Contacts of the helix formed by residues 162 - 185 (chain A) in PDB entry 1N54
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 PRO 162 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP 4.8 0.4 - - - +
161A VAL* 1.3 85.2 - - + +
163A GLN* 1.3 53.8 + - - +
164A VAL* 3.0 23.6 - - + -
165A ARG* 2.8 33.1 + - + +
166A ARG* 3.6 3.1 + - - +
276A HIS* 3.2 37.9 - - + +
282A TYR* 5.0 3.6 - - + -
789A GLN 4.2 15.5 - - - +
790A ALA* 4.3 6.1 - - + -
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL 3.3 2.8 + - - -
162A PRO* 1.3 71.0 - - - +
164A VAL* 1.3 52.5 + - - +
166A ARG* 3.1 16.5 + - - +
167A ASP* 2.7 51.8 + - - +
202A TYR* 3.3 7.2 + - + +
206A ARG* 3.4 30.7 - - + +
207A GLN* 2.5 64.5 + - - +
210A HIS* 4.1 7.3 - - - -
790A ALA* 3.0 22.8 + - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 3.4 24.0 - - + -
163A GLN* 1.3 77.8 - - - +
165A ARG* 1.3 63.5 + - - +
167A ASP* 3.4 10.4 + - - +
168A TRP* 3.1 23.4 + - - +
228A TYR* 5.3 0.2 + - - -
282A TYR* 3.8 32.1 - - + +
283A PRO 4.1 15.2 - - - +
285A PRO* 4.2 9.2 - - + -
788A LEU 3.2 24.5 - - - +
789A GLN* 4.4 4.7 - - - +
790A ALA 3.0 26.9 - - - +
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 5.4 1.4 + - - -
155A VAL* 3.5 21.7 - - + +
158A GLU* 3.6 11.6 + - - -
161A VAL* 4.6 6.7 - - - -
162A PRO* 2.8 13.8 + - + +
164A VAL* 1.3 78.9 - - - +
166A ARG* 1.3 67.3 + - + +
168A TRP* 3.2 9.5 + - - +
169A TYR* 3.3 35.3 + - + -
273A PRO* 3.6 8.5 + - - +
274A PRO 2.2 36.6 + - - -
275A PRO* 3.2 10.1 + - - +
276A HIS* 2.6 45.4 - - - +
280A SER* 4.7 1.2 + - - -
282A TYR* 2.8 55.6 + - + -
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 4.0 8.5 + - + +
156A THR* 2.8 44.4 + - + +
157A GLN 4.3 0.6 - - - -
158A GLU 2.8 28.4 + - - -
159A GLU* 4.4 2.0 + - - +
160A ASP* 4.2 4.8 - - - +
161A VAL* 3.1 41.4 + - + +
162A PRO 4.0 6.3 - - - +
163A GLN* 3.1 11.5 + - - +
165A ARG* 1.3 81.3 - - + +
167A ASP* 1.3 62.8 + - - +
168A TRP 2.8 1.7 + - - -
169A TYR* 3.2 4.9 + - - +
170A VAL* 3.2 23.6 + - - +
202A TYR* 2.8 39.2 - - + +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 2.7 39.6 + - - +
164A VAL* 3.6 11.0 - - - +
166A ARG* 1.3 72.4 - - - +
168A TRP* 1.3 57.5 + - - +
170A VAL* 3.4 2.9 - - - +
171A TYR* 2.9 23.6 + - - +
202A TYR* 2.8 18.8 + - - -
206A ARG* 2.5 38.5 + - - -
228A TYR* 3.3 21.8 + - - +
229A LEU* 3.3 19.0 - - + +
285A PRO* 4.9 7.8 - - - +
790A ALA 5.1 0.3 - - - +
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Residues in contact with TRP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 5.4 0.7 - - + -
