Contacts of the helix formed by residues 122 - 145 (chain c) in PDB entry 3J7Y
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 ASN 122 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90c THR 3.0 10.0 - - - +
91c ALA* 3.0 27.6 + - - +
93c VAL 2.7 22.7 + - - +
94c ASN* 3.1 32.9 + - - +
121c SER* 1.3 79.4 + - - +
123c GLN* 1.3 54.8 + - - +
124c GLU 2.7 3.1 + - - -
125c LEU* 2.6 37.1 + - - +
126c SER* 3.0 9.3 + - - -
193c GLN* 4.0 15.5 + - + +
194c THR* 4.1 10.7 - - - +
197c ALA* 3.9 15.3 - - + -
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Residues in contact with GLN 123 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94c ASN* 5.9 0.4 + - - -
95c SER* 4.7 14.1 + - - +
121c SER* 3.8 16.6 + - - +
122c ASN* 1.3 75.7 - - - +
124c GLU* 1.3 63.0 + - - +
126c SER* 3.2 8.6 + - - -
127c GLU* 3.2 47.0 + - + +
193c GLN* 3.0 26.6 + - - +
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Residues in contact with GLU 124 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120c LYS* 5.2 12.5 + - - +
121c SER 4.9 4.2 + - - +
122c ASN 2.7 5.8 + - - +
123c GLN* 1.3 77.5 - - - +
125c LEU* 1.3 63.6 + - + +
127c GLU* 4.6 3.4 - - - +
128c GLN* 3.3 39.9 + - - +
204c GLN* 5.4 8.1 + - - -
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Residues in contact with LEU 125 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87c LEU* 4.1 7.4 - - + +
90c THR* 4.0 18.4 - - - +
91c ALA* 3.9 29.4 - - + +
121c SER 4.9 5.2 - - - +
122c ASN* 2.6 14.8 + - - +
124c GLU* 1.3 83.6 - - + +
126c SER* 1.3 59.7 + - - +
127c GLU 3.3 0.4 - - - -
128c GLN* 3.2 8.8 + - - +
129c GLY* 2.9 26.7 + - - -
196c PHE 4.2 0.2 - - - +
197c ALA* 3.8 14.6 - - - +
200c GLY* 4.0 6.7 - - - -
201c ALA* 3.9 20.0 - - + +
204c GLN* 3.4 35.4 - - + +
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Residues in contact with SER 126 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122c ASN 3.0 11.9 + - - -
123c GLN* 3.2 19.9 + - - -
125c LEU* 1.3 77.7 - - - +
127c GLU* 1.3 67.9 + - - +
129c GLY* 3.2 2.1 + - - -
130c THR* 2.9 30.0 + - - +
193c GLN* 3.7 40.2 + - - +
196c PHE* 3.6 8.2 - - - +
197c ALA* 3.7 15.5 - - - +
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Residues in contact with GLU 127 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123c GLN* 3.2 31.5 + - + +
124c GLU* 4.6 3.8 - - - +
126c SER* 1.3 85.1 + - - +
128c GLN* 1.3 62.6 - - + +
130c THR* 2.5 21.9 + - - -
131c SER* 2.9 20.1 + - - +
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Residues in contact with GLN 128 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124c GLU* 3.3 30.9 + - - +
125c LEU* 3.2 14.6 + - - +
127c GLU* 1.3 79.7 - - + +
129c GLY* 1.3 57.0 + - - +
131c SER* 3.2 4.5 + - - -
132c PHE* 2.9 35.7 + - - +
200c GLY* 4.8 6.1 - - - +
203c LEU* 5.7 6.1 - - + -
204c GLN* 3.7 31.2 + - - +
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Residues in contact with GLY 129 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125c LEU 2.9 11.2 + - - -
126c SER 3.2 0.4 + - - -
128c GLN* 1.3 75.2 - - - +
130c THR* 1.3 57.2 + - - +
132c PHE* 4.1 2.4 - - - +
133c SER* 2.9 34.1 + - - -
196c PHE* 3.4 28.7 - - - -
199c ILE* 4.3 6.9 - - - +
200c GLY* 4.0 11.7 - - - -
