Contacts of the helix formed by residues 138 - 165 (chain A) in PDB entry 3BQY
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 GLY 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY 3.7 2.8 + - - -
137A PHE* 1.3 76.0 - - - +
139A ASP* 1.3 67.4 + - - -
140A GLY 3.3 2.9 - - - -
141A ASP* 3.3 13.1 + - - +
142A ALA* 2.9 21.4 + - - +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 5.5 0.9 - - - +
133A ARG* 2.7 47.5 + - - +
138A GLY* 1.3 71.1 - - - +
140A GLY* 1.3 57.9 + - - +
142A ALA* 3.9 3.2 - - - +
143A ALA* 3.0 32.1 + - - +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY 3.3 0.8 - - - -
139A ASP* 1.3 78.2 - - - +
141A ASP* 1.3 56.7 + - - +
143A ALA* 4.1 3.3 - - - +
144A ARG* 2.9 59.8 + - - +
303A PO4 5.4 0.4 - - - -
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 4.2 21.3 - - + -
138A GLY* 3.3 14.2 + - - +
140A GLY* 1.3 74.2 - - - +
142A ALA* 1.3 58.5 + - - +
144A ARG* 2.8 25.7 + - - +
145A ALA* 2.8 32.6 + - - +
216A LEU* 4.8 3.3 - - + +
219A VAL* 4.1 30.3 - - + +
220A ARG* 5.4 0.2 - - - -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.9 13.5 - - + +
132A LEU* 3.8 31.0 - - + +
133A ARG* 3.6 28.9 - - + +
137A PHE* 4.3 3.3 - - + +
138A GLY 2.9 17.1 + - - +
139A ASP 3.9 2.2 - - - +
141A ASP* 1.3 77.7 - - - +
143A ALA* 1.3 62.6 + - - +
145A ALA* 3.4 3.1 + - - +
146A LEU* 3.1 21.3 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 4.3 16.5 - - + +
139A ASP 3.0 17.9 + - - +
140A GLY* 4.1 3.6 - - - +
142A ALA* 1.3 74.2 - - - +
144A ARG* 1.3 67.9 + - + +
146A LEU* 3.2 18.5 + - + +
147A TYR* 3.4 19.8 - - + -
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 2.9 39.0 + - - +
141A ASP* 2.8 31.1 + - - +
143A ALA* 1.3 76.8 - - + +
145A ALA* 1.3 57.9 + - - +
147A TYR* 3.2 11.3 + - + +
148A SER* 3.0 31.4 + - - +
303A PO4 2.7 49.8 + - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.7 0.9 - - - -
132A LEU* 3.4 27.6 - - + -
141A ASP 2.8 19.7 + - - +
142A ALA 3.6 0.4 - - - +
143A ALA 3.2 0.2 - - - -
144A ARG* 1.3 74.1 - - - +
146A LEU* 1.3 65.0 + - - +
148A SER* 3.7 8.0 - - - -
149A VAL* 2.8 31.2 + - + +
216A LEU* 3.8 26.2 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 4.2 17.9 - - + -
125A ALA* 3.8 40.8 - - + +
128A LEU* 3.9 19.7 - - + +
129A VAL* 3.7 30.7 - - + -
142A ALA 3.1 6.2 + - - +
143A ALA* 3.2 12.5 + - + +
145A ALA* 1.3 76.5 - - - +
147A TYR* 1.3 74.4 + - + +
149A VAL* 4.0 1.0 - - - +
150A ALA* 2.9 37.4 + - + +
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Residues in contact with TYR 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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143A ALA* 3.4 25.3 + - + -
144A ARG* 3.2 11.2 + - + +
146A LEU* 1.3 91.7 - - + +
148A SER* 1.3 61.9 + - - +
150A ALA* 4.7 3.8 - - + -
151A ASN* 2.8 54.4 + - - +
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 3.0 17.4 + - - +
145A ALA* 3.7 10.1 - - - -
147A TYR* 1.3 76.5 - - - +
149A VAL* 1.3 58.3 + - - +
151A ASN* 4.3 2.2 - - - +
152A PHE* 2.9 32.7 + - - +
212A LEU* 4.0 19.7 - - - +
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Residues in contact with VAL 149 (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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90A THR* 4.5 18.4 - - + -
94A ALA* 3.7 29.6 - - + -
124A PHE* 5.6 1.1 - - + -
128A LEU* 4.0 21.3 - - + -
145A ALA* 2.8 21.3 + - + +
146A LEU 4.0 1.8 - - - +
148A SER* 1.3 76.0 - - - +
150A ALA* 1.3 59.4 + - - +
152A PHE* 3.8 1.6 - - - +
153A THR* 2.7 39.1 + - - +
209A LEU* 4.6 9.4 - - + -
212A LEU* 4.0 24.0 - - + -
213A LEU* 5.7 0.7 - - + -