116A LEU* 3.7 20.6 - - + -
121A TYR* 3.2 50.5 + + + +
122A ASN* 5.3 0.2 - - - +
124A ALA* 3.8 13.2 - - + -
125A VAL* 2.8 38.3 - - + +
128A VAL* 5.2 2.2 - - + -
152A PHE* 4.7 7.0 - + - -
164A VAL 3.1 10.0 + - - +
165A ARG* 3.6 9.2 - - - +
166A ARG 2.8 4.8 + - - -
167A ASP* 1.3 72.7 - - - +
169A TYR* 1.3 108.2 - + - +
170A VAL 2.9 1.6 - - - -
171A TYR* 2.3 38.8 + + + +
172A ALA* 2.7 28.9 + - + -
228A TYR* 5.1 2.5 - - - -
282A TYR* 5.4 2.0 - + + -
283A PRO* 4.6 17.3 - - + +
286A ARG* 6.4 0.4 - - - -
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Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.9 9.8 - - + +
121A TYR* 5.0 8.6 + + - -
152A PHE* 3.2 60.6 - + - +
155A VAL* 4.2 12.8 - - + -
165A ARG* 3.3 46.1 + - + -
166A ARG* 3.2 6.7 + - - +
168A TRP* 1.3 107.5 - + - +
170A VAL* 1.3 61.3 + - - +
172A ALA* 3.5 2.1 + - - -
173A PHE* 3.2 21.5 + - - +
273A PRO* 3.2 36.0 - - + +
274A PRO* 3.6 21.0 + - - +
282A TYR* 5.5 0.9 - + - -
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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
----------------------------------------------------------
152A PHE 5.2 1.8 - - - +
153A VAL* 5.4 6.1 - - + -
156A THR* 4.0 16.8 - - + -
166A ARG 3.2 15.0 - - - +
167A ASP 3.4 6.3 - - - +
168A TRP 2.9 0.6 - - - -
169A TYR* 1.3 74.1 - - + +
171A TYR* 1.3 68.6 + - - +
173A PHE* 3.4 5.6 + - + +
174A LEU* 3.2 35.6 + - + +
199A THR* 3.4 33.4 - - + +
202A TYR* 3.9 25.8 - - + -
203A LEU* 5.8 1.6 - - + -
229A LEU* 4.1 10.1 - - + -
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.2 18.2 - - + -
129A ARG* 4.1 15.5 - - - -
167A ASP 2.9 14.4 + - - +
168A TRP* 2.3 36.2 + + + +
170A VAL* 1.3 66.8 - - - +
172A ALA* 1.3 58.2 + - - -
173A PHE 2.8 1.6 + - - -
175A SER* 2.6 41.7 + - - -
228A TYR* 3.7 29.8 - + + -
229A LEU* 4.1 7.2 - - + -
232A LEU* 3.7 28.7 - - + -
286A ARG* 3.3 30.6 + - - -
312A PHE* 3.5 25.9 - + - -
316A GLU* 3.6 13.0 + - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.2 15.1 - - + +
128A VAL* 3.4 14.2 - - + +
149A PHE* 4.9 0.2 - - - -
152A PHE* 3.8 22.0 - - + -
168A TRP* 2.7 35.5 + - + +
169A TYR 3.7 9.4 - - - +
171A TYR* 1.3 72.4 - - - +
173A PHE* 1.3 54.1 + - - +
175A SER* 3.2 7.7 + - - -
176A SER* 2.7 27.7 + - - -
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.4 51.8 - + + -
152A PHE* 4.7 2.9 - - + -
153A VAL* 4.6 13.9 - - + -
169A TYR 3.2 11.0 + - - +
170A VAL* 3.5 9.0 - - + +
171A TYR 2.8 1.4 + - - -
172A ALA* 1.3 76.7 - - - +
174A LEU* 1.3 80.0 + - + +
175A SER 2.4 21.2 + - - -
176A SER* 2.5 21.8 + - - -
177A LEU* 3.3 43.8 + - + -
