Contacts of the helix formed by residues 117 - 138 (chain A) in PDB entry 3A7H
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PRO 4.2 0.2 + - - -
116A LEU* 1.3 77.0 - - - +
118A GLU* 1.3 64.6 + - - +
119A THR* 3.4 15.0 + - - -
120A GLN* 2.6 57.8 + - - +
121A ILE* 2.9 19.5 + - - +
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Residues in contact with GLU 118 (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 ASP* 1.3 74.9 - - - +
119A THR* 1.3 57.3 + - - +
121A ILE* 3.8 11.4 - - + -
122A ALA* 2.9 30.7 + - - +
242A ASN 4.5 1.2 - - - +
243A TYR* 3.1 19.7 - - + +
244A SER* 2.5 50.7 + - - -
247A LEU* 3.9 17.7 - - + +
273A PHE* 3.5 18.7 - - + -
277A ASN* 4.0 12.6 + - - +
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Residues in contact with THR 119 (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 ASP* 3.0 16.5 + - - +
118A GLU* 1.3 76.9 - - - +
120A GLN* 1.3 68.1 + - + +
122A ALA* 3.8 1.4 - - - +
123A THR* 2.8 35.5 + - - +
277A ASN* 3.7 28.9 + - - +
279A LYS* 3.7 34.1 - - + +
283A TYR* 5.8 4.5 - - + -
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Residues in contact with GLN 120 (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 PRO 4.3 1.4 - - - +
116A LEU* 3.3 16.9 - - + +
117A ASP* 2.6 51.3 + - - +
119A THR* 1.3 75.9 - - + +
121A ILE* 1.3 66.0 + - - +
123A THR* 3.2 1.7 + - - -
124A ILE* 3.0 30.9 + - - +
283A TYR 5.3 4.4 + - - +
284A LEU* 4.3 14.8 - - + -
286A GLU* 5.3 6.5 - - - +
287A LEU* 3.4 49.2 - - + +
290A ARG* 5.7 0.2 + - - -
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Residues in contact with ILE 121 (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* 3.8 18.6 - - + +
117A ASP 2.9 21.2 + - - +
118A GLU* 3.7 16.6 - - + +
119A THR 3.3 0.2 - - - -
120A GLN* 1.3 76.8 - - - +
122A ALA* 1.3 57.0 + - - +
124A ILE* 3.3 4.0 + - - +
125A LEU* 2.9 50.3 + - + +
209A ALA 4.9 3.4 - - - +
212A LEU* 3.8 28.2 - - + +
213A ALA* 3.7 30.5 - - + -
243A TYR* 5.0 4.0 - - + -
247A LEU* 4.2 14.8 - - + -
273A PHE* 4.0 9.6 - - + -
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Residues in contact with ALA 122 (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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118A GLU 2.9 20.7 + - - +
119A THR 3.8 0.4 - - - +
121A ILE* 1.3 71.1 - - - +
123A THR* 1.3 61.6 + - - +
125A LEU* 4.5 0.4 - - - -
126A ARG* 2.9 31.9 + - - +
273A PHE* 3.6 23.5 - - + +
274A ILE* 3.8 8.3 - - + +
277A ASN* 3.6 11.7 - - + -
278A ALA* 3.5 29.0 - - + +
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Residues in contact with THR 123 (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 THR* 2.8 23.9 + - - +
120A GLN* 3.2 4.0 + - - -
122A ALA* 1.3 75.4 - - - +
124A ILE* 1.3 63.7 + - - +
126A ARG* 3.3 9.1 + - - +
127A GLU* 3.2 27.8 + - - +
278A ALA* 4.2 6.1 - - - -
279A LYS* 3.0 40.6 + - - +
280A LYS 4.1 8.7 + - - +
281A THR* 4.1 7.9 - - + -
283A TYR* 5.9 1.1 - - + +
284A LEU* 3.6 34.1 - - + -
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Residues in contact with ILE 124 (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 ALA* 4.5 14.8 - - + -
110A LEU* 5.2 6.5 - - + -
116A LEU* 4.0 25.8 - - + -
120A GLN 3.0 21.7 + - - +
121A ILE* 3.8 3.4 - - - +
123A THR* 1.3 75.9 - - - +
125A LEU* 1.3 63.7 + - - +
127A GLU* 3.2 4.5 + - - +
128A ILE* 3.0 44.9 + - + +
150A VAL* 4.3 11.7 - - + -
152A LEU* 5.1 3.4 - - + -
158A VAL* 4.5 11.2 - - + +
212A LEU* 3.9 15.9 - - + -