216A LEU* 4.9 10.8 - - + -
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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
----------------------------------------------------------
97A LEU* 4.6 8.3 - - + -
111A PHE* 6.2 1.8 - - + -
124A PHE* 4.6 20.2 - - + -
128A LEU* 5.4 0.4 - - - +
146A LEU* 2.9 24.1 + - + +
147A TYR* 4.2 4.3 - - + +
149A VAL* 1.3 79.8 - - - +
151A ASN* 1.3 61.2 + - - +
153A THR* 3.3 5.6 + - - -
154A VAL* 2.9 37.0 + - + +
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Residues in contact with ASN 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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147A TYR* 2.8 47.8 + - - +
148A SER* 4.3 1.8 - - - +
150A ALA* 1.3 72.8 - - - +
152A PHE* 1.3 59.9 + - - +
154A VAL* 4.1 6.0 - - - +
155A GLY* 2.9 27.0 + - - -
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Residues in contact with PHE 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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148A SER 2.9 20.0 + - - +
149A VAL 3.8 0.7 - - - +
151A ASN* 1.3 78.6 - - - +
153A THR* 1.3 64.0 + - - +
155A GLY* 5.1 0.7 - - - -
156A HIS* 2.8 44.0 + + + +
204A HIS 4.6 1.6 - - - -
205A PHE* 3.6 39.9 - + - -
208A GLY* 3.7 22.2 - - - -
209A LEU* 3.8 18.8 - - + -
212A LEU* 3.7 24.2 - - + -
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Residues in contact with THR 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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94A ALA* 3.7 34.3 - - - +
97A LEU* 3.9 17.9 - - + -
98A ARG* 3.8 25.1 - - + +
101A LEU* 5.4 1.1 - - + -
149A VAL* 2.7 24.0 + - - +
150A ALA 3.3 3.8 + - - -
152A PHE* 1.3 82.8 - - - +
154A VAL* 1.3 56.0 + - - +
156A HIS* 3.7 1.4 - - - +
157A THR* 2.7 37.0 + - - +
205A PHE* 3.8 16.0 - - + -
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Residues in contact with VAL 154 (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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97A LEU* 4.6 4.9 - - + -
101A LEU* 4.5 8.7 - - + -
108A ALA* 4.3 4.8 - - + +
111A PHE* 3.8 31.6 - - + -
112A ALA* 3.8 29.4 - - + -
150A ALA* 2.9 23.4 + - + +
151A ASN* 4.1 7.0 - - - +
153A THR* 1.3 73.7 - - - +
155A GLY* 1.3 61.4 + - - +
157A THR* 3.2 4.1 + - - -
158A LEU* 2.8 41.7 + - + +
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Residues in contact with GLY 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 ASN 2.9 18.0 + - - -
152A PHE* 3.8 0.7 - - - -
154A VAL* 1.3 75.8 - - - +
156A HIS* 1.3 62.8 + - - +
158A LEU* 3.7 10.9 - - - +
159A GLU* 3.1 31.5 + - - +
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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
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98A ARG* 3.3 21.6 + - - -
152A PHE* 2.8 40.4 + - + +
153A THR 3.7 3.1 - - - +
155A GLY* 1.3 74.1 - - - +
157A THR* 1.3 66.2 + - - +
159A GLU* 3.3 5.2 + - - +
160A GLU* 2.8 47.9 + - + +
201A PHE* 3.4 29.4 + + + -
204A HIS* 4.3 9.0 - - + +
205A PHE* 3.6 29.0 + + + +
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Residues in contact with THR 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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98A ARG* 3.6 24.5 - - + +
101A LEU* 3.9 29.8 - - + -
102A LEU* 3.6 29.6 - - + -
108A ALA* 3.9 10.3 - - + -
153A THR* 2.7 23.3 + - - +
154A VAL 4.0 1.8 - - - -
156A HIS* 1.3 79.3 - - - +
158A LEU* 1.3 60.8 + - - +
160A GLU* 3.7 3.1 - - - +
161A GLN* 2.8 33.0 + - - +
