Contacts of the helix formed by residues 152 - 175 (chain A) in PDB entry 3PEI
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 ILE 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.8 25.8 - - + -
109A VAL* 4.3 18.6 - - + +
110A LYS* 4.5 3.1 - - - +
113A THR* 3.6 25.0 - - + +
144A LEU* 3.5 32.5 - - + -
146A TYR* 3.7 35.2 - - + -
150A GLN* 3.4 12.5 + - + +
151A ASP* 1.3 77.0 + - - +
153A GLU* 1.3 67.0 + - - +
154A ASP 3.3 3.1 - - - -
155A SER* 3.5 8.8 + - - -
156A ALA* 3.2 18.7 + - - +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE 5.0 7.1 - - - +
4A VAL* 5.3 1.4 - - - -
5A VAL* 4.3 28.5 + - + +
151A ASP* 3.4 13.6 + - - +
152A ILE* 1.3 77.9 - - - +
154A ASP* 1.3 66.7 + - + +
156A ALA* 3.2 13.9 + - - +
157A LYS* 3.2 14.3 + - - +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP* 4.8 3.1 + - - +
152A ILE 3.3 0.2 - - - -
153A GLU* 1.3 80.3 - - - +
155A SER* 1.3 67.0 + - - +
157A LYS* 2.9 25.4 + - - +
158A ILE* 2.9 23.7 + - + +
491A EDO 2.9 34.1 + - - -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 3.2 51.1 + - - +
113A THR* 4.2 2.9 - - - -
114A LEU* 3.4 23.3 - - - +
151A ASP 5.0 0.6 + - - -
152A ILE* 3.5 13.3 - - - +
154A ASP* 1.3 78.3 - - - +
156A ALA* 1.3 61.7 + - - -
158A ILE* 4.6 9.2 - - - +
159A GLY 3.0 18.9 + - - -
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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
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3A ILE* 3.9 23.6 - - + +
5A VAL* 4.4 13.0 - - + -
113A THR* 4.0 8.0 - - + +
117A VAL* 3.7 23.3 - - + +
144A LEU* 5.5 0.7 - - + -
152A ILE 3.2 8.3 + - - +
153A GLU 3.2 10.8 + - - +
154A ASP 3.1 1.0 - - - -
155A SER* 1.3 79.5 - - - +
157A LYS* 1.3 62.8 + - - +
160A SER* 3.0 24.8 + - - -
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 5.7 2.9 - - - -
153A GLU* 3.2 11.7 + - - +
154A ASP* 2.9 18.9 + - - +
156A ALA* 1.3 78.6 - - - +
158A ILE* 1.3 57.9 - - - +
160A SER* 3.2 8.9 - - - -
161A ALA* 2.9 26.2 + - + +
289A MSE 4.3 10.2 + - - -
290A LEU* 4.0 30.8 + - + +
291A ASN* 5.8 1.2 - - - +
491A EDO 3.5 20.4 + - - +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.8 21.8 - - + -
154A ASP* 2.9 32.4 + - + +
155A SER* 3.8 8.3 - - - +
157A LYS* 1.3 72.4 - - - +
159A GLY* 1.3 67.2 + - - +
160A SER 3.1 1.3 - - - -
161A ALA* 3.1 1.7 + - - +
162A ILE* 2.9 39.9 + - + +
290A LEU* 3.9 16.2 - - + -
472A HIS* 5.6 0.2 - - - +
475A ILE* 3.9 23.8 - - + -
479A LYS* 6.4 0.2 - - - +
491A EDO 3.9 27.6 - - - +
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.5 35.4 - - - +
117A VAL* 4.7 0.4 - - - -
118A ARG* 3.4 22.2 - - - +
155A SER 3.0 11.2 + - - -
156A ALA 4.0 0.9 - - - -
158A ILE* 1.3 79.8 - - - +
160A SER* 1.3 61.2 + - - +
162A ILE* 4.6 1.3 - - - -
163A ALA* 3.1 18.9 + - - +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 5.0 3.6 - - - +
3A ILE* 3.9 24.7 - - - +
117A VAL* 3.8 3.7 - - - +
121A ILE* 4.0 17.9 - - - +
156A ALA 3.0 15.2 + - - -
157A LYS* 3.2 12.3 - - - -
158A ILE 3.1 0.2 - - - -
