Contacts of the helix formed by residues 154 - 178 (chain A) in PDB entry 4N78
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 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 4.0 10.7 + - - -
152A PHE* 3.9 8.5 - - - -
153A VAL* 1.3 77.7 - - - +
155A GLU* 1.3 64.6 + - - +
156A ALA* 4.0 6.1 + - - +
157A TYR* 3.4 22.3 + - - +
158A LEU* 3.2 19.3 + - - +
560A TYR* 4.1 8.6 + - - -
564A THR* 4.3 26.2 - - - -
567A GLU* 3.1 12.3 - - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL 5.3 0.9 - - - +
154A SER* 1.3 71.6 - - - +
156A ALA* 1.3 64.4 + - - +
158A LEU* 3.2 4.8 + - + -
159A ILE* 3.0 27.9 + - - +
244A LEU* 3.4 29.4 - - + +
248A TYR* 2.4 41.5 + - - +
563A ARG* 5.1 3.0 + - - +
567A GLU* 2.6 34.4 + - - +
596A HIS* 4.2 19.7 - - - -
600A PHE* 5.7 0.3 - - - -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 3.4 17.5 - - + +
154A SER* 3.2 5.0 - - - +
155A GLU* 1.3 79.1 - - - +
157A TYR* 1.3 56.4 + - - +
159A ILE* 3.6 8.8 - - - +
160A THR* 3.1 28.2 + - - -
248A TYR* 5.6 0.4 - - - -
560A TYR* 4.3 17.3 - - + -
567A GLU* 5.0 1.0 + - - -
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 3.8 22.4 - - - +
65A VAL* 3.6 4.5 - - + +
66A HIS* 3.6 44.2 - + + +
69A MET* 3.4 23.8 - - + +
139A GLU* 2.7 43.5 + - + +
142A ARG* 4.6 0.2 - - - -
143A LEU* 4.1 7.4 - - + -
153A VAL* 4.3 15.0 - - + -
154A SER* 3.2 20.3 + - - +
155A GLU 3.2 0.6 - - - -
156A ALA* 1.3 78.7 - - - +
158A LEU* 1.3 59.9 + - - +
159A ILE 3.2 0.2 - - - -
160A THR* 4.3 2.7 - - + -
161A LEU* 2.9 60.7 + - + +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 3.9 28.0 - - + +
154A SER 3.2 14.0 + - - +
155A GLU* 3.6 4.0 - - + +
157A TYR* 1.3 75.8 - - - +
159A ILE* 1.3 57.4 + - - +
161A LEU* 3.2 9.0 + - + +
162A GLY* 2.8 25.8 + - - -
237A LEU* 4.0 19.5 - - + -
240A ASP* 4.1 24.7 - - + +
241A ILE* 3.7 30.7 - - + +
244A LEU* 3.6 29.4 - - + -
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU 3.0 18.6 + - - +
156A ALA* 3.6 11.2 - - - +
158A LEU* 1.3 76.1 - - - +
160A THR* 1.3 52.8 + - - +
162A GLY* 2.9 4.6 + - - -
163A LYS* 2.8 54.1 + - + +
241A ILE* 5.6 0.9 - - + -
244A LEU* 3.9 12.1 - - + -
245A CYS* 4.5 11.9 - - - +
248A TYR* 3.7 37.9 - - + -
262A MET* 6.1 1.8 - - + -
263A LEU* 4.4 14.8 - - + -
266A VAL* 5.6 0.2 - - - +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 2.6 36.5 + - + -
69A MET* 4.2 18.4 - - + -
70A ASN* 3.2 23.8 + - - +
73A LEU* 3.9 10.4 - - + +
156A ALA 3.1 4.5 + - - -
157A TYR* 3.3 11.4 + - + -
159A ILE* 1.3 79.5 - - - +
161A LEU* 1.3 63.4 + - + +
163A LYS* 3.2 13.9 + - - +
164A PHE* 3.0 23.8 + - + -
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 4.1 18.6 - - + -
136A PHE* 3.6 21.6 - - + -
139A GLU* 4.4 7.2 - - + -
140A VAL* 6.0 0.9 - - + -
143A LEU* 4.0 18.2 - - + -
157A TYR* 2.9 57.1 + - + +
158A LEU* 3.5 15.5 - - + +
160A THR* 1.3 73.0 - - + +
162A GLY* 1.3 65.4 + - - +
164A PHE* 3.1 20.6 + - - +
165A ILE* 3.3 8.1 + - - +
237A LEU* 4.5 10.5 - - + -
241A ILE* 3.6 20.9 - - + -
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 2.8 15.2 + - - -
159A ILE* 2.9 5.6 + - - -
161A LEU* 1.3 78.0 - - - +
163A LYS* 1.3 59.0 + - - +
165A ILE* 2.9 27.4 - - - +
166A ASN 3.3 3.1 + - - -
241A ILE* 3.7 19.7 - - - +