192A MET* 4.0 21.5 - - + -
195A ILE* 4.3 17.5 - - + -
196A PHE* 4.8 10.8 - + - -
199A THR* 4.9 7.4 - - + -
233A TRP* 6.0 0.4 - + - -
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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
----------------------------------------------------------
170A VAL* 3.2 34.9 + - + +
173A PHE* 1.3 102.5 - - + +
175A SER* 1.3 61.0 + - - +
176A SER 3.3 0.2 - - - -
177A LEU* 3.4 9.4 - - + +
178A PRO* 3.3 8.8 - - - +
196A PHE* 6.0 1.6 - - + -
199A THR* 4.3 1.8 - - + -
203A LEU* 5.0 3.6 - - + -
229A LEU* 3.7 19.3 - - + +
232A LEU* 3.7 16.6 - - + +
233A TRP* 3.8 38.8 - - + -
236A ILE* 2.7 42.0 - - + +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.2 1.4 - - - +
129A ARG* 3.6 28.5 + - - -
171A TYR* 2.6 30.3 + - - -
172A ALA* 3.2 10.7 + - - -
173A PHE 2.4 11.5 + - - -
174A LEU* 1.3 68.9 - - - +
176A SER* 1.3 58.3 + - - +
178A PRO* 2.6 23.9 - - - +
179A TRP* 3.6 13.2 - - - -
232A LEU* 3.9 16.1 - - - +
312A PHE* 4.1 14.9 - - - -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL 5.3 0.2 + - - -
128A VAL* 3.3 17.0 - - - +
129A ARG* 3.9 19.1 + - - +
132A SER* 3.3 26.6 + - - -
149A PHE* 3.9 8.2 - - - -
172A ALA 2.7 22.5 + - - -
173A PHE 2.5 12.6 + - - -
175A SER* 1.3 73.8 + - - +
177A LEU* 1.3 49.4 + - - -
178A PRO* 2.8 2.0 - - - +
179A TRP* 2.7 40.4 + - - +
180A VAL* 3.4 3.9 + - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 4.1 13.5 - - + -
173A PHE* 3.3 56.5 - - + +
174A LEU* 3.4 28.5 - - + +
176A SER* 1.3 76.9 - - - +
178A PRO* 1.3 61.4 - - - +
179A TRP 2.9 2.3 + - - -
180A VAL* 4.1 4.5 - - + -
181A GLY* 3.1 26.2 + - - +
182A LYS 4.6 0.9 + - - -
184A LEU* 4.6 1.6 - - + -
192A MET* 4.3 10.8 - - + -
196A PHE* 4.6 6.1 - - + -
236A ILE* 3.9 21.8 - - + -
239A LEU* 3.6 8.7 - - - +
244A TRP* 4.1 17.2 - - + -
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Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU 3.3 8.3 - - - +
175A SER* 2.6 34.8 - - - +
176A SER 3.1 1.6 - - - +
177A LEU* 1.3 81.9 - - + +
179A TRP* 1.3 61.4 + - + +
182A LYS* 5.9 0.7 - - - +
232A LEU* 5.3 2.7 - - + -
236A ILE* 5.0 3.6 - - + -
239A LEU* 3.9 14.9 - - + +
244A TRP 5.8 0.3 - - - +
246A GLU* 3.7 17.1 - - + +
249A ILE* 3.2 23.8 - - + +
251A ARG* 3.9 0.7 + - - -
309A VAL* 4.3 28.7 - - + -
312A PHE* 4.6 14.4 - - + -
313A VAL* 4.8 7.4 - - + -
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Residues in contact with TRP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.6 25.1 - - + +
84A THR* 3.8 11.9 - - + +
129A ARG* 2.9 54.3 - - + +
132A SER* 5.6 0.2 - - - -
