Contacts of the helix formed by residues 137 - 168 (chain A) in PDB entry 2Y4U
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 SER 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 3.1 22.4 + - - -
136A PRO* 1.3 76.4 - - - +
138A GLU* 1.3 96.9 + - - +
140A GLU* 3.3 24.7 + - - +
141A GLU* 3.4 15.9 + - - +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 1.3 114.4 + - - +
139A ASN* 1.3 80.8 + - + +
140A GLU* 3.2 28.1 - - - +
141A GLU* 3.1 20.0 + - - +
142A LYS* 3.2 18.1 + - - +
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 1.3 85.1 - - + +
140A GLU* 1.3 64.6 + - + +
142A LYS* 2.9 41.1 + - - +
143A GLU* 3.3 26.0 + - - +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 3.7 18.8 + - - -
106A ALA* 3.9 27.5 + - - +
109A LEU* 4.3 22.5 - - + +
131A VAL* 5.1 10.8 - - + +
135A ASN 4.5 2.8 - - - +
137A SER* 3.3 21.0 + - - +
138A GLU* 3.2 22.7 - - - +
139A ASN* 1.3 80.2 - - + +
141A GLU* 1.3 62.9 + - - +
142A LYS 3.1 0.2 + - - -
143A GLU* 3.2 8.8 + - - +
144A ALA* 2.9 26.9 + - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 5.7 0.6 - - - +
132A LEU* 3.6 25.7 - - + +
136A PRO* 3.6 13.7 - - + +
137A SER* 3.4 35.1 + - - +
138A GLU 3.1 12.4 + - - +
140A GLU* 1.3 76.9 - - - +
142A LYS* 1.3 59.8 - - + +
145A GLN* 3.1 35.3 + - - +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 3.2 27.8 + - - +
139A ASN* 2.9 35.3 + - - +
141A GLU* 1.3 76.0 - - + +
143A GLU* 1.3 65.5 + - - +
145A GLN* 3.3 7.7 + - - +
146A SER* 2.9 27.9 + - - -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.8 18.8 - - + +
110A GLN* 5.4 0.2 - - - +
113A HIS* 2.8 33.3 + - + +
139A ASN* 3.3 25.2 + - - +
140A GLU* 3.2 9.5 + - - +
142A LYS* 1.3 81.8 - - - +
144A ALA* 1.3 64.0 + - - +
146A SER* 3.2 3.9 + - - -
147A GLN* 3.1 28.6 + - + +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.2 6.2 - - + +
128A PHE* 4.1 20.8 - - + +
131A VAL* 4.1 17.0 - - + -
132A LEU* 3.8 26.2 - - + -
140A GLU 2.9 19.6 + - - +
143A GLU* 1.3 74.7 - - - +
145A GLN* 1.3 62.4 + - - +
147A GLN* 3.3 3.5 + - - +
148A LEU* 2.9 29.2 + - - +
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.4 16.8 - - + +
141A GLU* 3.1 20.0 + - - +
142A LYS* 3.7 6.1 - - - +
144A ALA* 1.3 79.5 - - - +
146A SER* 1.3 63.3 + - - +
147A GLN 3.0 1.4 + - - -
148A LEU* 3.1 19.4 + - - +
149A ILE* 3.5 20.0 + - + +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS 2.9 22.1 + - - -
143A GLU* 3.9 4.3 - - - -
145A GLN* 1.3 72.2 - - - +
147A GLN* 1.3 60.8 + - - +
149A ILE* 3.6 20.8 + - - +
150A LYS* 3.7 22.4 + - - +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 2.9 38.1 + - + -
116A LEU* 3.6 19.7 - - + +
128A PHE* 3.4 31.2 - - + -
143A GLU* 3.1 22.4 + - - +
144A ALA 3.5 2.5 - - - +
145A GLN 3.0 1.0 - - - -
146A SER* 1.3 75.4 - - - +
148A LEU* 1.3 56.8 + - - +
149A ILE 2.9 6.1 + - - -
150A LYS* 3.1 34.5 + - - +
151A SER* 2.8 29.0 + - - -
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 4.8 11.2 - - + +
128A PHE* 3.1 37.0 - - + +
129A LYS* 3.7 39.9 - - + -
132A LEU* 4.8 8.1 - - + -
144A ALA 2.9 32.6 + - - +
145A GLN* 3.1 10.9 + - - +
147A GLN* 1.3 75.6 - - - +
