Contacts of the helix formed by residues 131 - 153 (chain A) in PDB entry 2YW7
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 ASP 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.9 23.1 - - + +
71A ARG* 2.8 19.7 + - - -
75A LEU* 4.6 2.2 - - - +
127A LEU* 3.0 12.0 + - + +
128A GLU 4.6 0.4 + - - -
130A LEU* 1.3 81.9 - - - +
132A LEU* 1.3 59.8 + - - +
133A VAL* 3.1 19.4 + - - +
134A SER* 2.6 32.5 + - - +
135A GLN* 3.1 26.7 + - - +
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Residues in contact with LEU 132 (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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127A LEU 5.2 0.2 - - - -
128A GLU* 4.4 22.2 - - - +
131A ASP* 1.3 72.0 + - - +
133A VAL* 1.3 56.2 + - + +
135A GLN* 3.6 18.2 - - - +
136A ASP* 2.8 34.8 + - - +
124D ILE* 3.9 23.1 - - + +
125D GLU* 4.7 16.8 - - + +
128D GLU* 4.2 24.2 - - - +
135D GLN* 5.4 3.1 - - - +
139D ILE* 3.9 18.3 - - + +
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.7 28.9 - - - +
131A ASP* 3.1 12.1 + - - +
132A LEU* 1.3 75.3 - - + +
134A SER* 1.3 67.7 + - - +
136A ASP* 3.0 5.2 + - - +
137A LEU* 2.9 22.0 + - + +
121D ARG* 6.1 3.4 - - + +
124D ILE* 4.9 7.0 - - + -
139D ILE* 3.9 18.4 - - + +
142D ALA* 4.1 22.9 - - + -
143D GLY* 4.2 20.0 - - - +
146D GLU* 4.4 9.4 - - - +
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.3 16.9 - - - +
21A LEU* 3.8 19.0 - - - +
71A ARG* 3.1 24.5 + - - +
127A LEU* 3.8 11.9 - - - -
131A ASP* 2.6 31.2 + - - -
133A VAL* 1.3 73.1 - - - +
135A GLN* 1.3 56.4 + - - +
137A LEU* 3.4 8.6 + - - +
138A LEU* 3.0 31.9 + - - +
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Residues in contact with GLN 135 (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 ILE* 2.6 48.8 + - + +
125A GLU* 4.1 1.0 - - - +
127A LEU* 3.7 13.8 - - + +
128A GLU* 3.7 34.1 + - - +
131A ASP 3.1 19.4 + - - +
132A LEU* 3.6 19.2 - - - +
134A SER* 1.3 74.8 - - - +
136A ASP* 1.3 55.8 + - - +
138A LEU* 3.2 3.3 + - - +
139A ILE* 2.6 49.5 + - + +
132B LEU* 4.1 10.7 - - - +
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU 2.8 21.9 + - - +
133A VAL 3.0 5.4 + - - +
135A GLN* 1.3 73.4 - - - +
137A LEU* 1.3 64.1 + - - +
139A ILE* 3.2 16.9 - - - +
140A ALA* 3.1 21.8 + - - +
136B ASP* 4.8 1.4 - - - +
136D ASP* 2.9 29.6 - - - +
139D ILE* 3.4 27.0 - - + +
140D ALA* 5.2 3.6 + - - +
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Residues in contact with LEU 137 (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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21A LEU* 5.3 2.0 - - + -
67A GLU* 3.2 33.0 - - + +
68A VAL* 3.8 38.8 - - + +
71A ARG* 4.8 12.8 - - + -
133A VAL* 2.9 12.3 + - + +
134A SER* 3.4 9.9 - - - +
136A ASP* 1.3 78.6 + - - +
138A LEU* 1.3 64.5 + - + +
140A ALA* 3.1 11.9 + - - +
141A HIS* 3.0 38.2 + - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 6.3 0.9 - - + -
21A LEU* 4.8 6.5 - - + -
24A GLN* 3.6 36.1 - - + +
28A TYR* 3.4 24.0 - - - +
68A VAL* 4.0 17.3 - - + -
120A THR* 4.0 7.9 - - + +
123A SER* 3.8 23.1 - - - -
124A ILE* 3.9 13.2 - - + +
127A LEU* 4.3 12.3 - - + -
134A SER 3.0 19.0 + - - +
135A GLN* 3.7 4.3 - - - +
137A LEU* 1.3 76.8 - - + +
139A ILE* 1.3 65.8 + - - +
141A HIS* 3.5 7.4 + - - +
142A ALA* 3.0 24.3 + - - +
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Residues in contact with ILE 139 (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 ILE* 3.6 18.8 - - + +
135A GLN* 2.6 34.7 + - + +
136A ASP* 3.2 18.6 - - - +
138A LEU* 1.3 75.4 - - - +
140A ALA* 1.3 67.4 + - - +
142A ALA* 3.3 13.7 - - - +
143A GLY* 3.5 3.5 + - - -