245A CYS* 5.8 0.7 - - - -
266A VAL* 3.5 21.6 - - - +
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 5.4 1.6 - - - -
73A LEU* 3.6 26.7 - - + +
159A ILE* 2.8 36.1 + - + +
160A THR* 3.2 12.5 + - - +
162A GLY* 1.3 71.9 - - - +
164A PHE* 1.3 57.9 + - - +
166A ASN* 3.5 10.1 + - - +
167A MET* 3.0 28.1 + - - +
262A MET* 4.2 33.4 - - + +
266A VAL* 5.6 0.2 - - + -
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Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 3.4 55.0 - - + -
72A MET* 3.9 25.6 - - + -
73A LEU* 3.8 18.8 - - + -
132A ALA 4.1 10.1 - - - -
136A PHE* 3.6 39.9 - + + -
160A THR* 3.0 20.7 + - + +
161A LEU* 3.1 15.7 - - - +
162A GLY 3.0 0.4 - - - -
163A LYS* 1.3 75.5 - - - +
165A ILE* 1.3 63.7 + - - +
167A MET* 3.1 29.4 + - + +
168A PHE* 3.2 30.3 + + - -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.5 31.6 - - + -
161A LEU 3.3 4.5 + - - +
162A GLY* 2.9 25.1 - - - +
164A PHE* 1.3 76.3 - - - +
166A ASN* 1.3 62.7 + - + +
168A PHE* 3.2 11.5 + - + +
169A ALA 3.1 6.4 + - - -
224A LEU* 5.1 0.2 - - + -
238A LEU* 4.6 11.0 - - + -
241A ILE* 5.1 4.3 - - + -
242A VAL* 6.2 0.2 - - + -
266A VAL* 3.9 34.1 - - + +
269A PHE* 3.0 37.7 - - + -
270A GLY* 4.1 17.3 - - - +
273A LEU* 4.2 17.0 - - + -
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Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY 3.3 6.7 + - - +
163A LYS 3.7 7.2 + - - +
164A PHE 3.2 0.6 - - - -
165A ILE* 1.3 80.3 - - + +
167A MET* 1.3 61.3 + - - +
169A ALA* 3.1 8.1 + - - +
170A VAL* 2.8 41.9 + - - +
262A MET* 3.5 40.5 - - - +
265A LYS* 3.5 35.7 - - + +
266A VAL* 4.7 4.9 - - + -
269A PHE* 4.7 2.9 - - - -
307A LEU* 4.2 8.0 - - - +
318A TYR* 5.4 1.2 + - - -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET 4.1 9.4 - - - +
73A LEU* 3.9 21.3 - - + +
76A GLY* 3.9 28.7 - - - -
77A GLN 5.2 0.2 - - - +
128A PHE* 4.1 7.2 - - + -
132A ALA* 4.3 11.0 - - + -
163A LYS 3.0 14.9 + - - +
164A PHE* 3.1 28.2 + - + +
166A ASN* 1.3 80.0 - - - +
168A PHE* 1.3 87.4 + - + +
170A VAL* 3.4 6.0 + - - +
171A LEU* 2.9 46.1 + - + +
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN* 4.8 2.7 - - + -
132A ALA* 3.7 29.2 - - + -
133A ILE* 3.9 20.2 - - + -
136A PHE* 3.9 26.7 - + + -
164A PHE* 3.2 30.2 + + - -
165A ILE* 3.4 11.2 - - - +
167A MET* 1.3 95.0 - - + +
169A ALA* 1.3 65.7 + - - +
171A LEU* 3.5 6.0 + - + -
172A ASP* 2.9 27.3 + - - +
220A ILE* 4.0 27.5 - - + +
221A THR* 5.2 0.9 - - - +
224A LEU* 3.6 31.4 - - + -
269A PHE* 4.3 3.8 - - + -
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE 3.1 6.6 + - - +
166A ASN* 3.1 14.3 + - - +
168A PHE* 1.3 76.1 - - - +
170A VAL* 1.3 61.7 + - - +
172A ASP* 3.3 5.1 + - - +
173A GLU* 3.0 33.5 + - + +
221A THR* 5.0 1.1 - - - -
269A PHE* 3.7 32.0 - - + -
307A LEU* 5.0 4.7 - - + -
318A TYR* 3.8 20.2 - - + +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 6.1 0.7 - - - +
80A ALA* 4.3 7.4 - - + -
166A ASN* 2.8 40.5 + - - +
167A MET* 3.7 6.3 - - - +
169A ALA* 1.3 73.0 - - - +
171A LEU* 1.3 64.7 + - + +
173A GLU* 3.9 1.2 - - - +
174A LEU* 2.9 49.7 + - + +
307A LEU* 3.7 37.0 - - + +
308A PHE* 3.8 24.0 - - + -
311A MET* 4.4 0.2 - - - +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 3.7 19.1 - - - +
