Contacts of the helix formed by residues 131 - 153 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ARG* 5.8 2.1 + - - -
146C GLU* 5.1 2.3 - - - +
17E VAL* 4.0 22.6 - - + +
71E ARG* 2.9 19.9 + - - -
75E LEU* 5.1 4.2 - - + +
127E LEU* 3.2 8.5 + - - +
130E LEU* 1.3 82.7 - - - +
132E LEU* 1.3 64.1 + - - +
133E VAL* 3.6 12.3 + - - +
134E SER* 2.4 39.7 + - - -
135E GLN* 3.0 17.7 + - - +
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ILE* 4.4 10.1 - - + +
128C GLU* 4.1 20.4 - - - +
135C GLN* 3.7 25.8 - - - +
139C ILE* 4.0 22.7 - - + +
127E LEU 5.1 0.4 - - - -
128E GLU* 4.4 18.2 - - - +
129E ASP 6.0 0.2 - - - -
130E LEU 5.2 3.4 - - - +
131E ASP* 1.3 76.3 + - - +
133E VAL* 1.3 52.4 + - + +
135E GLN* 2.9 21.9 + - - +
136E ASP* 2.6 37.4 + - - +
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ARG* 5.9 3.6 - - + -
124C ILE* 5.1 6.7 - - + -
139C ILE* 4.6 13.0 - - + +
142C ALA* 3.9 24.9 - - + -
143C GLY* 4.2 19.3 - - - +
146C GLU* 3.9 11.4 - - - +
71E ARG* 3.6 28.7 - - - +
131E ASP* 3.1 15.0 - - - +
132E LEU* 1.3 79.2 - - + +
134E SER* 1.3 63.5 + - - +
136E ASP* 3.1 14.5 + - - +
137E LEU* 3.1 11.8 + - - +
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Residues in contact with SER 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 3.6 22.3 - - - +
21E LEU* 3.7 15.5 - - - +
71E ARG* 3.0 21.3 + - - +
75E LEU* 3.8 0.2 - - - +
127E LEU* 4.2 10.1 - - - -
131E ASP* 2.4 35.8 + - - -
133E VAL* 1.3 72.8 - - - +
135E GLN* 1.3 62.4 + - - +
137E LEU* 3.1 11.7 + - - +
138E LEU* 3.0 24.4 + - - +
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE* 3.2 46.5 + - + +
127E LEU* 4.2 15.8 - - + +
128E GLU* 3.3 35.9 - - - +
131E ASP 3.0 7.2 + - - +
132E LEU* 2.9 29.0 + - - +
134E SER* 1.3 73.6 - - - +
136E ASP* 1.3 54.8 + - - +
138E LEU* 3.1 2.8 + - - +
139E ILE* 2.6 53.6 + - + +
132J LEU* 4.1 9.6 - - - +
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Residues in contact with ASP 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP* 3.2 23.9 - - - +
139C ILE* 3.6 26.6 - - + +
140C ALA* 5.0 9.7 + - - +
132E LEU 2.6 15.5 + - - +
133E VAL 3.3 9.6 - - - +
135E GLN* 1.3 71.2 + - - +
137E LEU* 1.3 65.7 + - - +
139E ILE* 3.0 18.7 - - - +
140E ALA* 3.0 25.6 + - - +
136J ASP* 4.6 2.9 - - - +
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LYS* 5.8 8.1 - - - +
21E LEU* 5.2 3.1 - - + -
67E GLU* 3.4 24.0 - - + +
68E VAL* 4.0 18.2 - - + -
71E ARG* 3.7 38.6 - - + -
133E VAL 3.1 5.8 + - - +
134E SER* 3.1 13.2 + - - +
135E GLN 3.1 0.4 - - - -
136E ASP* 1.3 83.1 + - - +
138E LEU* 1.3 62.4 + - + +
140E ALA* 3.4 5.1 + - + +
141E HIS* 2.8 55.3 + - + +
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Residues in contact with LEU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 6.3 1.1 - - + -
21E LEU* 4.2 15.9 - - + -
24E GLN* 3.3 44.2 - - + +
28E TYR* 3.6 9.4 - - + +
68E VAL* 5.6 1.3 - - + -
120E THR* 4.2 8.2 - - + +
123E SER* 4.1 17.9 - - - -
124E ILE* 4.1 16.2 - - + +
127E LEU* 3.4 32.1 - - + -
134E SER 3.0 10.7 + - - +
135E GLN 3.8 4.5 - - - +
137E LEU* 1.3 73.7 - - + +
139E ILE* 1.3 68.0 + - - +
140E ALA 3.0 2.8 + - - -
141E HIS* 3.2 5.8 + - + +