159A GLY* 1.3 77.2 - - - +
161A ALA* 1.3 62.6 + - - +
163A ALA* 3.3 3.3 + - - +
164A CYS* 2.9 22.6 + - - +
289A MSE 5.1 6.1 - - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LYS 2.9 8.6 + - - +
158A ILE 3.1 3.6 + - - +
160A SER* 1.3 74.9 + - - +
162A ILE* 1.3 64.3 + - - +
164A CYS* 3.1 5.2 + - - +
165A GLY 3.0 17.7 + - - -
286A ALA* 3.6 17.9 - - - +
289A MSE 4.1 23.5 - - + +
290A LEU* 3.5 41.7 - - + -
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 4.3 7.2 - - + -
118A ARG* 3.5 23.3 - - - -
158A ILE* 2.9 31.2 + - + +
159A GLY 3.9 3.6 - - - +
161A ALA* 1.3 75.9 - - + +
163A ALA* 1.3 56.4 + - - +
165A GLY* 3.0 4.3 + - - -
166A GLN* 2.8 26.4 + - - +
286A ALA* 4.3 6.5 - - - -
467A VAL* 4.1 5.1 - - + +
468A PRO* 3.7 24.7 - - + +
471A VAL* 3.7 31.6 - - + -
472A HIS* 3.8 34.1 - - + +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ARG* 3.4 32.0 - - + +
121A ILE* 3.5 26.2 - - + -
122A SER* 4.0 4.0 - - - +
159A GLY 3.1 19.7 + - - +
160A SER 3.7 2.5 - - - +
162A ILE* 1.3 76.0 - - - +
164A CYS* 1.3 58.3 + - - +
166A GLN* 4.3 7.2 - - - -
167A ASN* 3.0 35.2 + - - +
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Residues in contact with CYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.6 1.1 - - + +
160A SER* 2.9 14.0 + - - +
161A ALA 3.1 9.4 + - - +
163A ALA* 1.3 78.1 - - - +
165A GLY* 1.3 55.7 + - - +
167A ASN* 3.5 2.8 + - - +
168A TYR* 3.1 26.9 + - - +
285A LYS* 3.9 21.7 + - - -
289A MSE 3.7 30.5 - - + -
505A CL 4.2 20.6 - - + -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA 3.0 12.9 + - - -
162A ILE 3.0 4.2 + - - -
164A CYS* 1.3 74.8 - - - +
166A GLN* 1.3 58.5 + - - +
168A TYR* 3.3 3.7 + - - +
169A ALA* 2.9 25.5 + - - +
282A GLY* 3.3 36.7 - - - -
285A LYS* 4.7 5.3 - - - +
286A ALA* 4.7 2.2 - - - +
467A VAL* 4.1 5.2 - - - -
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Residues in contact with GLN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 5.0 2.8 + - - -
118A ARG* 2.8 42.9 + - - +
122A SER* 3.9 16.5 + - - +
162A ILE 2.8 16.4 + - - +
163A ALA* 3.4 8.3 + - - +
165A GLY* 1.3 71.3 - - - +
167A ASN* 1.3 63.7 + - - +
169A ALA* 3.3 3.3 + - - +
170A LYS* 2.8 32.6 + - - +
463A SER 2.9 25.8 + - - +
464A GLY* 3.5 24.9 - - - +
465A ARG* 4.5 5.3 - - - +
467A VAL* 4.0 2.4 - - + +
468A PRO* 3.6 25.3 - - + +
501A FMT 4.8 1.8 + - - -
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Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.2 25.4 + - - +
122A SER* 3.6 7.5 + - - -
125A TYR* 3.6 22.5 - - + +
163A ALA 3.0 17.8 + - - +
164A CYS 3.9 3.4 - - - +
166A GLN* 1.3 74.6 - - - +
168A TYR* 1.3 67.2 + - - +
170A LYS* 2.9 34.5 + - - +
171A ASP* 2.9 28.6 + - - +
505A CL 3.4 26.9 - - + +
507A EDO 3.9 4.6 + - - -
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A CYS 3.1 17.3 + - - +
165A GLY 3.6 3.8 - - - +
166A GLN 3.2 0.2 - - - -
167A ASN* 1.3 77.1 - - - +
169A ALA* 1.3 63.0 + - - +
171A ASP* 3.0 27.3 + - + +
172A LEU* 3.1 28.9 + - + +
188A GLU* 2.9 33.3 + - - +