149A ILE* 1.3 62.4 + - + +
151A SER* 3.8 10.3 - - - -
152A ASP* 3.0 34.7 + - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 3.5 20.4 - - + +
146A SER* 3.6 13.5 - - - +
147A GLN 2.9 0.6 - - - -
148A LEU* 1.3 83.9 - - + +
150A LYS* 1.3 67.7 + - + +
152A ASP* 3.4 9.8 + - + +
153A GLU* 3.2 19.8 + - - +
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 5.0 1.3 - - + -
146A SER* 3.7 24.4 + - - +
147A GLN* 3.1 34.5 + - - +
149A ILE* 1.3 76.7 - - - +
151A SER* 1.3 51.4 + - - +
153A GLU* 2.8 11.8 + - - +
154A MSE 2.6 45.1 + - + +
183A VAL* 4.1 32.8 - - + +
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.9 19.9 - - - +
121A LEU* 4.2 9.0 + - - +
124A ALA* 5.3 0.2 - - - +
125A GLU* 2.7 37.8 + - - +
128A PHE* 5.2 4.3 - - - -
147A GLN 2.8 17.3 + - - -
148A LEU* 3.8 11.2 - - - -
150A LYS* 1.3 76.9 - - - +
152A ASP* 1.3 56.2 + - - +
154A MSE 3.6 10.1 - - - +
155A GLN* 2.9 30.3 + - - +
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.4 20.3 - - - +
148A LEU* 3.0 24.2 + - - +
149A ILE* 3.9 11.6 - - + +
150A LYS 3.1 0.6 + - - -
151A SER* 1.3 76.0 - - - +
153A GLU* 1.3 60.9 + - - +
155A GLN* 4.0 6.6 - - - +
156A ARG* 3.7 16.3 + - - +
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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
----------------------------------------------------------
149A ILE 3.2 10.8 + - - +
150A LYS* 2.8 8.5 + - - +
152A ASP* 1.3 77.9 - - - +
154A MSE 1.3 74.9 + - - +
155A GLN 3.3 0.2 - - - -
156A ARG* 2.9 18.2 + - - +
157A LEU* 2.6 51.0 + - + +
160A GLN* 6.0 0.2 - - - +
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Residues in contact with MSE 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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116A LEU* 4.9 0.4 - - + -
121A LEU* 3.9 21.3 - - + -
150A LYS* 2.6 32.4 + - + +
151A SER* 3.6 7.4 - - - +
153A GLU* 1.3 98.5 - - - +
155A GLN* 1.3 57.1 + - - +
157A LEU* 2.6 38.8 + - + +
158A ARG* 3.0 13.7 + - - +
179A LYS 5.6 0.7 - - - +
180A ILE* 4.0 29.3 - - + +
183A VAL* 3.5 46.4 - - + -
184A CYS* 4.4 8.5 - - - -
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.3 29.6 - - - +
122A ASP* 2.8 29.8 + - - +
125A GLU* 3.0 23.8 - - - +
151A SER 2.9 14.7 + - - +
152A ASP* 4.0 9.4 - - - +
154A MSE 1.3 75.4 - - - +
156A ARG* 1.3 57.3 + - - +
158A ARG* 4.0 15.1 - - - +
159A SER* 3.0 19.4 + - - -
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Residues in contact with ARG 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 ASP 3.7 12.1 + - - +
153A GLU* 2.9 19.9 + - - +
154A MSE 2.7 4.4 + - - -
155A GLN* 1.3 77.2 - - - +
157A LEU* 1.3 62.2 + - - +
159A SER* 3.5 8.7 - - - -
160A GLN* 2.9 46.4 + - + +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 2.6 29.1 + - + +
154A MSE 2.6 39.9 + - + +
156A ARG* 1.3 70.1 - - - +
158A ARG* 1.3 58.8 + - - +
160A GLN* 3.1 24.7 + - - +
161A ALA 2.9 23.4 + - - -
176A PHE* 4.1 19.1 - - + +
179A LYS* 4.4 16.6 - - + -
180A ILE* 3.4 37.3 - - + +
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY 3.7 21.6 + - - -
120A LYS* 5.7 0.2 - - - +
121A LEU* 4.3 20.5 - - + +
154A MSE 3.0 9.3 + - - +