203c LEU* 5.9 0.7 - - - -
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Residues in contact with THR 130 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126c SER* 2.9 11.8 + - - +
127c GLU* 2.5 27.7 + - - -
129c GLY* 1.3 72.4 - - - +
131c SER* 1.3 58.8 + - - +
133c SER* 2.4 24.5 + - - -
134c GLN* 2.9 30.5 + - - +
192c GLN* 5.7 1.6 - - - +
193c GLN* 6.3 0.4 - - - -
196c PHE* 3.3 39.6 - - + -
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Residues in contact with SER 131 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127c GLU* 2.9 22.5 + - - +
128c GLN* 3.7 5.1 - - - -
130c THR* 1.3 78.6 + - - +
132c PHE* 1.3 59.3 + - - +
134c GLN* 3.2 15.2 + - - +
135c THR* 2.9 35.6 + - - +
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Residues in contact with PHE 132 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128c GLN 2.9 17.2 + - - +
129c GLY 4.1 1.1 - - - +
131c SER* 1.3 77.4 - - - +
133c SER* 1.3 61.3 + - - +
135c THR* 2.4 29.4 + - - -
136c CYS* 2.9 42.5 + - - +
199c ILE* 4.6 8.7 - - + -
203c LEU* 3.4 30.5 - - + -
208c PRO* 3.5 35.0 - - + -
211c THR* 3.5 17.5 - - - -
212c ALA 4.2 0.4 - - - -
215c ILE* 3.6 15.7 - - + -
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Residues in contact with SER 133 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129c GLY 2.9 17.3 + - - -
130c THR 2.4 24.3 + - - -
132c PHE* 1.3 77.6 - - - +
134c GLN* 1.3 61.0 + - - +
136c CYS* 3.2 4.3 + - - +
137c LEU* 2.9 34.5 + - - +
161c THR* 4.5 2.7 - - - +
196c PHE* 3.2 26.2 - - - -
199c ILE* 4.8 3.1 - - - -
215c ILE* 3.9 25.2 - - - +
219c LEU* 4.7 9.9 - - - -
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Residues in contact with GLN 134 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130c THR* 2.9 27.3 + - - +
131c SER* 3.2 15.1 + - - +
133c SER* 1.3 77.5 + - - +
135c THR* 1.3 58.8 + - + +
137c LEU* 3.2 6.4 + - - +
138c THR* 2.9 34.3 + - + +
157c VAL* 4.0 24.4 - - + +
158c ASP* 5.1 7.5 + - - -
161c THR* 4.5 16.5 + - + -
196c PHE* 6.4 0.2 - - + -
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Residues in contact with THR 135 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131c SER* 2.9 22.5 + - - +
132c PHE* 2.4 36.2 + - - -
134c GLN* 1.3 78.0 - - + +
136c CYS* 1.3 58.0 + - - +
138c THR* 2.4 26.4 + - - -
139c GLN* 2.9 22.2 + - - +
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Residues in contact with CYS 136 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132c PHE* 2.9 50.4 + - - +
133c SER 3.2 9.4 + - - +
135c THR* 1.3 77.2 + - - +
137c LEU* 1.3 58.1 + - - +
139c GLN* 3.2 8.2 + - - +
140c PHE* 2.9 44.7 + - + -
212c ALA* 3.8 22.2 - - - -
215c ILE* 4.2 12.8 - - + -
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Residues in contact with LEU 137 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133c SER 2.9 17.5 + - - +
134c GLN 3.4 7.2 - - - +
136c CYS* 1.3 77.3 - - - +
138c THR* 1.3 56.1 + - - +
140c PHE* 3.2 3.2 + - - +
141c LEU* 2.9 41.4 + - + +
157c VAL* 3.9 18.2 - - + -
160c LEU* 3.8 24.2 - - + -
161c THR* 3.3 35.7 - - + -
215c ILE* 3.9 12.8 - - + -
219c LEU* 4.7 8.3 - - + -
220c ILE* 3.3 38.8 - - + -
