Contacts of the helix formed by residues 146 - 171 (chain A) in PDB entry 3D4S
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 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 4.4 2.5 - - - -
144A LEU 3.8 5.4 + - - +
145A LEU* 1.3 77.3 - - - +
147A LYS* 1.3 59.6 + - - +
148A ASN* 4.0 6.5 + - - +
149A LYS* 3.3 24.1 + - - +
150A ALA* 2.9 28.1 + - - +
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Residues in contact with LYS 147 (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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62A GLU 5.8 0.2 + - - -
65A GLN* 3.4 31.4 + - - +
66A THR* 5.1 2.5 - - - +
67A VAL* 4.5 13.7 - - + +
70A TYR* 4.0 26.8 + - + +
146A THR* 1.3 73.4 - - - +
148A ASN* 1.3 62.5 + - - +
150A ALA* 3.4 8.1 + - - +
151A ARG* 3.2 42.2 + - - +
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Residues in contact with ASN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 3.4 5.9 + - - +
147A LYS* 1.3 78.0 - - - +
149A LYS* 1.3 58.1 + - - +
151A ARG* 2.8 32.7 + - - +
152A VAL* 3.3 25.8 + - - +
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.1 19.2 - - + +
146A THR* 3.3 26.4 + - - +
147A LYS 3.2 0.4 - - - -
148A ASN* 1.3 75.9 - - - +
150A ALA* 1.3 65.3 + - - +
151A ARG 3.2 0.2 - - - -
152A VAL* 3.1 21.9 + - + +
153A ILE* 3.1 49.0 + - + +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.9 26.5 - - + -
70A TYR* 4.7 12.1 - - + -
71A PHE* 4.0 10.7 - - + -
145A LEU* 4.7 4.6 - - + +
146A THR 2.9 17.3 + - - +
147A LYS* 3.4 8.3 + - - +
149A LYS* 1.3 77.4 - - - +
151A ARG* 1.3 60.6 + - - +
153A ILE* 3.4 10.9 + - - +
154A ILE* 3.2 29.6 + - - +
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 2.9 45.0 + - + -
147A LYS* 3.2 34.5 + - - +
148A ASN* 2.8 36.9 + - - +
149A LYS 3.2 0.2 - - - -
150A ALA* 1.3 74.7 - - - +
152A VAL* 1.3 59.7 + - + +
154A ILE* 3.6 8.5 + - - +
155A LEU* 2.9 29.8 + - - +
402A CLR 3.5 39.4 + - + +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN 3.3 18.4 - - - +
149A LYS* 3.1 26.6 + - + +
151A ARG* 1.3 76.1 - - + +
153A ILE* 1.3 65.5 + - + +
155A LEU* 3.3 14.2 + - + +
156A MET* 2.9 34.7 + - + +
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.3 5.2 - - + -
126A VAL* 3.7 31.9 - - + -
145A LEU* 4.3 15.5 - - + -
149A LYS* 3.1 40.6 + - - +
150A ALA* 3.6 10.3 - - - +
152A VAL* 1.3 75.5 - - + +
154A ILE* 1.3 57.8 + - - +
156A MET* 3.2 6.4 + - - +
157A VAL* 2.9 42.1 + - + +
404A OLC 4.0 21.8 - - + +
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.2 44.0 - - + +
71A PHE* 3.7 20.9 - - + -
74A SER* 3.5 26.2 - - - +
123A THR* 5.9 0.9 - - + -
150A ALA 3.2 17.0 + - - +
151A ARG* 3.6 7.2 - - - +
152A VAL 3.3 0.2 - - - -
153A ILE* 1.3 78.4 - - - +
155A LEU* 1.3 63.0 + - - +
157A VAL* 3.1 8.8 + - - +
158A TRP* 3.1 35.2 + - + -
402A CLR 3.9 31.6 - - + -
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Residues in contact with LEU 155 (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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151A ARG 2.9 19.2 + - - +
152A VAL* 3.5 15.7 - - + +
153A ILE 3.3 0.2 - - - -
154A ILE* 1.3 78.3 - - - +
156A MET* 1.3 57.9 + - + +
158A TRP* 3.3 7.4 + - + +
159A ILE* 3.0 51.2 + - + +
402A CLR 5.0 22.2 - - + -
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Residues in contact with MET 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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152A VAL* 2.9 30.8 + - + +