192A LEU* 4.6 7.3 - - + +
281A MSE 3.3 60.2 - - + +
282A GLY* 4.2 0.7 - - - -
285A LYS* 3.9 37.0 - - + +
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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
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165A GLY 2.9 14.4 + - - +
166A GLN 3.5 7.6 - - - +
168A TYR* 1.3 76.9 - - - +
170A LYS* 1.3 61.6 + - - +
172A LEU* 3.2 2.3 + - - -
173A GLN* 2.9 30.5 + - - +
278A ALA* 3.4 37.7 + - + +
279A ALA* 4.1 2.9 - - + +
464A GLY* 4.0 15.9 - - - -
467A VAL* 4.2 8.3 - - + -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER* 2.9 43.4 + - - -
123A GLU* 5.6 1.6 + - - -
125A TYR* 3.6 32.5 - - + +
166A GLN* 2.8 19.4 + - - +
167A ASN* 2.9 25.2 + - - +
169A ALA* 1.3 72.2 - - - +
171A ASP* 1.3 63.7 + - - +
173A GLN* 3.2 1.8 + - - +
174A ASN* 2.9 32.2 + - - +
462A ALA* 3.9 24.9 - - + +
463A SER* 3.6 22.4 - - - +
464A GLY 3.9 12.8 - - - +
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 2.6 35.0 + - - -
126A VAL 5.0 1.0 - - - +
127A PHE* 3.7 17.6 - - + -
129A GLN* 5.3 5.6 - - - +
167A ASN 2.9 17.5 + - - +
168A TYR* 3.2 22.2 - - + +
170A LYS* 1.3 74.2 - - - +
172A LEU* 1.3 66.0 + - + +
174A ASN* 3.2 2.8 + - - +
175A LEU* 3.1 29.3 + - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR* 3.1 28.5 + - + +
169A ALA 3.2 4.9 + - - +
171A ASP* 1.3 83.7 - - + +
173A GLN* 1.3 61.4 + - - +
174A ASN 3.4 0.3 + - - -
175A LEU* 3.6 20.1 + - + +
180A CYS* 4.1 10.3 - - - -
184A TYR* 4.2 12.1 - - + +
185A MSE 4.0 26.9 - - + -
188A GLU* 4.0 23.1 - - + +
274A MSE 4.3 8.7 - - + +
277A VAL* 6.5 0.2 - - + -
278A ALA* 4.0 17.3 - - + +
281A MSE 3.5 39.5 - - + -
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA* 2.9 24.5 + - - +
170A LYS 3.8 4.0 - - - +
172A LEU* 1.3 77.3 - - - +
174A ASN* 1.3 61.6 + - - +
175A LEU 3.6 5.5 + - - +
273A ASP* 2.6 37.2 + - - +
274A MSE 4.7 6.8 - - - +
275A GLY* 4.1 13.4 - - - +
278A ALA* 3.7 14.4 - - + +
453A ALA* 3.1 30.3 + - - +
462A ALA* 3.9 13.5 - - + +
464A GLY* 3.6 27.5 + - - -
465A ARG 4.8 1.4 - - - +
503A EDO 3.6 20.8 - - - -
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 3.1 33.9 + - - -
127A PHE* 3.8 34.2 - - + +
130A LEU* 5.4 0.2 - - - +
170A LYS* 2.9 17.6 + - - +
171A ASP 3.2 4.2 + - - +
173A GLN* 1.3 77.8 - - - +
175A LEU* 1.3 63.9 + - - +
176A PRO* 3.6 4.9 - - - +
462A ALA* 3.8 13.8 + - - +
503A EDO 3.3 18.8 + - - -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 4.1 14.6 - - + -
129A GLN* 3.9 24.9 - - - +
130A LEU* 4.6 4.3 - - + -
171A ASP* 3.1 20.1 + - + +
172A LEU* 4.0 12.7 - - + +
173A GLN 3.4 8.1 - - - +
174A ASN* 1.3 77.6 - - - +
176A PRO* 1.3 77.4 - - + +
177A ALA* 4.0 1.0 + - - -
179A ILE* 4.2 12.8 - - + -
180A CYS* 3.8 23.8 - - + +
184A TYR* 3.4 43.7 - - + +
274A MSE 6.0 1.0 - - - +
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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
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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