Contacts of the helix formed by residues 126 - 149 (chain C) in PDB entry 4NEF
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 THR 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 4.1 1.8 - - - -
124C SER 4.5 5.8 - - - +
125C THR* 1.3 75.4 - - - +
127C ALA* 1.4 52.3 + - - +
128C GLY* 3.8 4.0 + - - -
129C GLN* 3.0 38.8 + - - +
130C ALA* 2.8 32.1 + - - +
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.7 20.0 - - + +
126C THR* 1.4 71.9 - - - +
128C GLY* 1.3 56.0 + - - +
130C ALA* 3.7 5.2 - - - +
131C VAL* 2.9 32.4 + - - +
200C ASP* 4.9 6.3 - - + +
202C TRP* 3.7 27.5 - - + +
203C VAL* 3.7 12.7 - - + +
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Residues in contact with GLY 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C THR* 3.2 5.8 + - - -
127C ALA* 1.3 75.8 - - - +
129C GLN* 1.4 54.4 + - - +
131C VAL* 3.4 15.8 - - - +
132C THR* 2.7 27.5 + - - -
202C TRP* 5.0 2.9 - - - -
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Residues in contact with GLN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU 2.7 24.8 + - - +
107A ILE* 3.3 40.1 - - + +
108A THR 4.1 7.7 + - - +
109A PRO* 4.3 10.1 - - - +
113A ARG* 4.6 4.8 - - - +
124C SER 4.8 0.9 - - - +
125C THR* 3.8 11.0 - - + +
126C THR* 3.0 40.9 + - - +
128C GLY* 1.4 74.0 - - - +
130C ALA* 1.4 63.5 + - - +
132C THR* 3.4 5.9 + - - -
133C VAL* 3.2 25.3 + - - +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.2 35.0 - - + -
125C THR* 3.9 8.0 - - + +
126C THR 2.8 8.0 + - - +
127C ALA* 3.7 5.2 - - - +
129C GLN* 1.4 74.5 - - - +
131C VAL* 1.4 59.3 + - - +
133C VAL* 3.2 9.1 + - - +
134C GLU* 3.0 31.7 + - - +
178C TYR* 5.2 0.7 - - - -
179C THR* 3.6 16.7 - - + +
203C VAL* 3.8 8.3 - - + -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ALA 2.9 20.5 + - - +
128C GLY* 3.4 21.3 - - - +
130C ALA* 1.4 72.3 - - - +
132C THR* 1.4 57.9 + - - +
134C GLU* 3.7 2.1 + - - -
135C LEU* 3.1 27.4 + - - +
202C TRP* 3.8 28.9 - - + -
203C VAL* 3.6 15.0 - - + +
206C ILE* 3.9 10.5 - - + -
207C GLY* 3.5 28.4 - - - +
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 5.5 0.4 - - - -
103A LEU* 4.3 7.6 - - + -
106A GLU* 4.6 8.1 + - - +
107A ILE* 3.7 19.9 - - + +
128C GLY 2.7 21.8 + - - -
129C GLN* 3.4 9.2 + - - -
130C ALA 3.2 0.4 - - - -
131C VAL* 1.4 77.6 - - - +
133C VAL* 1.4 63.2 + - - +
135C LEU* 3.4 10.0 - - + +
136C PHE* 3.1 47.9 + - + -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.6 7.8 - - + -
107A ILE* 3.7 29.6 - - + -
129C GLN 3.2 15.8 + - - +
130C ALA* 3.2 8.0 + - - +
132C THR* 1.4 73.8 - - - +
134C GLU* 1.4 51.5 + - + +
136C PHE* 3.0 7.8 + - - +
137C LEU* 2.9 58.7 + - + +
174C LEU* 4.4 9.2 - - + -
175C GLY* 4.5 1.8 - - - -
178C TYR* 3.8 42.0 - - + -
179C THR* 5.5 2.0 - - - +
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ALA 3.0 17.5 + - - +
131C VAL 3.9 0.9 - - - +
133C VAL* 1.4 73.8 - - + +
135C LEU* 1.3 58.3 + - - +
137C LEU* 3.7 14.3 - - + +
138C THR* 2.8 30.8 + - - -
179C THR* 2.7 34.6 + - + +
182C SER* 2.8 30.1 + - - -
183C MET* 2.8 29.3 + - - -
203C VAL* 4.2 13.5 - - + +
204C PHE* 4.9 1.3 - - + -
207C GLY* 3.6 25.2 - - - +