133A ASP* 4.0 14.1 - - + +
136A ASN* 3.7 4.9 - - - +
175A SER 3.6 11.4 - - - -
176A SER* 2.7 16.8 + - - +
178A PRO* 1.3 85.6 - - + +
180A VAL* 1.3 68.6 + - + +
181A GLY 3.1 2.2 + - - -
182A LYS* 3.8 11.4 + - - +
249A ILE* 2.8 53.9 - - + +
251A ARG* 3.0 25.6 + - - +
312A PHE* 4.7 5.6 - + - -
313A VAL* 4.3 15.0 - - + -
316A GLU* 5.2 3.4 - - + -
317A ASN* 4.8 19.3 - - - -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.2 53.2 - - - +
135A VAL* 3.8 13.2 - - + -
136A ASN* 3.5 22.1 + - - +
145A MET* 5.4 0.9 - - + -
149A PHE* 4.5 2.9 - - + -
176A SER* 3.9 15.5 - - - +
177A LEU* 4.1 3.6 - - - +
179A TRP* 1.3 78.5 - - - +
181A GLY* 1.3 60.2 + - - +
182A LYS 3.4 1.3 + - - -
183A GLU 3.7 2.1 + - - -
184A LEU* 2.8 53.5 + - + +
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.1 22.3 + - - -
179A TRP 3.1 0.4 + - - -
180A VAL* 1.3 79.7 - - - +
182A LYS* 1.3 66.3 + - - +
183A GLU 3.3 0.2 - - - -
184A LEU* 3.1 17.8 + - - -
185A TYR* 3.2 11.3 + - - +
192A MET* 5.8 1.1 - - - -
244A TRP* 3.7 29.0 - - - -
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU 4.6 1.2 + - - -
178A PRO 5.8 0.4 + - - +
179A TRP 3.8 9.2 + - - +
180A VAL 3.4 0.8 + - - -
181A GLY* 1.3 77.0 - - - +
183A GLU* 1.3 59.8 + - + +
185A TYR* 4.0 6.8 + - - +
186A GLU* 4.7 2.8 + - - +
243A ARG 4.5 3.4 + - - +
244A TRP* 2.9 36.1 + - + +
245A GLN* 3.1 38.8 + - - +
246A GLU* 4.7 13.5 - - + +
251A ARG* 5.9 4.0 - - - +
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.8 24.2 - - - +
136A ASN* 4.2 28.4 - - + +
138A HIS* 4.6 13.2 - - - -
142A ALA* 5.0 8.7 - - - +
180A VAL 3.7 2.0 + - - -
182A LYS* 1.3 76.1 - - + +
184A LEU* 1.3 56.7 + - - +
185A TYR 3.1 6.1 - - - -
186A GLU* 3.1 53.8 - - - +
187A LYS* 5.8 0.2 - - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 4.7 3.8 - - + -
142A ALA* 3.3 37.0 - - + +
145A MET* 5.0 4.7 - - + -
146A VAL* 3.7 17.2 - - + +
149A PHE* 4.2 17.0 - - + -
177A LEU* 4.6 2.5 - - + -
180A VAL* 2.8 52.5 + - + +
181A GLY* 3.1 8.4 + - - +
183A GLU* 1.3 79.2 - - - +
185A TYR* 1.3 61.2 + - - +
186A GLU 3.4 0.7 - - - -
187A LYS* 2.7 20.2 - - + +
192A MET* 4.1 22.7 - - + +
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY 3.2 13.2 + - - +
182A LYS 4.0 3.3 + - - +
183A GLU 3.1 0.8 - - - -
184A LEU* 1.3 79.5 - - - +
186A GLU* 1.3 57.4 + - - +
187A LYS 2.7 9.8 + - - +
189A ASP* 3.5 35.3 - - + +
192A MET* 3.1 43.2 + - + -
193A ASP* 2.1 35.3 + - - -
240A LYS* 4.0 13.3 - - + -
244A TRP* 3.4 46.0 - + + +
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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