Contacts of the helix formed by residues 157 - 178 (chain B) in PDB entry 3PJF
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 ASN 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.5 20.2 - - - -
99B GLN 2.9 26.6 + - - +
101B ASP 3.5 15.8 + - - +
102B GLY 3.1 24.4 + - - +
104B TYR* 3.4 39.7 + - + +
107B ALA* 4.1 2.8 - - - +
108B VAL* 6.0 0.7 - - + -
153B ILE 4.6 0.9 - - - +
154B PRO* 4.5 0.5 - - - +
155B ASN 3.4 20.3 + - - -
156B TYR* 1.3 77.1 - - - +
158B VAL* 1.3 60.3 + - + +
160B GLY* 2.9 22.3 + - - -
161B LEU* 3.8 3.8 - - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 4.8 3.1 - - + -
99B GLN* 3.7 31.4 - - + +
100B LEU* 4.9 1.3 - - + -
104B TYR* 3.6 6.5 - - + -
108B VAL* 3.9 19.3 - - + -
112B GLY 4.4 2.5 - - - +
113B PHE* 3.8 38.8 - - + -
116B ALA* 3.9 17.5 - - + -
117B HIS* 4.0 7.2 - - + +
156B TYR 3.3 0.2 + - - -
157B ASN* 1.3 76.3 - - + +
159B MET* 1.3 66.6 + - - +
160B GLY 2.9 2.5 - - - -
161B LEU* 3.0 19.4 + - + -
162B ALA* 3.0 12.0 + - - +
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.5 23.6 - - + -
94B PHE 3.4 17.5 - - - +
95B ALA* 3.5 18.6 - - + +
100B LEU* 4.0 8.9 - - + +
116B ALA* 4.3 3.8 - - + -
120B SER* 3.3 29.2 - - - +
156B TYR* 3.0 48.6 + - + +
158B VAL* 1.3 81.3 - - - +
160B GLY* 1.3 56.0 + - - +
162B ALA* 3.3 4.9 + - - -
163B LYS* 2.8 40.8 + - - +
504B TCL 4.2 12.6 - - + -
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ALA* 4.0 1.8 - - - +
172A TYR* 3.5 13.0 - - - -
148B GLY 3.5 20.9 - - - -
149B ALA* 3.4 11.3 - - - -
156B TYR* 3.4 8.4 - - - -
157B ASN 2.9 12.9 + - - -
159B MET* 1.3 80.0 - - - +
161B LEU* 1.3 55.8 + - - +
164B ALA* 3.0 23.9 + - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 4.1 0.4 - - - +
165A SER* 3.5 20.5 - - - +
168A ALA* 3.9 8.1 - - - -
169A ASN* 3.5 28.9 - - + +
172A TYR* 3.8 17.9 - - + -
104B TYR* 3.2 31.2 - - + +
113B PHE* 3.7 26.9 - - + -
117B HIS* 3.4 15.7 + - + +
157B ASN 3.8 15.7 - - - +
158B VAL* 3.0 9.9 + - + +
160B GLY* 1.3 73.6 - - - +
162B ALA* 1.3 60.0 + - - +
164B ALA* 3.2 3.6 + - - +
165B SER* 2.9 25.1 + - - -
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.7 32.3 - - + +
117B HIS* 3.4 16.5 + - + +
120B SER* 4.1 4.9 - - - -
121B SER* 3.6 5.0 - - - -
158B VAL 3.0 11.5 + - - +
159B MET* 3.3 20.8 + - - +
161B LEU* 1.3 78.2 - - - +
163B LYS* 1.3 58.0 + - - +
165B SER* 3.2 4.5 + - - -
166B LEU* 2.8 26.7 + - - +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE 4.8 2.8 + - - -
93B VAL* 4.1 17.4 - - - +
120B SER* 5.1 4.3 + - - -
144B LEU 2.8 23.6 + - - -
145B SER* 3.8 13.9 - - - +
146B TYR 4.6 2.2 - - - +
149B ALA* 3.5 21.1 - - + +
156B TYR* 3.5 29.2 - - + +
159B MET* 2.8 26.6 + - + +
160B GLY 3.9 1.1 - - - +
162B ALA* 1.3 73.5 - - - +
164B ALA* 1.3 62.2 + - - +
166B LEU* 3.2 20.3 + - + +
167B GLU* 2.9 33.1 + - - +
503B NAD 2.9 32.0 + - - -
504B TCL 4.1 0.4 - - - -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA* 3.5 34.8 - - + +
