Contacts of the helix formed by residues 148 - 173 (chain A) in PDB entry 2GDZ
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 GLN 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASN* 2.8 38.0 + - - +
97A GLU* 3.3 12.3 - - + +
145A VAL* 3.0 31.1 + - + +
147A GLN* 1.3 85.8 - - - +
149A PRO* 1.3 60.8 - - - +
150A VAL 3.2 2.9 + - - -
151A TYR* 3.3 26.4 + - + -
152A CYS* 2.8 28.1 + - - +
190A ILE* 5.8 2.8 - - - +
194A ILE* 4.8 6.2 - - - +
200A MET* 4.2 6.5 - - + -
210A ILE* 3.7 20.4 - - + +
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 3.3 13.2 - - - +
145A VAL 3.9 6.5 - - - +
146A ALA* 3.6 13.0 - - - +
147A GLN 3.6 2.2 - - - -
148A GLN* 1.3 88.1 - - - +
150A VAL* 1.3 59.1 + - + +
152A CYS* 3.4 6.8 - - + +
153A ALA* 2.9 26.2 + - - +
203A TYR* 3.4 36.6 - - + +
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 2.9 18.6 + - - +
100A TRP* 3.6 45.5 - - + +
103A THR* 4.6 7.2 - - + -
104A LEU* 3.6 33.4 - - + -
149A PRO* 1.3 77.8 - - + +
151A TYR* 1.3 68.5 + - - +
153A ALA* 3.1 6.9 + - + +
154A SER* 2.8 23.0 + - - -
203A TYR* 6.1 0.9 - - + +
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Residues in contact with TYR 151 (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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94A VAL 3.4 27.8 - - - -
95A ASN* 4.2 14.6 - - + +
97A GLU* 2.8 17.7 + - - +
103A THR* 4.6 7.5 - - + +
107A ASN* 3.5 10.8 - - - -
138A SER* 4.2 3.8 - - - -
140A ALA* 3.8 25.4 - - + -
148A GLN* 3.6 30.7 - - + +
150A VAL* 1.3 75.8 - - - +
152A CYS* 1.3 63.2 + - - +
154A SER* 2.7 22.6 + - - -
155A LYS* 2.9 24.5 + - + +
190A ILE* 4.6 8.1 - - + +
300A NAD 2.6 50.9 + + - -
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Residues in contact with CYS 152 (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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140A ALA* 3.3 27.6 - - - +
143A MET 3.5 10.8 - - - -
144A PRO* 3.9 12.8 - - - -
145A VAL* 4.0 12.8 - - + +
148A GLN 2.8 21.3 + - - +
149A PRO* 3.4 9.0 - - + +
151A TYR* 1.3 73.9 - - - +
153A ALA* 1.3 55.7 + - - +
155A LYS 3.2 0.9 + - - -
156A HIS* 2.9 54.7 + - - -
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Residues in contact with ALA 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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104A LEU* 4.6 9.9 - - + -
108A LEU* 4.9 1.7 - - - +
149A PRO 2.9 17.0 + - - +
150A VAL* 3.1 14.3 + - + +
152A CYS* 1.3 73.0 - - - +
154A SER* 1.3 54.0 + - - +
156A HIS* 3.2 7.6 + - - +
157A GLY* 2.8 32.4 + - - -
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 4.8 1.8 - - - -
104A LEU* 3.9 19.5 - - - +
107A ASN* 3.2 42.3 + - - +
108A LEU* 3.9 12.0 - - - +
150A VAL 2.8 14.5 + - - -
151A TYR* 2.7 18.8 + - - -
153A ALA* 1.3 71.7 - - - +
155A LYS* 1.3 62.7 + - - +
157A GLY* 3.3 2.9 + - - -
158A ILE* 3.0 30.6 + - - +
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Residues in contact with LYS 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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92A ALA 5.3 1.0 + - - -
93A GLY* 5.2 0.2 - - - -
107A ASN* 4.2 13.0 + - - +
136A MET 3.0 17.4 + - - -
137A SER* 2.8 40.0 + - - +
138A SER* 4.0 4.3 - - - +
140A ALA* 3.8 3.1 - - + -
141A GLY* 3.4 24.8 - - - +
151A TYR* 2.9 50.8 + - + +
152A CYS 3.9 0.2 - - - +
154A SER* 1.3 78.3 - - - +
156A HIS* 1.3 64.8 + - - +
158A ILE* 3.3 12.5 + - + +
159A VAL* 3.2 12.3 + - - +
300A NAD 2.9 43.9 + - - -
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Residues in contact with HIS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA 2.9 28.7 + - - -
141A GLY 3.3 26.1 + - - -
142A LEU* 3.7 9.4 + - - -
143A MET 3.6 12.9 - - - -
144A PRO* 4.8 0.4 - - + -