153A ILE* 3.7 4.7 - - - +
155A LEU* 1.3 75.3 - - + +
157A VAL* 1.3 60.8 + - + +
158A TRP 3.2 0.7 - - - -
159A ILE* 4.2 24.7 - - + -
160A VAL* 2.9 54.1 + - + +
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Residues in contact with VAL 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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119A ALA* 4.0 7.4 - - - +
122A TRP* 3.9 28.7 - - + +
123A THR* 3.9 20.9 - - - +
126A VAL* 4.1 24.0 - - + -
153A ILE* 2.9 25.3 + - + +
154A ILE* 3.1 11.6 + - - +
156A MET* 1.3 77.4 - - + +
158A TRP* 1.3 58.3 + - + +
160A VAL* 4.9 2.0 - - - +
161A SER* 2.7 32.9 + - - +
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Residues in contact with TRP 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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74A SER* 2.9 44.8 + - - -
77A CYS 4.7 1.1 - - - -
78A ALA* 3.7 28.7 - - + -
81A VAL* 5.4 1.3 - - + -
115A LEU* 3.9 35.2 - - + +
116A CYS* 4.8 7.4 - - - -
119A ALA* 3.8 18.9 - - + +
123A THR* 4.8 0.8 + - - -
154A ILE* 3.1 26.5 + - + +
155A LEU* 3.7 8.1 - - + +
156A MET 3.2 0.2 - - - -
157A VAL* 1.3 81.9 - - + +
159A ILE* 1.3 58.8 + - + +
161A SER* 4.5 2.0 - - - -
162A GLY* 2.9 25.2 + - - -
402A CLR 3.8 71.6 - - + +
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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
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155A LEU* 3.0 44.6 + - + +
156A MET* 3.3 25.3 + - + +
158A TRP* 1.3 75.0 - - + +
160A VAL* 1.3 63.4 + - + +
162A GLY* 3.2 2.2 + - - -
163A LEU* 3.0 50.0 + - + +
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Residues in contact with VAL 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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156A MET* 2.9 40.4 + - + +
157A VAL* 4.9 2.0 - - - +
159A ILE* 1.3 77.1 - - + +
161A SER* 1.3 58.6 + - - +
163A LEU* 3.3 10.5 + - + +
164A THR* 2.9 39.9 + - + +
404A OLC 4.2 38.8 - - + -
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Residues in contact with SER 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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115A LEU* 3.6 15.4 - - - +
118A THR* 3.4 28.1 + - - +
119A ALA* 4.1 10.5 + - - -
122A TRP* 4.5 6.1 - - - -
157A VAL* 2.7 25.5 + - - +
158A TRP* 4.3 0.9 - - - -
159A ILE 3.4 0.4 - - - -
160A VAL* 1.3 77.0 - - - +
162A GLY* 1.3 58.0 + - - +
164A THR* 3.4 8.3 - - - -
165A SER* 2.8 36.6 + - - -
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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
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115A LEU* 3.6 12.1 - - - +
158A TRP 2.9 20.7 + - - -
159A ILE* 3.2 3.5 + - - -
161A SER* 1.3 76.1 - - - +
163A LEU* 1.3 58.3 + - - +
166A PHE* 2.9 43.6 + - - +
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Residues in contact with LEU 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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159A ILE* 3.0 40.9 + - + +
160A VAL* 3.3 10.7 + - + +
162A GLY* 1.3 76.7 - - - +
164A THR* 1.3 62.5 + - + +
166A PHE* 5.4 0.2 - - - -
167A LEU* 3.1 46.6 + - + +
168A PRO* 3.3 1.7 - - - +
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Residues in contact with THR 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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114A VAL* 5.3 0.5 - - - +
118A THR* 4.4 8.3 - - - +
160A VAL* 2.9 33.0 + - + +