79A TYR* 4.2 2.2 - - + -
80A ALA* 3.8 23.8 - - + +
83A LEU* 3.8 7.7 - - + +
125A PHE* 3.9 23.3 - - + -
128A PHE* 3.9 23.8 - - + -
129A GLN* 5.2 3.1 - - + -
167A MET* 2.9 42.4 + - + +
168A PHE* 4.0 7.0 - - + +
170A VAL* 1.3 78.6 - - + +
172A ASP* 1.3 56.0 - - - +
174A LEU* 3.6 3.5 + - - -
175A LYS* 3.0 29.8 + - - +
220A ILE* 3.8 19.6 - - + +
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE 2.9 20.0 + - - +
169A ALA* 3.7 3.8 - - - +
171A LEU* 1.3 75.0 - - - +
173A GLU* 1.3 56.9 + - + +
175A LYS* 3.3 7.9 + - - +
176A ASN* 2.8 42.0 + - - +
218A ASN* 3.2 22.9 + - - +
219A LYS 3.6 5.5 + - - -
220A ILE* 3.2 27.7 + - + +
221A THR* 2.6 42.5 + - - +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 3.0 21.9 + - + +
170A VAL 4.0 0.2 - - - +
172A ASP* 1.3 74.5 - - + +
174A LEU* 1.3 60.4 + - - +
176A ASN* 3.3 20.5 + - - +
177A MET* 3.0 29.8 + - - +
218A ASN* 4.3 6.2 - - - +
307A LEU* 3.8 15.5 - - + -
311A MET* 3.8 26.0 - - + +
313A ILE* 6.0 0.2 - - + -
317A ARG* 3.0 32.4 + - - +
318A TYR* 6.1 0.7 - - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.5 36.3 - - + +
83A LEU* 3.8 19.1 - - + -
84A TYR* 4.2 14.1 - - + -
170A VAL* 2.9 38.3 + - + +
171A LEU* 4.7 0.7 - - - -
173A GLU* 1.3 76.5 - - - +
175A LYS* 1.3 61.8 + - - +
177A MET* 3.1 36.6 - - + +
178A LYS* 3.1 15.3 + - - +
308A PHE* 4.0 17.5 - - + -
311A MET* 3.5 23.6 - - + -
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.1 16.1 - - + +
125A PHE* 4.2 7.6 - - + -
171A LEU 3.0 19.7 + - - +
172A ASP* 3.6 13.7 - - - +
173A GLU 3.3 0.2 - - - -
174A LEU* 1.3 76.5 - - - +
176A ASN* 1.3 68.3 + - - +
177A MET 3.4 0.5 + - - -
178A LYS* 3.6 16.2 + - - +
181A VAL* 6.5 0.4 - - + -
213A PHE* 2.8 71.9 + - + -
214A LEU* 4.1 17.2 + - + +
216A ASN 2.9 21.8 + - - -
217A HIS* 5.0 0.2 - - - +
219A LYS* 4.2 5.1 - - - +
220A ILE* 4.6 3.6 - - + -
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Residues in contact with ASN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 2.8 31.3 + - - +
173A GLU* 3.6 23.6 + - - +
175A LYS* 1.3 79.2 + - - +
177A MET* 1.3 60.3 + - - +
178A LYS 4.9 1.0 - - - -
179A CYS* 5.0 6.1 + - - -
216A ASN 4.8 0.7 - - - +
217A HIS* 3.3 40.2 + - + -
218A ASN* 2.8 48.5 + - - +
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Residues in contact with MET 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 4.7 7.0 - - + -
173A GLU 3.0 13.2 + - - +
174A LEU* 3.1 51.4 - - + +
175A LYS 3.3 0.2 - - - -
176A ASN* 1.3 79.8 - - - +
178A LYS* 1.3 82.0 + - + +
179A CYS* 2.9 16.3 + - - -
311A MET* 4.6 4.0 - - - +
625A GLU 5.3 0.2 - - - -
626A PHE* 3.4 54.7 - - + -
629A GLU* 3.4 23.5 - - + +
630A LEU* 5.7 5.0 - - + +
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.2 27.8 - - + +
84A TYR 3.7 13.8 + - - -
86A TRP 2.6 31.5 + - - +
87A ARG* 4.5 3.2 - - - +
174A LEU 3.1 12.2 + - - +
175A LYS* 3.6 12.7 + - - +
176A ASN 3.5 2.5 - - - -
177A MET* 1.3 96.5 - - + +
179A CYS* 1.3 64.6 + - - +
180A SER* 3.1 4.7 - - - -
181A VAL* 3.3 31.2 + - + +
182A LYS* 3.6 5.4 + - - +
625A GLU* 4.5 12.0 + - - -
629A GLU* 3.2 30.2 + - - +
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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