132B LEU* 3.5 50.9 - - + +
133B VAL* 4.3 8.4 - - + +
136B ASP* 3.1 31.9 - - + +
136D ASP* 5.5 0.2 - - - +
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Residues in contact with ALA 140 (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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64A TYR* 4.9 1.3 + - + -
136A ASP* 3.1 9.4 + - - +
137A LEU* 3.1 12.0 + - - +
139A ILE* 1.3 83.3 - - - +
141A HIS* 1.3 71.2 + - + +
143A GLY* 2.9 17.0 + - - -
144A GLU* 3.7 5.7 + - - +
136B ASP* 3.9 10.5 - - - +
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Residues in contact with HIS 141 (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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28A TYR* 2.6 36.6 + + - +
64A TYR* 3.2 57.1 + + + -
67A GLU* 2.4 29.2 + - - -
120A THR* 5.4 0.2 - - + -
137A LEU* 3.0 36.4 + - + +
138A LEU* 3.7 6.8 - - + +
140A ALA* 1.3 76.0 - - + +
142A ALA* 1.3 65.3 + - - +
144A GLU* 2.9 6.2 + - - +
145A LEU* 2.9 31.5 + - + +
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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
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117A ILE* 6.0 0.7 - - + -
120A THR* 3.9 21.3 - - + +
121A ARG* 5.8 1.1 - - - -
124A ILE* 4.3 6.7 - - + -
138A LEU 3.0 10.8 + - - +
139A ILE 3.3 12.6 - - - +
140A ALA 3.2 0.2 + - - -
141A HIS* 1.3 76.9 - - - +
143A GLY* 1.3 52.3 + - - +
145A LEU* 4.3 6.0 - - - +
146A GLU* 2.7 51.0 + - - +
133B VAL* 3.8 17.9 - - + -
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Residues in contact with GLY 143 (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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139A ILE 3.5 3.0 + - - -
140A ALA 2.9 10.3 + - - -
142A ALA* 1.3 79.8 - - - +
144A GLU* 1.3 56.9 + - - +
146A GLU* 4.2 1.9 - - - +
147A LYS* 3.1 29.8 + - - +
71B ARG* 5.1 3.0 + - - -
133B VAL* 3.8 21.9 - - - +
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Residues in contact with GLU 144 (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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57A GLN* 3.8 6.3 - - - +
60A LEU* 3.5 19.2 - - + +
64A TYR* 3.0 27.4 - - - +
140A ALA 3.7 5.2 + - - +
141A HIS 2.9 5.4 + - - +
143A GLY* 1.3 73.4 - - - +
145A LEU* 1.3 59.3 + - - +
147A LYS* 3.9 26.4 + - - +
148A PHE* 3.2 24.9 + - - +
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Residues in contact with LEU 145 (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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28A TYR* 4.0 24.9 - - + +
31A LEU* 4.0 14.8 - - + -
57A GLN* 3.5 22.7 - - - +
61A VAL* 4.6 1.6 - - + -
64A TYR* 4.3 14.8 - - + -
113A TYR* 3.8 25.1 - - + -
116A VAL* 4.2 14.1 - - + -
117A ILE* 4.5 10.3 - - + -
120A THR* 4.4 10.1 - - + +
141A HIS* 2.9 27.8 + - + +
142A ALA* 3.7 7.2 - - - +
144A GLU* 1.3 75.8 - - - +
146A GLU* 1.3 64.9 + - - +
147A LYS 3.2 0.2 - - - -
148A PHE* 3.2 5.2 + - - +
149A GLN* 3.2 17.7 + - - +
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Residues in contact with GLU 146 (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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117A ILE* 3.3 40.3 - - + +
121A ARG* 3.3 39.8 + - - -
142A ALA* 2.7 30.5 + - - +
143A GLY 4.2 2.5 - - - +
145A LEU* 1.3 72.2 - - - +
147A LYS* 1.3 61.9 + - - +
149A GLN* 3.3 13.7 + - - +
150A TRP 3.4 7.8 + - - -
71B ARG* 3.2 26.9 + - - +
74B THR* 3.6 14.5 - - + +
75B LEU* 5.5 1.0 - - - +
133B VAL* 3.6 12.8 - - - +
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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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143A GLY 3.1 21.7 + - - +