142E ALA* 2.8 28.1 + - - +
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Residues in contact with ILE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE* 3.4 39.7 - - + +
135E GLN* 2.6 37.4 + - + +
136E ASP* 3.0 23.1 - - - +
138E LEU* 1.3 73.7 - - - +
140E ALA* 1.3 68.6 + - + +
142E ALA* 3.6 3.1 - - - +
143E GLY* 3.5 12.0 + - - -
132J LEU* 3.7 39.3 - - + +
133J VAL* 4.4 9.7 - - - +
136J ASP* 3.5 29.8 - - + +
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E TYR* 5.1 1.8 - - + -
136E ASP* 3.0 11.1 + - - +
137E LEU* 3.5 12.3 - - + +
139E ILE* 1.3 81.7 - - + +
141E HIS* 1.3 73.2 + - + +
143E GLY* 2.9 17.2 + - - -
144E GLU* 3.5 5.7 + - - +
136J ASP* 4.6 7.4 - - - +
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Residues in contact with HIS 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E TYR* 2.6 30.9 + + - +
64E TYR* 3.3 63.6 - + + -
67E GLU* 2.9 22.1 + - - -
68E VAL* 4.8 2.7 - - + -
120E THR* 5.3 0.7 - - + -
137E LEU* 2.8 41.5 + - + +
138E LEU* 3.2 7.5 + - + +
140E ALA* 1.3 75.0 - - + +
142E ALA* 1.3 67.7 + - - +
144E GLU* 2.6 16.5 + - - +
145E LEU* 2.8 25.3 + - + +
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Residues in contact with ALA 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 5.9 1.1 - - + -
120E THR* 4.0 16.3 - - + +
121E ARG* 5.5 0.9 - - - -
124E ILE* 3.8 21.8 - - + -
138E LEU 2.8 20.4 + - - +
139E ILE 3.6 6.7 - - - +
141E HIS* 1.3 71.6 - - - +
143E GLY* 1.3 62.8 + - - +
145E LEU* 3.2 6.2 + - - +
146E GLU* 2.9 39.2 + - - +
133J VAL* 4.0 11.0 - - + -
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Residues in contact with GLY 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ILE 3.5 3.7 + - - -
140E ALA 2.9 10.1 + - - -
141E HIS 2.9 0.2 + - - -
142E ALA* 1.3 79.3 - - - +
144E GLU* 1.3 60.6 + - - +
146E GLU* 3.9 3.7 + - - +
147E LYS* 3.2 20.4 + - - +
71J ARG* 4.9 2.5 + - - -
74J THR* 5.8 0.3 - - - +
133J VAL* 3.7 24.3 - - - +
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLN* 4.8 4.3 - - - +
60E LEU* 4.0 20.8 - - + +
64E TYR* 3.1 29.4 - - + +
140E ALA 3.5 5.6 + - - +
141E HIS 2.6 9.8 + - - +
143E GLY* 1.3 71.2 - - - -
145E LEU* 1.3 64.6 + - - +
147E LYS* 2.9 27.9 + - - +
148E PHE* 2.9 14.4 + - - +
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Residues in contact with LEU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 4.2 14.6 - - + +
31E LEU* 4.2 15.0 - - + -
57E GLN* 3.3 26.5 - - - +
61E VAL* 4.6 4.5 - - + -
64E TYR* 4.1 11.2 - - + -
113E TYR* 3.5 19.8 - - + -
116E VAL* 4.0 15.3 - - + -
117E ILE* 4.3 15.7 - - + -
120E THR* 5.0 5.8 - - + +
141E HIS* 2.8 47.5 + - + +
142E ALA* 3.7 9.4 - - - +
144E GLU* 1.3 70.4 - - - +
146E GLU* 1.3 64.2 + - - +
148E PHE* 3.0 15.4 + - - +
149E GLN 3.0 10.0 + - - -
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Residues in contact with GLU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ILE* 3.3 39.5 - - + +
121E ARG* 2.8 41.3 + - - -
142E ALA* 2.9 24.8 + - - +
143E GLY 4.0 3.6 - - - +
145E LEU* 1.3 75.2 - - - +
147E LYS* 1.3 63.2 + - - +
149E GLN* 3.2 4.6 - - - +
150E TRP 3.1 17.5 + - - -
71J ARG* 2.9 28.5 + - - +