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Residues in contact with LEU 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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108A ALA* 3.6 10.4 - - + +
109A ARG* 3.5 48.8 - - + +
112A ALA* 4.4 7.6 - - + -
154A VAL* 2.8 37.2 + - + +
155A GLY* 3.7 9.9 - - - +
157A THR* 1.3 77.1 - - - +
159A GLU* 1.3 64.2 + - + +
161A GLN* 3.4 3.1 + - - +
162A ALA* 2.9 28.4 + - - +
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Residues in contact with GLU 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 GLY* 3.1 19.6 + - - +
156A HIS* 3.9 3.6 - - - +
158A LEU* 1.3 78.1 - - + +
160A GLU* 1.3 64.7 + - - +
162A ALA* 3.4 8.4 + - - +
163A ALA* 3.2 23.2 + - - +
169A GLY 4.7 1.4 - - - +
170A GLY* 3.6 20.4 - - - -
171A PRO* 3.3 29.2 - - - +
201A PHE* 5.0 1.5 - - - -
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Residues in contact with GLU 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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98A ARG* 2.9 32.0 + - - -
102A LEU* 3.7 21.3 - - + +
156A HIS* 2.8 32.2 + - + +
157A THR* 3.7 5.6 - - - +
159A GLU* 1.3 75.9 - - - +
161A GLN* 1.3 62.3 + - - +
163A ALA* 3.2 5.2 + - - +
164A LEU* 3.2 37.8 + - + +
201A PHE* 3.3 45.3 - - + +
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Residues in contact with GLN 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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101A LEU 3.0 13.6 + - - -
102A LEU* 3.5 28.5 + - + +
104A HIS 2.9 27.5 + - - -
105A ARG* 4.6 1.4 - - - +
106A ASP* 3.9 16.2 - - - +
107A GLY 3.4 5.1 + - - -
108A ALA* 2.9 34.8 + - - +
109A ARG* 4.6 1.0 + - + -
157A THR* 2.8 16.5 + - - +
158A LEU* 4.0 3.6 - - - +
160A GLU* 1.3 73.8 - - + +
162A ALA* 1.3 58.5 + - - +
164A LEU* 3.2 10.7 + - + +
165A THR* 2.7 34.0 + - - -
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Residues in contact with ALA 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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158A LEU 2.9 18.0 + - - +
159A GLU* 3.7 14.8 - - - +
161A GLN* 1.3 76.0 - - - +
163A ALA* 1.3 60.7 + - - +
165A THR* 3.5 13.8 + - - -
168A GLY 3.1 25.1 - - - +
169A GLY* 3.7 20.4 - - - +
170A GLY* 4.0 3.8 - - - +
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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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159A GLU 3.2 13.3 + - - +
160A GLU 3.5 9.6 - - - +
161A GLN 3.2 0.2 - - - -
162A ALA* 1.3 76.3 - - - +
164A LEU* 1.3 61.7 + - - +
165A THR 3.6 1.4 + - - +
168A GLY* 3.6 13.3 + - - -
169A GLY 3.7 2.4 + - - +
173A ASP* 3.6 25.6 - - + +
174A GLU* 4.0 15.5 - - + +
201A PHE* 3.8 21.8 - - + -
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Residues in contact with LEU 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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102A LEU* 5.2 2.7 - - + -
160A GLU* 3.2 43.1 + - + +
161A GLN* 3.2 11.4 + - + +
163A ALA* 1.3 77.1 - - - +
165A THR* 1.3 64.4 + - - +
166A PRO* 3.5 5.4 - - - +
174A GLU* 5.3 2.0 - - - +
199A THR* 6.4 1.6 - - + -
201A PHE* 3.9 20.6 - - + -
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Residues in contact with THR 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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105A ARG* 5.1 9.2 - - - +
106A ASP* 4.5 12.9 + - - +
161A GLN 2.7 22.7 + - - -
162A ALA* 3.5 15.1 + - - -
163A ALA 3.3 1.3 - - - +
164A LEU* 1.3 78.4 - - - +
166A PRO* 1.4 74.8 - - + +
167A GLY 3.0 0.5 + - - -
168A GLY* 2.7 37.3 + - - +
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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