161A SER* 3.4 12.3 + - - -
163A LEU* 1.3 77.0 - - + +
165A SER* 1.3 60.4 + - - +
168A PRO* 3.4 21.2 - - - +
199A TYR* 5.3 2.4 + - - -
203A SER* 5.0 5.9 + - - -
206A VAL* 5.0 16.9 - - + +
207A SER* 4.7 12.0 + - - -
404A OLC 5.7 3.6 - - + -
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Residues in contact with SER 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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111A SER* 3.9 4.9 - - - -
114A VAL* 3.5 22.0 + - - +
115A LEU* 3.4 33.6 - - - -
118A THR* 3.6 7.8 + - - -
161A SER 2.8 23.1 + - - -
162A GLY 4.2 0.7 - - - -
164A THR* 1.3 78.5 + - - +
166A PHE* 1.3 66.3 + - - +
168A PRO* 3.6 5.2 - - - +
169A ILE* 3.4 27.9 - - - +
199A TYR* 4.7 1.8 + - - -
207A SER* 5.2 0.5 + - - -
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Residues in contact with PHE 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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108A PHE* 4.0 33.4 - + - -
111A SER* 3.6 34.8 - - - -
112A ILE* 3.7 23.6 - - + -
115A LEU* 3.7 29.4 - - + -
162A GLY* 2.9 23.0 + - - +
163A LEU* 5.4 0.2 - - - -
165A SER* 1.3 77.6 - - - +
167A LEU* 1.3 56.7 + - - +
169A ILE* 2.9 5.7 + - - +
170A GLN* 2.8 51.3 + - + +
402A CLR 5.0 4.5 - - + -
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Residues in contact with LEU 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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162A GLY 4.1 0.4 + - - -
163A LEU* 3.1 35.8 + - + +
166A PHE* 1.3 76.7 - - - +
168A PRO* 1.4 58.1 - - + +
170A GLN* 4.5 5.4 - - + +
171A MET* 2.9 57.0 + - + +
173A TRP* 3.7 26.5 - - + -
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Residues in contact with PRO 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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163A LEU 3.3 13.7 - - - +
164A THR* 3.4 24.5 - - - +
165A SER 3.6 6.5 - - - +
167A LEU* 1.4 88.0 - - + +
169A ILE* 1.3 56.7 + - - +
171A MET 4.3 0.2 - - - -
173A TRP* 3.1 53.9 + - + -
174A TYR* 3.2 10.3 + - - -
199A TYR* 3.7 26.9 - - + -
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Residues in contact with ILE 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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107A GLU* 3.7 31.9 - - + +
110A THR* 3.8 23.8 - - + +
111A SER* 3.3 36.3 - - - +
114A VAL* 4.1 6.1 - - + -
165A SER 3.4 18.4 - - - +
166A PHE 2.9 3.6 + - - +
168A PRO* 1.3 77.7 - - - +
170A GLN* 1.3 66.3 + - - +
171A MET 3.3 0.2 - - - -
172A HIS* 3.5 4.9 + - - -
174A TYR* 3.4 35.7 - - + -
193A PHE* 4.6 2.2 - - + -
199A TYR* 3.8 24.0 - - + +
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Residues in contact with GLN 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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104A PHE* 5.6 5.4 - - - -
107A GLU* 3.9 28.1 + - - +
108A PHE* 4.0 17.5 - - - +
111A SER* 3.2 21.2 + - - -
166A PHE* 2.8 46.1 + - + +
167A LEU* 4.2 4.9 - - + +
169A ILE* 1.3 72.0 - - - +
171A MET* 1.3 66.1 + - + +
172A HIS* 3.4 15.7 + - - -
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Residues in contact with MET 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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167A LEU* 2.9 43.4 + - + +
170A GLN* 1.3 80.8 - - + +
172A HIS* 1.3 72.9 + - - +
173A TRP* 3.2 41.9 + - + +
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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