155A GLN* 4.0 17.5 - - - +
157A LEU* 1.3 76.4 - - - +
159A SER* 1.3 60.8 + - - +
161A ALA* 3.1 1.9 + - - +
162A LEU* 2.7 62.9 + - + +
180A ILE* 3.8 17.8 - - + +
187A ASP* 4.9 4.2 + - - -
189A GLU* 6.2 2.0 - - - +
190A LEU* 4.5 26.6 - - + +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLN 3.0 17.2 + - - -
156A ARG* 3.5 10.4 + - - -
158A ARG* 1.3 82.2 - - - +
160A GLN* 1.3 52.2 + - - +
162A LEU* 3.7 5.8 - - - +
163A ASN* 2.8 36.3 + - - +
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Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 6.0 0.2 - - - +
156A ARG* 2.9 49.5 + - + +
157A LEU* 3.1 32.2 + - - +
159A SER* 1.3 80.0 - - - +
161A ALA* 1.3 61.2 + - - +
163A ASN* 3.3 7.9 - - - +
164A ALA* 3.2 22.2 + - - +
176A PHE* 3.5 35.5 - - + -
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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
----------------------------------------------------------
157A LEU 2.9 13.1 + - - +
158A ARG* 3.1 7.8 + - - +
160A GLN* 1.3 72.7 - - - +
162A LEU* 1.3 68.8 + - + +
163A ASN 3.1 1.1 - - - -
164A ALA 3.1 12.0 + - - -
165A PHE* 3.1 12.5 + - - +
173A ALA* 3.5 12.2 - - - +
176A PHE* 3.9 16.7 - - + -
177A LEU* 3.9 21.8 - - + -
180A ILE* 3.8 17.9 - - + -
193A LEU* 5.5 1.6 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 2.7 46.1 + - + +
159A SER* 3.9 4.9 - - - +
161A ALA* 1.3 77.4 - - + +
163A ASN* 1.3 60.0 + - - +
165A PHE* 3.9 6.7 - - - +
166A GLY* 3.1 20.8 + - - -
177A LEU* 5.5 0.2 - - + -
190A LEU* 4.5 17.9 - - + -
193A LEU* 3.9 23.3 - - + -
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER 2.8 22.9 + - - +
160A GLN* 3.3 10.8 - - - +
162A LEU* 1.3 74.5 - - - +
164A ALA* 1.3 68.2 + - - +
165A PHE 3.1 0.3 + - - -
166A GLY* 3.8 0.3 - - - -
167A SER* 3.0 29.0 + - - -
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLN 3.2 7.5 + - - +
161A ALA 3.1 4.3 + - - +
163A ASN* 1.3 82.8 + - - +
165A PHE* 1.3 53.9 + - - +
167A SER* 2.8 13.1 + - - -
168A GLY 2.9 1.6 + - - -
169A ASP* 2.6 47.8 + - + +
172A ALA* 3.8 11.7 - - + -
173A ALA* 3.6 23.6 - - + +
176A PHE* 4.6 4.3 - - + -
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA 3.1 13.5 + - - +
162A LEU* 3.9 7.2 - - - +
164A ALA* 1.3 77.5 - - - +
166A GLY* 1.3 63.9 - - - +
168A GLY* 2.6 27.7 + - - -
169A ASP 3.7 6.7 + - - -
170A TYR* 4.0 24.3 - + - -
173A ALA* 3.9 4.5 - - + +
193A LEU* 3.4 38.6 - - + -
196A GLU* 4.6 17.3 - - + -
197A CYS* 3.6 27.8 - - - -
200A LYS* 5.6 3.6 - - + -
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU 3.1 13.2 + - - -
163A ASN 3.8 2.5 - - - -
165A PHE* 1.3 86.7 - - - +
167A SER* 1.3 58.9 + - - +
168A GLY* 3.3 1.0 + - - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 3.0 19.6 + - - -
164A ALA* 2.8 25.5 + - - -
166A GLY* 1.3 72.9 - - - +
168A GLY* 1.3 57.9 + - - +
169A ASP* 3.6 4.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA 2.9 0.8 + - - -
165A PHE 2.6 22.6 + - - -
166A GLY 3.1 1.1 - - - -
167A SER* 1.3 73.7 - - - +
169A ASP* 1.3 63.0 + - - +
170A TYR* 3.3 29.1 + - - -
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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