168A ALA* 3.6 12.6 - - + -
171A ARG* 4.7 1.6 - - - +
149B ALA* 3.5 17.2 - - - +
160B GLY 3.0 16.0 + - - +
161B LEU 3.4 8.5 - - - +
163B LYS* 1.3 77.1 - - - +
165B SER* 1.3 62.3 + - - +
167B GLU* 3.4 5.4 + - - +
168B ALA 3.1 17.5 + - - -
171B ARG* 4.8 1.4 + - - -
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.8 0.5 - - - -
117A HIS* 2.9 31.9 + - - -
161A LEU* 3.5 23.8 - - - +
164A ALA* 4.4 1.3 - - - +
165A SER* 4.3 1.3 - - - +
117B HIS* 3.8 11.2 - - - -
121B SER* 2.9 15.0 + - - -
161B LEU 2.9 12.6 + - - -
162B ALA 3.2 9.9 - - - -
164B ALA* 1.3 77.6 - - - +
166B LEU* 1.3 57.0 + - - -
168B ALA* 3.2 1.4 + - - +
169B ASN* 2.9 27.4 + - - +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B HIS* 4.5 1.3 - - + +
120B SER 3.6 26.5 - - - +
121B SER* 3.3 10.7 + - - +
124B PHE* 3.8 29.4 - - + -
143B THR* 3.5 29.8 - - + +
144B LEU 3.4 26.7 - - - +
145B SER* 4.7 3.8 - - - -
162B ALA 2.8 14.5 + - - +
163B LYS* 3.2 24.0 + - + +
165B SER* 1.3 77.0 - - - +
167B GLU* 1.3 58.6 + - + +
169B ASN* 3.0 6.9 + - + +
170B VAL* 3.0 26.4 + - - +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B SER* 2.5 34.9 + - - +
146B TYR 3.9 3.8 - - - +
149B ALA* 3.4 18.4 - - - +
150B GLU* 4.1 20.1 - - - +
163B LYS 2.9 16.4 + - - +
164B ALA* 3.9 5.2 - - - +
166B LEU* 1.3 75.7 - - + +
168B ALA* 1.3 61.8 + - - +
170B VAL* 3.2 19.3 + - - +
171B ARG* 3.3 28.4 + - - +
186B ALA* 5.3 2.2 - - + -
188B SER* 4.6 2.6 + - - -
244B VAL* 3.9 36.4 - - + +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA 4.2 2.9 - - - +
160A GLY 4.1 3.6 - - - +
161A LEU* 3.8 16.4 - - + +
164A ALA* 3.6 28.9 - - + -
164B ALA 3.1 5.3 + - - -
165B SER 3.5 8.3 - - - +
167B GLU* 1.3 74.4 - - - +
169B ASN* 1.3 66.4 + - - +
171B ARG* 3.1 21.2 + - - +
172B TYR* 3.0 32.7 + - + -
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 2.8 22.7 + - - -
161A LEU* 3.4 20.1 - - + +
121B SER* 2.9 32.5 + - - -
122B TYR* 4.4 0.4 - - - +
124B PHE* 4.2 2.4 - - + +
125B VAL* 3.6 19.5 - - - +
165B SER 2.9 13.5 + - - +
166B LEU* 3.0 17.5 - - + +
168B ALA* 1.3 76.9 - - - +
170B VAL* 1.3 54.5 + - - +
172B TYR* 4.7 0.2 - - - -
173B MET* 2.8 54.1 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 3.9 9.0 - - + -
143B THR* 3.6 29.4 - - + -
166B LEU 3.0 18.1 + - - +
167B GLU* 3.3 12.6 - - - +
168B ALA 3.2 0.2 - - - -
169B ASN* 1.3 77.1 - - - +
171B ARG* 1.3 56.6 + - - +
173B MET* 3.8 1.2 - - - +
174B ALA* 2.9 31.0 + - - +
184B VAL* 3.6 28.5 - - - +
185B ASN* 3.7 15.0 - - - +
186B ALA* 3.7 13.2 - - + +
242B GLY* 3.9 15.3 - - - +
243B GLU 4.2 2.7 - - - +
244B VAL* 5.2 2.5 - - + -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA 3.2 22.8 + - - -
150A GLU* 3.0 31.3 + - - +
151A ARG* 4.3 4.8 - - - +
152A ALA* 3.4 16.3 - - + +
164A ALA* 4.9 1.6 - - - +
164B ALA 4.8 2.0 + - - -
167B GLU* 3.4 28.0 + - - +
168B ALA* 3.1 24.5 + - - +
170B VAL* 1.3 75.4 - - + +