284A LEU* 4.1 17.9 - - + -
287A LEU* 4.2 17.3 - - + -
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Residues in contact with LEU 125 (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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121A ILE* 2.9 41.1 + - + +
122A ALA 3.9 3.4 - - - +
124A ILE* 1.3 73.6 - - - +
126A ARG* 1.3 62.8 + - - +
128A ILE* 3.2 7.4 + - + +
129A LEU* 2.9 30.8 + - + +
205A LEU* 3.7 27.4 - - + +
208A THR* 5.0 0.9 - - + -
209A ALA* 3.9 28.5 - - + +
212A LEU* 3.9 20.4 - - + -
247A LEU* 4.8 0.7 - - + -
250A PHE* 4.0 17.3 - - + -
273A PHE* 3.9 16.8 - - + -
274A ILE* 4.1 8.3 - - + -
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Residues in contact with ARG 126 (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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122A ALA 2.9 18.7 + - - +
123A THR* 3.6 7.4 - - - +
124A ILE 3.2 0.2 - - - -
125A LEU* 1.3 77.1 - - - +
127A GLU* 1.3 86.6 + - - +
129A LEU* 3.2 12.6 + - - +
130A LYS* 3.1 38.9 + - - +
269A LEU* 3.8 18.6 - - + -
274A ILE* 3.8 16.4 - - + +
278A ALA* 3.6 27.8 + - + +
279A LYS* 2.8 31.3 + - - +
280A LYS* 4.5 1.6 - - - +
281A THR* 4.2 10.5 - - - +
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Residues in contact with GLU 127 (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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81A TYR* 3.6 28.6 + - + +
123A THR 3.3 13.5 - - - +
124A ILE 3.2 4.7 + - - +
126A ARG* 1.3 107.2 + - - +
128A ILE* 1.3 64.6 + - - +
130A LYS* 3.1 17.8 + - - +
131A GLY* 3.1 17.5 + - - -
157A GLU* 6.2 0.2 - - - +
158A VAL* 3.5 39.9 + - + +
160A LEU* 5.7 0.3 - - - +
281A THR* 3.6 25.7 - - + +
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Residues in contact with ILE 128 (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 ALA* 6.0 0.2 - - + -
124A ILE* 3.0 34.8 + - + +
125A LEU* 3.2 19.5 + - + +
127A GLU* 1.3 77.4 - - - +
129A LEU* 1.3 53.0 + - - +
131A GLY* 3.2 2.8 + - - -
132A LEU* 2.8 41.5 + - + +
145A ILE* 4.4 10.3 - - + -
150A VAL* 3.7 34.8 - - + -
158A VAL* 4.4 2.2 - - + -
160A LEU* 4.0 22.6 - - + +
205A LEU* 3.7 20.0 - - + -
208A THR* 4.6 13.7 - - + -
212A LEU* 4.6 0.7 - - + -
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Residues in contact with LEU 129 (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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125A LEU 2.9 21.9 + - - +
126A ARG* 3.3 8.3 - - - +
128A ILE* 1.3 75.3 - - - +
130A LYS* 1.3 64.7 + - - +
132A LEU* 4.4 4.3 - - + +
133A ASP* 3.0 24.9 + - - +
202A ILE* 5.5 0.2 - - + -
205A LEU* 3.3 30.5 - - + -
250A PHE* 4.0 16.2 - - + -
265A ALA* 3.7 23.1 - - + +
268A LEU* 3.8 43.5 - - + +
269A LEU* 3.8 15.0 - - + +
274A ILE* 4.1 12.1 - - + -
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Residues in contact with LYS 130 (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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81A TYR* 3.5 47.9 + - + +
126A ARG* 3.1 36.0 + - - +
127A GLU* 3.6 29.1 + - - +
128A ILE 3.1 0.6 - - - -
129A LEU* 1.3 78.9 - - - +
131A GLY* 1.3 61.6 + - - +
133A ASP* 3.4 6.8 + - - +
134A TYR* 3.1 21.7 + - - +
269A LEU* 4.2 18.6 - - + -
113B PRO 5.1 7.7 + - - -
294B TRP* 5.6 8.3 - - - +
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Residues in contact with GLY 131 (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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81A TYR* 3.4 24.3 - - - +