208C PRO* 3.8 4.4 - - + +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C VAL 3.1 15.3 + - - +
132C THR* 3.4 15.3 - - + +
133C VAL 3.2 0.2 - - - -
134C GLU* 1.3 75.5 - - - +
136C PHE* 1.4 84.1 + - + +
138C THR 3.4 1.2 + - - -
139C LEU* 2.9 32.4 + - + +
207C GLY* 3.4 12.8 + - - +
210C VAL* 3.7 27.4 - - + -
211C GLY* 3.3 22.2 - - - +
214C LEU* 4.2 19.3 - - + -
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Residues in contact with PHE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.9 2.7 - - + -
21A LEU* 4.1 20.0 - - + -
22A LEU* 3.6 22.6 - - + +
25A PHE* 3.7 26.7 - + + -
26A PHE* 3.5 8.0 - - + -
103A LEU* 3.7 39.5 - - + -
132C THR* 3.1 30.2 + - + -
133C VAL 3.0 7.3 + - - +
135C LEU* 1.4 94.2 - - + +
137C LEU* 1.4 63.7 + - - +
139C LEU* 3.9 14.3 - - + +
140C GLN* 3.4 24.8 + - - +
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.6 24.9 - - + -
133C VAL* 2.9 26.2 + - + +
134C GLU* 3.7 34.3 - - - +
135C LEU 3.4 0.2 - - - -
136C PHE* 1.4 75.5 - - - +
138C THR* 1.3 59.9 + - - +
140C GLN* 2.8 24.5 + - - +
141C LEU* 3.7 2.3 + - - +
171C GLY* 3.3 21.3 - - - +
174C LEU* 3.9 14.8 - - + -
175C GLY* 3.8 20.6 - - - +
179C THR* 4.9 0.4 - - - +
181C CYS* 3.9 13.7 - - - -
183C MET* 3.5 20.6 - - + +
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Residues in contact with THR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASN* 5.1 0.9 - - - +
70C ALA* 4.1 9.9 - - + -
71C VAL* 5.5 0.4 - - + -
134C GLU 2.8 19.9 + - - -
135C LEU 4.1 1.8 - - - -
136C PHE 3.3 0.2 - - - -
137C LEU* 1.3 74.0 - - - +
139C LEU* 1.3 59.7 + - - +
140C GLN 3.4 0.2 - - - -
141C LEU* 3.3 10.8 + - + +
142C VAL* 2.9 35.0 + - + +
183C MET* 3.5 33.9 - - - +
208C PRO* 3.3 34.9 - - + +
211C GLY 4.2 2.0 - - - -
212C ALA* 4.2 7.9 - - + -
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.6 9.6 - - + -
22A LEU* 3.9 28.3 - - + -
135C LEU* 2.9 25.1 + - + +
136C PHE* 3.9 14.8 - - + +
137C LEU 3.5 0.2 - - - -
138C THR* 1.3 76.4 - - - +
140C GLN* 1.4 54.5 + - - +
142C VAL* 3.4 2.1 + - - +
143C LEU* 2.9 49.8 + - + +
211C GLY 3.4 11.6 + - - +
214C LEU* 3.7 27.6 - - + -
215C GLY* 3.6 25.7 - - - +
218C LEU* 4.4 7.0 - - + -
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Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.6 16.4 - - + -
26A PHE* 3.6 17.7 - - + -
54A THR* 3.4 18.7 - - + +
55A LEU* 5.4 4.9 - - + -
58A ALA* 5.2 0.5 - - - +
136C PHE 3.4 16.4 + - - +
137C LEU* 2.8 19.7 + - - +
139C LEU* 1.4 75.2 - - - +
141C LEU* 1.3 70.2 + - - +
143C LEU* 3.5 11.7 + - - +
144C CYS* 3.0 28.4 + - - +
167C SER* 2.7 39.3 + - - -
170C LEU* 3.6 14.2 - - + +
171C GLY* 3.9 13.7 - - - -
183C MET* 4.3 1.2 - - - -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ASN* 4.0 23.3 - - - +
71C VAL* 4.1 12.1 - - + -
137C LEU 3.7 11.0 + - - +
138C THR* 3.3 11.4 + - + +
139C LEU 3.3 0.6 - - - -
140C GLN* 1.3 82.8 - - - +
142C VAL* 1.3 58.2 + - - +
144C CYS* 3.1 4.9 + - - +
145C ILE* 2.9 51.0 + - + +
164C ILE* 4.1 6.5 - - + +
167C SER* 3.3 24.0 - - - +
168C VAL* 3.8 30.1 - - + +
183C MET* 4.6 17.7 - - + +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 4.4 16.8 - - + -
74C ALA* 3.8 8.5 - - + -