74J THR* 3.6 16.8 - - + +
75J LEU* 4.9 2.8 - - - +
133J VAL* 4.0 6.5 - - - +
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Residues in contact with LYS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E GLY 3.2 15.9 + - - +
144E GLU* 2.9 30.4 + - - +
146E GLU* 1.3 76.3 - - - +
148E PHE* 1.3 62.7 + - - +
150E TRP* 3.2 48.3 + - + +
151E PHE* 3.1 22.8 + - + +
70J GLU* 2.6 42.8 + - + +
74J THR* 4.4 15.9 + - - +
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Residues in contact with PHE 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 4.4 2.5 - - + -
53E MET* 3.8 33.7 - - + -
54E ILE* 4.5 8.1 - - + -
57E GLN* 3.4 47.3 - - + +
109E LEU* 4.1 16.6 - - + -
113E TYR* 3.1 39.0 - + + -
144E GLU 2.9 7.7 + - - +
145E LEU 3.4 8.1 - - - +
147E LYS* 1.3 76.2 - - - +
149E GLN* 1.3 55.2 + - - +
151E PHE* 2.8 14.9 + + - +
152E VAL* 2.6 66.0 + - + +
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Residues in contact with GLN 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP* 2.4 33.9 + - - +
113E TYR* 3.3 21.1 - - + -
114E ASN* 3.3 15.8 + - - +
117E ILE* 3.0 34.5 - - + +
145E LEU 3.0 6.0 + - - +
146E GLU* 3.2 11.9 - - - +
148E PHE* 1.3 75.6 - - - +
150E TRP* 1.3 62.4 + - - +
152E VAL* 3.3 10.3 + - - +
153E ARG* 2.9 60.2 + - - +
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Residues in contact with TRP 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLU 3.1 8.4 + - - +
147E LYS* 3.2 43.1 - - - +
149E GLN* 1.3 78.1 - - - +
151E PHE* 1.3 86.8 + + + +
153E ARG* 2.8 44.8 + - + +
40H TRP* 5.1 7.4 - - - -
42H VAL 5.2 1.1 - - - -
43H VAL* 4.4 17.4 - - + +
47H PHE* 3.8 29.2 - + - -
51H HIS* 4.6 10.3 - + - -
99H ARG* 4.3 20.2 - - - +
70J GLU* 5.9 0.9 - - + -
73J ALA* 3.1 41.7 + - + +
74J THR* 4.2 22.0 - - + +
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Residues in contact with PHE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLY 5.7 0.2 - - - -
53E MET* 3.5 50.8 - - + +
147E LYS* 3.1 12.9 + - - +
148E PHE* 2.8 21.5 + + - +
150E TRP* 1.3 91.1 - + + +
152E VAL* 1.3 63.6 + - - +
153E ARG 3.1 0.9 + - - -
154E ALA* 3.1 16.9 + - + +
47H PHE* 3.3 19.5 - + - -
48H ILE* 3.1 38.4 - - + -
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Residues in contact with VAL 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E MET* 4.2 12.5 - - - -
106E LEU* 3.5 49.1 - - + +
109E LEU* 4.5 7.9 - - + +
110E ASP* 4.0 19.7 - - + +
113E TYR* 5.3 2.0 - - + -
148E PHE* 2.6 58.2 + - + +
149E GLN* 3.3 12.6 - - - +
151E PHE* 1.3 71.7 - - - +
153E ARG* 1.3 58.6 + - + +
154E ALA* 2.8 10.9 + - - +
155E HIS 4.4 2.4 - - - +
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Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP* 3.0 27.1 + - - +
114E ASN* 3.7 14.1 + - - +
149E GLN* 2.9 51.0 + - - +
150E TRP* 2.8 24.9 + - + +
151E PHE 3.6 0.2 - - - -
152E VAL* 1.3 75.3 - - + +
154E ALA* 1.3 51.2 + - - +
155E HIS* 2.6 23.2 + - + +
43H VAL* 4.9 4.9 - - - +
47H PHE* 5.5 1.1 - - - -
99H ARG* 4.4 24.8 + - - +
74J THR 5.4 5.3 + - - -
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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