172B TYR* 1.3 61.8 + - + +
174B ALA* 3.4 6.2 + - - +
175B ASN* 2.9 29.8 + - - +
242B GLY* 3.6 20.8 + - - +
244B VAL* 4.4 10.9 - - + +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 3.6 29.2 - + + +
148A GLY* 2.6 39.1 + - - -
149A ALA 5.6 0.2 - - - -
151A ARG 3.1 16.2 + - - -
152A ALA* 3.9 9.9 - - + -
153A ILE 3.4 30.0 + - - -
156A TYR* 3.6 5.7 - - - +
157A ASN* 3.6 30.5 - - - -
160A GLY* 3.5 16.5 - - - -
161A LEU* 3.7 13.5 - - + -
168B ALA* 3.0 30.5 + - + +
169B ASN 4.0 0.7 - - - +
171B ARG* 1.3 75.3 - - + +
173B MET* 1.3 61.5 + - - +
175B ASN* 3.4 4.0 + - + +
176B ALA* 3.0 29.5 + - - +
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Residues in contact with MET 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 3.9 12.6 - - + -
105A VAL* 4.3 7.9 - - + -
124B PHE* 3.5 46.2 - - + +
125B VAL* 3.8 12.3 - - + -
128B ALA* 3.7 28.9 - - + -
141B LEU* 3.8 16.2 - - + -
169B ASN* 2.8 43.1 + - - +
170B VAL 3.8 2.9 - - - +
172B TYR* 1.3 75.2 - - - +
174B ALA* 1.3 60.1 + - - +
176B ALA 3.2 0.7 + - - -
177B MET* 2.8 37.5 + - - +
184B VAL* 3.9 11.7 - - + -
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL 2.9 18.8 + - - +
171B ARG 3.7 3.8 - - - +
173B MET* 1.3 76.4 - - - +
175B ASN* 1.3 58.2 + - - +
177B MET 4.8 0.2 - - - +
178B GLY* 3.0 29.4 + - - +
182B VAL 4.5 0.8 - - - +
184B VAL* 3.8 13.6 - - - +
241B SER* 3.5 19.0 + - - +
242B GLY* 3.4 26.9 - - - +
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA* 3.6 30.3 + - + +
153A ILE 5.2 0.4 - - - -
154A PRO* 4.6 19.4 - - - +
171B ARG 2.9 18.7 + - - +
172B TYR* 3.8 4.6 - - + +
173B MET 3.2 0.2 - - - -
174B ALA* 1.3 78.1 - - - +
176B ALA* 1.3 60.6 + - - +
179B PRO* 3.6 16.6 - - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASP* 3.5 28.6 - - - +
104A TYR* 4.2 11.4 - - + +
105A VAL* 4.2 14.6 - - + +
132B ARG* 3.4 12.5 + - - -
172B TYR 3.0 17.1 + - - +
173B MET 3.2 1.8 + - - +
175B ASN* 1.3 79.5 - - - +
177B MET* 1.3 61.2 + - - +
178B GLY 3.5 0.2 - - - -
179B PRO* 3.5 11.4 - - - +
180B GLU* 3.9 1.9 - - - +
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Residues in contact with MET 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.9 24.5 - - + -
128B ALA* 4.2 19.3 - - + +
132B ARG* 4.0 30.1 - - + +
135B LEU* 3.8 28.5 - - + -
141B LEU* 4.1 18.2 - - + -
173B MET* 2.8 23.6 + - - +
176B ALA* 1.3 72.6 - - - +
178B GLY* 1.3 65.0 + - - +
179B PRO* 3.3 2.9 - - - -
180B GLU* 3.0 32.3 + - - +
182B VAL* 3.3 26.8 + - + +
184B VAL* 4.4 6.5 - - + -
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA 3.0 17.5 + - - -
177B MET* 1.3 77.1 - - - +
179B PRO* 1.3 57.3 - - - +
181B GLY* 2.8 26.2 + - - -
182B VAL 3.3 14.0 + - - -
241B SER* 5.8 0.9 - - - -
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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
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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