138C THR* 2.9 24.5 + - + +
139C LEU 3.9 2.9 - - - +
141C LEU* 1.3 72.8 - - + +
143C LEU* 1.4 61.8 + - - +
145C ILE* 3.4 6.0 + - - +
146C PHE* 3.0 57.0 + - + -
212C ALA* 3.5 44.4 - - + +
215C GLY* 3.7 3.8 - - - -
216C SER 3.6 9.0 - - - +
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 19.3 - - + -
22A LEU* 4.2 11.0 - - + -
55A LEU* 6.0 1.1 - - + -
58A ALA* 3.8 17.4 - - + +
59A LEU* 5.1 6.1 - - + -
139C LEU* 2.9 43.6 + - + +
140C GLN* 3.7 6.3 - - - +
141C LEU 3.3 0.2 - - - -
142C VAL* 1.4 76.8 - - - +
144C CYS* 1.4 60.7 + - - +
146C PHE* 3.9 3.8 - - - +
147C ALA* 3.2 23.9 + - - +
215C GLY* 3.3 33.0 - - - +
218C LEU* 4.6 2.9 - - + -
219C TYR* 4.2 18.4 - - + +
223C LEU* 4.4 16.6 - - + -
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Residues in contact with CYS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 3.9 20.6 - - + +
57A GLN* 3.8 24.9 - - - -
58A ALA* 3.9 8.5 - - + +
140C GLN 3.0 18.5 + - - +
141C LEU 3.1 4.5 + - - +
143C LEU* 1.4 73.1 - - - +
145C ILE* 1.4 59.8 + - + +
147C ALA* 3.5 2.1 + - - +
148C SER* 3.0 37.9 + - - -
163C SER* 3.9 25.8 - - - -
164C ILE* 4.4 3.8 - - - -
167C SER* 4.0 10.5 - - - +
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C HIS 5.8 0.7 - - - +
71C VAL* 3.7 41.3 - - + -
75C CYS* 5.2 10.5 - - - -
141C LEU* 2.9 42.6 + - + +
142C VAL* 3.4 6.5 + - + +
144C CYS* 1.4 70.9 - - - +
146C PHE* 1.3 57.3 + - + +
148C SER* 3.8 4.2 - - - -
149C THR* 2.7 50.4 + - + +
164C ILE* 3.9 31.2 - - + -
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 3.7 18.2 - - + -
75C CYS* 4.5 4.3 - - - -
77C VAL 3.7 5.4 - - - -
78C GLY 3.8 19.5 - - - -
79C CYS* 4.3 12.1 - - - -
142C VAL* 3.0 49.7 + - + +
143C LEU 3.9 2.2 - - - +
145C ILE* 1.3 81.5 - - + +
147C ALA* 1.3 59.8 + - - +
149C THR* 3.6 6.6 + - - -
150C ASP* 3.4 22.3 + - - +
216C SER* 3.4 31.0 - - - -
219C TYR* 3.5 36.6 + + + -
220C ASN* 3.1 24.0 - - - -
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Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 3.2 25.6 - - - +
58A ALA* 3.5 25.6 - - - +
61A HIS* 3.6 9.4 - - + -
143C LEU 3.2 8.1 + - - +
144C CYS 3.9 2.0 - - - +
146C PHE* 1.3 76.8 - - - +
148C SER* 1.3 62.4 + - - +
150C ASP* 3.2 6.6 + - - +
153C ARG* 3.2 29.0 - - - +
219C TYR* 3.6 12.5 - - + +
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.9 33.4 + - - +
144C CYS* 3.0 26.9 + - - -
145C ILE 3.9 3.4 - - - -
146C PHE 3.4 0.2 - - - -
147C ALA* 1.3 74.3 - - - +
149C THR* 1.3 61.4 + - - +
150C ASP 3.5 1.9 + - - +
153C ARG* 5.0 1.1 - - - +
158C GLY 4.4 4.2 - - - +
159C THR* 4.1 4.5 + - - -
160C PRO* 3.3 33.8 - - - +
163C SER* 4.2 1.4 - - - -
164C ILE* 4.0 18.1 - - - +
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Residues in contact with THR 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLY 6.1 0.9 - - - +
79C CYS* 5.2 8.7 - - - -
145C ILE* 2.7 34.3 + - + +
146C PHE* 3.7 8.1 + - - -
147C ALA 3.2 0.4 - - - -
148C SER* 1.3 80.0 - - - +
150C ASP* 1.3 59.1 + - - +
151C GLU 3.9 1.7 + - - -
159C THR* 4.0 25.1 - - + +
164C ILE* 4.9 3.1 - - + -
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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