82A VAL* 5.1 1.1 - - - -
127A GLU 3.1 11.8 + - - -
128A ILE 3.2 3.6 + - - -
130A LYS* 1.3 77.2 - - - +
132A LEU* 1.3 61.0 + - - +
134A TYR* 3.2 4.1 + - - +
135A LEU* 3.0 26.2 + - - +
160A LEU* 3.8 17.9 - - - -
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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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128A ILE* 2.8 38.8 + - + +
129A LEU* 3.9 2.9 - - + +
130A LYS 3.4 0.2 - - - -
131A GLY* 1.3 68.8 - - - +
133A ASP* 1.3 57.8 + - - +
135A LEU* 4.5 4.3 - - + +
136A HIS* 2.7 50.0 + - + +
142A HIS* 4.4 2.9 - - + -
145A ILE* 3.9 25.6 - - + -
160A LEU* 4.2 6.7 - - + -
201A ASP* 3.8 33.7 - - + +
202A ILE* 4.7 7.2 - - + -
205A LEU* 4.2 30.3 - - + -
265A ALA* 3.9 12.3 - - + -
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Residues in contact with ASP 133 (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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129A LEU 3.0 18.1 + - - +
130A LYS* 3.6 7.1 - - - +
132A LEU* 1.3 75.8 - - - +
134A TYR* 1.3 59.0 + - - +
136A HIS* 3.8 4.4 - - - +
137A SER* 2.9 33.5 + - - -
264A THR* 5.8 0.3 - - - -
265A ALA* 3.7 12.4 + - + +
266A LYS* 3.6 35.4 + - - +
269A LEU* 4.8 7.7 - - + +
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLN 3.9 4.2 + - - -
77A CYS* 3.3 28.8 - - + -
78A ASP* 2.7 41.2 + - - +
79A SER* 3.7 27.6 - - - +
81A TYR* 5.1 2.5 - - + -
82A VAL* 4.1 11.2 - - + -
130A LYS 3.1 14.1 + - - +
131A GLY* 3.5 7.2 - - - +
132A LEU 3.2 0.2 - - - -
133A ASP* 1.3 74.1 + - - +
135A LEU* 1.3 73.0 + - + +
137A SER* 2.5 25.6 + - - -
138A GLU* 3.0 40.2 + - + +
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Residues in contact with LEU 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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77A CYS* 3.7 24.2 - - - -
82A VAL* 4.3 5.4 - - + -
131A GLY 3.0 15.5 + - - +
132A LEU* 3.8 6.5 - - + +
134A TYR* 1.3 87.1 - - + +
136A HIS* 1.3 65.9 + - + +
138A GLU* 3.1 8.8 + - - -
140A LYS* 2.8 50.4 + - + +
141A ILE 6.0 0.2 - - - -
142A HIS* 4.1 20.0 - - + +
160A LEU* 3.7 24.2 - - + -
163A PHE* 3.6 34.8 - - + -
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Residues in contact with HIS 136 (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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132A LEU* 2.7 44.0 + - + +
133A ASP* 4.0 4.5 - - - +
135A LEU* 1.3 76.6 - - + +
137A SER* 1.3 57.9 + - - +
139A LYS* 2.9 29.1 + - - +
140A LYS 3.4 17.3 - - - -
198A SER* 3.4 43.7 + - - +
201A ASP* 3.0 33.6 + - + +
202A ILE* 4.0 15.0 - - + +
264A THR* 6.0 0.2 - - - -
265A ALA* 4.5 7.5 + - + +
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Residues in contact with SER 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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133A ASP* 2.9 18.4 + - - -
134A TYR* 2.5 27.4 + - - -
136A HIS* 1.3 76.3 - - - +
138A GLU* 1.3 66.2 + - - +
139A LYS* 2.8 21.2 + - - +
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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
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76A GLN 4.9 4.2 - - - +
134A TYR* 3.0 49.9 + - + +
135A LEU* 3.1 8.9 + - - +
137A SER* 1.3 84.1 + - - +
139A LYS* 1.3 70.9 + - - +
140A LYS* 3.2 23.0 + - + +
168A GLN* 3.4 10.9 + - - -
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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