152A CYS* 2.9 33.8 + - - +
153A ALA* 3.5 7.6 - - - +
155A LYS* 1.3 73.6 - - - +
157A GLY* 1.3 66.6 + - - +
159A VAL* 3.1 4.7 + - - +
160A GLY* 3.0 21.0 + - - -
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Residues in contact with GLY 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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108A LEU* 3.6 21.7 - - - +
153A ALA 2.8 15.3 + - - -
154A SER 3.3 4.9 + - - -
155A LYS 3.2 0.2 - - - -
156A HIS* 1.3 76.8 - - - +
158A ILE* 1.3 62.2 + - - +
160A GLY* 3.4 1.0 + - - -
161A PHE* 2.9 26.3 + - - +
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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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107A ASN 3.2 26.7 - - - +
108A LEU* 4.0 8.7 - - + -
111A VAL* 4.1 15.9 - - + -
135A ASN* 3.6 29.4 - - + -
136A MET 3.3 20.9 - - - +
137A SER* 4.0 17.3 - - - +
154A SER 3.0 15.4 + - - +
155A LYS* 3.6 22.4 - - + +
156A HIS 3.2 0.4 - - - -
157A GLY* 1.3 76.8 - - - +
159A VAL* 1.3 56.8 + - - +
161A PHE* 4.4 4.7 - - - -
162A THR* 2.7 39.3 + - - +
180A ALA* 4.5 2.7 - - + -
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Residues in contact with VAL 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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137A SER* 3.4 26.7 - - - +
141A GLY 3.8 18.2 - - - +
142A LEU* 4.2 12.6 - - + -
155A LYS 3.2 5.6 + - - +
156A HIS* 3.1 7.5 + - - +
158A ILE* 1.3 75.6 - - - +
160A GLY* 1.3 64.6 + - - +
162A THR* 3.8 1.1 - - - -
163A ARG* 3.0 37.5 + - - +
180A ALA* 5.2 1.1 - - + -
182A CYS* 4.2 7.4 - - - -
242A ILE* 4.2 14.1 - - + -
256A TYR* 3.5 24.9 - - - +
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Residues in contact with GLY 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 HIS 3.0 12.8 + - - -
157A GLY 3.9 1.3 - - - -
159A VAL* 1.3 78.4 - - - +
161A PHE* 1.3 61.5 + - - +
163A ARG* 4.1 5.0 - - - +
164A SER* 2.8 31.8 + - - -
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Residues in contact with PHE 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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111A VAL* 4.4 5.2 - - + -
112A ILE* 3.9 44.9 - - + -
115A THR* 3.6 43.7 - - + -
116A TYR* 3.8 33.2 - + - -
135A ASN* 4.2 12.1 - - - -
157A GLY 2.9 20.7 + - - +
158A ILE* 3.8 2.9 - - - +
160A GLY* 1.3 74.9 - - - +
162A THR* 1.3 57.0 + - - +
164A SER* 3.3 6.0 + - - -
165A ALA* 2.8 43.9 + - + +
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Residues in contact with THR 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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135A ASN* 3.0 30.0 + - - +
158A ILE* 2.7 26.8 + - - +
159A VAL 4.0 1.6 - - - -
161A PHE* 1.3 77.2 - - - +
163A ARG* 1.4 64.9 - - - +
165A ALA* 3.3 4.3 + - - +
166A ALA* 2.9 23.2 + - - +
178A LEU* 3.7 11.1 - - + +
179A ASN* 3.5 43.3 - - - +
180A ALA* 3.9 8.3 - - + +
240A GLY* 5.2 0.9 - - - -
242A ILE* 4.8 4.3 - - + -
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Residues in contact with ARG 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 VAL* 3.0 23.6 + - - +
160A GLY* 4.1 4.7 - - - +
162A THR* 1.4 74.7 - - - +
164A SER* 1.3 63.5 + - - +
166A ALA* 3.5 7.0 + - - +
167A LEU* 3.2 29.4 + - + +
240A GLY* 4.2 13.2 + - - +
242A ILE* 3.8 17.7 - - + -
256A TYR* 3.4 71.8 - - - +
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Residues in contact with SER 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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160A GLY 2.8 23.3 + - - -
161A PHE* 3.5 5.6 - - - -
163A ARG* 1.3 75.7 - - - +
165A ALA* 1.3 65.3 + - - +
167A LEU* 3.1 13.6 + - - +
168A ALA* 3.0 21.9 + - - +