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Residues in contact with THR 138 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134c GLN* 2.9 18.9 + - + +
135c THR* 2.4 32.7 + - - -
137c LEU* 1.3 76.7 - - - +
139c GLN* 1.3 55.9 + - - +
141c LEU* 4.0 0.9 - - - +
142c GLU* 2.9 47.5 + - - +
153c ILE* 4.5 14.5 - - + +
154c LYS* 6.0 4.9 - - + -
157c VAL* 3.9 19.1 - - + -
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Residues in contact with GLN 139 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135c THR* 2.9 19.7 + - - +
136c CYS* 3.2 11.4 + - - +
138c THR* 1.3 77.6 + - - +
140c PHE* 1.3 61.1 + - + +
142c GLU* 3.7 7.9 - - - +
143c ASP* 2.4 48.7 + - - +
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Residues in contact with PHE 140 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136c CYS* 2.9 34.3 + - + +
137c LEU 3.8 3.8 - - - +
139c GLN* 1.3 79.3 - - + +
141c LEU* 1.3 58.5 + - + +
143c ASP* 3.2 10.2 + - + +
144c GLU* 2.9 34.9 + - + +
212c ALA* 4.2 36.3 - - + -
213c LEU* 5.7 4.0 - - + -
215c ILE* 6.0 0.4 - - + -
216c ARG* 4.5 22.7 - - + -
220c ILE* 4.1 24.9 - - + -
314c TRP* 4.2 21.5 - + + -
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Residues in contact with LEU 141 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137c LEU* 2.9 21.8 + - + +
138c THR 4.1 2.0 - - - +
140c PHE* 1.3 77.9 - - + +
142c GLU* 1.3 55.9 + - - +
144c GLU* 3.2 4.9 + - - +
145c TYR* 2.9 69.9 + - + +
153c ILE* 4.2 18.2 - - + +
156c LEU* 4.2 20.9 - - + -
157c VAL* 3.7 26.0 - - + -
160c LEU* 4.3 11.4 - - + -
220c ILE* 5.9 1.1 - - + -
223c MET* 4.1 20.2 - - + -
314c TRP* 4.7 6.7 - - + -
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Residues in contact with GLU 142 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138c THR* 2.9 35.4 + - - +
139c GLN* 3.7 9.0 - - - +
141c LEU* 1.3 79.1 - - - +
143c ASP* 1.3 65.0 + - - +
145c TYR 4.4 4.7 - - - -
146c PRO* 3.6 26.5 - - + +
150c THR* 5.8 3.3 - - - +
153c ILE* 4.0 25.9 - - + +
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Residues in contact with ASP 143 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139c GLN* 2.4 42.4 + - - +
140c PHE* 3.2 10.2 + - + +
142c GLU* 1.3 78.7 - - - +
144c GLU* 1.3 65.2 + - + +
146c PRO* 4.6 3.5 - - - +
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Residues in contact with GLU 144 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140c PHE* 2.9 18.9 + - + +
141c LEU 3.2 2.6 + - - +
143c ASP* 1.3 82.4 - - + +
145c TYR* 1.3 83.5 + - + +
146c PRO* 3.7 6.1 - - - +
312c ARG* 4.9 12.1 - - - +
314c TRP* 3.7 52.5 + - + -
315c ASN* 5.0 2.1 + - - +
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Residues in contact with TYR 145 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141c LEU* 2.9 45.7 + - + +
142c GLU* 3.7 5.1 - - - +
144c GLU* 1.3 99.0 - - + +
146c PRO* 1.4 65.7 - - - +
147c ASP* 3.3 1.6 - - + +
148c MET* 3.6 27.3 - - + +
153c ILE* 4.9 3.4 - - + +
156c LEU* 4.4 4.0 - - + -
223c MET* 3.2 25.5 - - - +
305c TYR 4.0 17.3 - - - +
306c GLY* 4.1 15.5 - - - +
307c PHE* 3.2 40.2 - + - -
311c ARG* 4.4 11.1 + - - -
314c TRP* 3.5 13.9 - + - -
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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