144A GLU* 3.9 29.1 + - - +
146A GLU* 1.3 78.3 - - - +
148A PHE* 1.3 56.7 + - - +
150A TRP* 2.8 28.0 + - + +
151A PHE* 3.1 11.6 + - - +
67B GLU* 5.5 13.0 - - - +
70B GLU* 3.3 36.2 + - + +
71B ARG* 5.5 0.6 - - - +
74B THR* 4.1 19.9 - - - +
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Residues in contact with PHE 148 (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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35A LEU* 4.5 5.2 - - + -
53A MET* 3.6 42.2 - - + -
54A ILE* 4.6 3.8 - - + -
57A GLN* 3.6 31.2 - - + +
109A LEU* 4.2 14.1 - - + -
113A TYR* 3.2 41.7 - + - -
144A GLU 3.2 18.3 + - - +
145A LEU 3.5 5.2 - - - +
147A LYS* 1.3 77.9 - - - +
149A GLN* 1.3 56.7 + - - +
151A PHE* 3.2 18.3 - + - +
152A VAL* 2.8 54.5 + - + +
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Residues in contact with GLN 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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110A ASP* 2.4 24.5 + - - +
113A TYR* 4.0 12.7 - - + +
114A ASN* 2.4 34.8 + - - +
117A ILE* 2.8 27.8 - - + +
145A LEU 3.2 9.8 + - - +
146A GLU 3.5 9.6 - - - +
147A LYS 3.1 0.6 - - - -
148A PHE* 1.3 78.7 - - - +
150A TRP* 1.3 54.6 + - - +
152A VAL* 3.0 10.4 + - + +
153A ARG* 2.7 71.9 + - + +
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Residues in contact with TRP 150 (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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146A GLU 3.4 3.2 + - - -
147A LYS* 2.8 16.5 + - + +
149A GLN* 1.3 76.7 - - - +
151A PHE* 1.3 76.1 + + + +
153A ARG* 3.0 43.1 + - + +
154A ALA* 3.3 13.4 + - + +
70B GLU* 4.7 24.9 - - + -
73B ALA* 3.7 39.8 + - + -
74B THR* 3.9 27.4 - - + +
40G TRP* 4.0 21.1 - - - -
42G VAL 4.6 13.5 - - - -
43G VAL* 4.7 7.1 - - + +
47G PHE* 5.3 6.5 - + - -
51G HIS* 5.0 15.9 - + - -
99G ARG* 3.8 18.8 - - - +
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Residues in contact with PHE 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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53A MET* 3.5 36.6 - - + -
147A LYS 3.1 7.9 + - - +
148A PHE* 3.2 28.9 - + + +
150A TRP* 1.3 90.8 - + + +
152A VAL* 1.3 52.2 + - - -
154A ALA* 3.9 3.8 - - - +
155A HIS* 2.5 70.4 + + - -
47G PHE* 3.8 7.2 - + - -
48G ILE* 3.8 24.0 - - + -
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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
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53A MET* 4.6 1.8 - - - -
106A LEU* 3.2 52.8 - - + +
109A LEU* 4.4 5.4 - - + -
110A ASP* 3.8 18.6 - - + +
113A TYR* 5.2 2.9 - - + -
148A PHE* 2.8 55.4 + - + +
149A GLN* 3.3 11.0 - - - +
151A PHE* 1.3 75.3 - - - +
153A ARG* 1.3 57.8 + - - +
154A ALA 3.3 3.8 + - - -
155A HIS* 3.9 6.1 + - - +
156A LEU* 3.6 14.9 + - - +
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Residues in contact with ARG 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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110A ASP* 3.6 17.0 + - - +
114A ASN* 4.1 10.8 + - - +
149A GLN* 2.7 75.2 + - + +
150A TRP* 3.0 23.9 + - + +
152A VAL* 1.3 69.2 - - - +
154A ALA* 1.3 57.4 + - - +
156A LEU* 4.1 21.3 - - + -
43G VAL* 5.5 0.7 - - - +
99G ARG* 5.8 0.3 + - - -
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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
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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) + - + + + + + -
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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