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Residues in contact with ALA 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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115A THR* 4.9 0.7 - - + -
116A TYR* 5.7 2.2 - - + -
119A LEU* 5.5 5.9 - - + +
161A PHE* 2.8 40.3 + - + +
162A THR* 3.9 2.9 - - - +
164A SER* 1.3 72.8 - - - +
166A ALA* 1.4 52.2 + - - +
168A ALA* 3.3 9.1 + - - +
169A ALA* 2.8 35.0 + - - +
178A LEU* 3.7 26.7 - - + +
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Residues in contact with ALA 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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162A THR 2.9 14.4 + - - +
163A ARG 3.6 4.0 - - - +
164A SER 3.2 0.2 - - - -
165A ALA* 1.4 75.5 - - - +
167A LEU* 1.3 63.3 + - + +
169A ALA* 3.3 3.1 + - - +
170A ASN* 3.3 13.7 + - - -
178A LEU* 3.7 11.6 - - - +
239A ASN* 3.2 31.6 + - - +
240A GLY* 3.3 40.4 - - - +
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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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163A ARG* 3.2 14.8 + - + +
164A SER* 3.1 13.1 + - - +
166A ALA* 1.3 78.7 - - + +
168A ALA* 1.3 60.8 - - - +
170A ASN* 3.1 28.8 + - + +
171A LEU* 3.1 20.6 + - + +
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Residues in contact with ALA 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 SER 3.0 13.0 + - - +
165A ALA* 3.4 12.8 - - - +
167A LEU* 1.3 73.6 - - - +
169A ALA* 1.3 58.8 + - - +
171A LEU* 3.1 14.1 + - - +
172A MET* 2.9 52.2 + - + +
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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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119A LEU* 5.6 2.5 - - + -
165A ALA 2.8 17.5 + - - +
166A ALA 3.5 9.6 - - - +
167A LEU 3.3 0.2 - - - -
168A ALA* 1.3 73.4 - - - +
170A ASN* 1.3 62.8 + - - +
172A MET* 3.4 5.3 + - - -
173A ASN* 3.0 19.1 + - - -
174A SER* 3.2 24.5 + - - +
175A GLY 4.7 0.5 + - - -
176A VAL* 3.2 27.1 - - + +
178A LEU* 3.7 9.6 - - + -
239A ASN* 5.0 2.0 - - - +
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Residues in contact with ASN 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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166A ALA 3.3 4.0 + - - -
167A LEU* 3.1 23.2 + - - +
169A ALA* 1.3 77.4 - - - +
171A LEU* 1.3 66.4 + - + +
173A ASN* 3.2 14.0 + - - +
239A ASN* 3.1 29.2 + - - +
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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
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167A LEU* 3.1 16.0 + - + +
168A ALA* 3.1 15.0 + - - +
170A ASN* 1.3 78.9 - - + +
172A MET* 1.3 64.1 + - + +
173A ASN* 3.6 0.9 + - - +
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Residues in contact with MET 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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119A LEU* 6.1 4.5 - - - -
125A GLN* 3.6 19.8 + - + +
168A ALA* 2.9 35.0 + - + +
169A ALA* 3.9 6.7 - - - +
171A LEU* 1.3 77.2 - - + +
173A ASN* 1.3 70.3 + - - +
174A SER* 4.2 11.0 - - - +
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Residues in contact with ASN 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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124A LYS* 3.9 18.9 + - - +
125A GLN* 3.2 25.4 + - - +
169A ALA 3.0 7.4 + - - -
170A ASN* 3.2 10.7 + - - +
171A LEU 3.3 1.3 - - - +
172A MET* 1.3 78.3 - - - +
174A SER* 1.3 62.4 + - - +
175A GLY* 3.2 7.2 + - - +
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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) + - + + + + + -
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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