
128B ALA 3.2 0.4 - - - -
129B ILE* 1.3 83.8 - - + +
131B ASP* 1.3 57.5 + - - +
133B VAL* 3.2 5.4 + - + +
134B GLY 2.8 24.4 + - - -
141B LEU* 3.6 19.4 - - + +
144B LEU* 4.0 20.6 - - + -
145B TRP* 3.3 51.1 - + + -
298B PRO* 3.7 14.4 - - + +
299B THR* 3.1 27.1 + - - +
302B LEU* 4.6 7.9 - - + -
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY* 3.5 2.3 - - - -
64B GLU* 2.8 39.9 + - - +
127B THR 3.2 10.4 + - - +
128B ALA 3.1 9.8 + - - +
130B TRP* 1.3 76.3 - - - +
132B ALA* 1.3 61.8 + - - +
134B GLY* 3.2 1.9 + - - -
135B LYS* 3.0 55.6 + - - +
141B LEU* 4.0 9.6 - - - +
370B GLY* 3.6 2.6 - - - -
371B LEU* 2.8 38.0 + - + +
372B GLY 4.1 1.2 + - - -
373B TRP 5.6 0.2 + - - -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.1 12.7 - - + +
55B VAL* 4.7 3.8 - - + +
57B THR* 4.7 7.9 - - + -
61B ILE* 3.8 16.2 - - + +
63B GLY* 3.6 25.3 - - - +
94B ALA* 5.2 2.9 - - + -
128B ALA 3.0 7.8 + - - +
129B ILE* 3.2 13.7 - - + +
131B ASP* 1.3 77.4 - - - +
133B VAL* 1.3 56.9 - - + +
135B LYS* 3.3 3.4 + - - +
136B ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MSE 5.2 2.2 - - + -
20B LEU* 4.8 0.7 - - + -
94B ALA* 3.5 29.2 - - + +
95B MSE 3.8 25.1 - - + +
97B ILE* 4.0 14.4 - - + -
129B ILE* 2.8 30.0 + - + +
130B TRP* 3.2 8.5 + - + +
132B ALA* 1.3 69.4 - - - +
134B GLY* 1.3 65.8 + - - +
136B ALA* 3.2 6.4 + - - +
137B LEU* 2.9 38.7 + - + +
144B LEU* 4.3 10.3 - - + -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TRP 2.8 14.3 + - - -
131B ASP 3.7 3.4 - - - -
133B VAL* 1.3 79.2 - - - +
135B LYS* 1.3 55.6 + - - +
137B LEU 3.4 0.3 + - - -
138B LYS 3.0 7.1 + - - -
139B MSE 2.8 47.3 + - - +
141B LEU* 4.2 7.8 - - - +
144B LEU* 4.4 6.5 - - - -
369B PRO* 3.6 0.5 - - - +
370B GLY* 3.5 8.7 - - - -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.9 20.1 - - + +
62B ILE 3.0 24.0 + - - +
64B GLU* 4.0 13.7 + - - +
131B ASP* 3.0 47.5 + - - +
132B ALA 3.6 4.0 - - - +
133B VAL 3.2 0.2 - - - -
134B GLY* 1.3 74.8 - - - +
136B ALA* 1.3 65.3 + - - +
138B LYS* 3.1 23.0 + - - +
369B PRO* 3.8 27.5 - - + +
370B GLY 3.8 0.2 - - - +
372B GLY* 5.5 2.9 - - - +
373B TRP 5.7 2.6 + - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.9 18.2 - - + -
61B ILE* 3.4 22.8 - - + +
95B MSE 4.0 15.7 - - + -
132B ALA 2.9 17.2 + - - +
133B VAL 3.6 5.2 - - - +
135B LYS* 1.3 75.8 - - - +
137B LEU* 1.3 61.4 + - + +
138B LYS* 3.3 19.4 - - - -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.6 35.6 - - + +
139A MSE 3.6 47.3 - - + -
144A LEU* 4.4 4.3 - - + -
95B MSE 4.8 6.1 - - + -
133B VAL* 2.9 32.8 + - + +
134B GLY* 4.1 1.6 - - - +
136B ALA* 1.3 79.2 - - + +
138B LYS* 1.3 73.5 + - - +
139B MSE 3.0 20.3 + - + +
144B LEU* 4.2 21.5 - - + -
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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