Contacts of the helix formed by residues 137 - 159 (chain D) in PDB entry 5JKL
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 TYR 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D GLU* 4.1 8.1 - - - -
65D HIS* 2.7 54.5 + + + -
68D LYS* 3.3 20.6 - - + +
69D LEU* 3.4 22.1 - - + +
114D LEU* 3.9 35.7 - - + -
132D PHE* 3.5 34.3 - + - -
133D ILE* 2.9 16.2 + - + +
135D THR 3.7 0.6 - - - -
136D HIS* 1.3 96.6 - - + +
138D LEU* 1.3 66.0 + - - +
139D ASN 3.4 2.0 - - - -
140D GLU* 3.2 6.0 + - - +
141D GLN* 3.0 28.9 + - - +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN* 4.2 7.7 - - - +
114D LEU* 3.9 23.3 - - + -
115D LEU* 4.0 17.3 - - + -
118D HIS* 4.4 1.8 - - + -
133D ILE* 3.0 38.4 + - + +
134D GLU* 3.9 22.7 + - + +
137D TYR* 1.3 72.5 - - - +
139D ASN* 1.3 58.7 + - - +
141D GLN* 3.3 7.1 + - - +
142D VAL* 3.1 28.9 + - - +
127F PRO* 3.8 34.5 - - + -
128F HIS* 3.9 23.3 - - + +
131F ASP* 6.3 0.9 - - + -
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Residues in contact with ASN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D GLU 4.2 9.4 + - - +
135D THR 5.8 2.5 - - - +
137D TYR 3.4 0.2 - - - -
138D LEU* 1.3 76.0 - - - +
140D GLU* 1.3 61.8 + - - +
142D VAL* 4.1 6.9 - - - +
143D LYS* 2.8 61.0 + - - +
75F GLN* 4.6 7.5 + - - +
128F HIS* 2.9 31.7 + - + +
131F ASP* 5.0 7.9 - - - +
136F HIS* 6.0 1.6 + - - -
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLU* 5.3 4.3 - - - +
65D HIS* 5.0 18.6 + - + +
135D THR 5.6 1.3 - - - +
136D HIS* 3.4 25.3 - - - +
137D TYR* 3.2 9.3 + - - +
139D ASN* 1.3 79.3 + - - +
141D GLN* 1.3 61.5 + - - +
143D LYS* 2.9 32.4 + - - +
144D ALA* 3.0 28.9 + - - +
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Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D HIS* 4.8 6.9 - - - -
107D GLU* 2.8 53.7 + - - +
110D VAL* 3.9 10.5 - - - +
111D ASN* 3.4 28.0 - - + +
114D LEU* 3.5 31.3 - - + +
137D TYR* 3.0 13.9 + - - +
138D LEU 3.6 4.0 - - - +
139D ASN 3.3 0.2 - - - -
140D GLU* 1.3 73.6 - - - +
142D VAL* 1.3 61.4 + - - +
144D ALA* 3.1 3.5 + - - +
145D ILE* 2.8 36.3 + - + +
201D FE 4.0 13.7 - - - -
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN* 5.0 11.2 - - - +
138D LEU 3.1 18.7 + - - +
139D ASN* 3.3 6.7 + - - +
141D GLN* 1.3 76.2 - - - +
143D LYS* 1.3 63.1 + - - +
145D ILE* 3.5 7.2 + - + +
146D LYS* 3.0 23.0 + - - +
75F GLN* 3.9 37.6 - - + +
76F ARG* 4.0 15.5 - - - +
128F HIS* 3.5 42.6 - - + +
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ASN* 2.8 41.3 + - - +
140D GLU* 2.9 37.7 + - - +
142D VAL* 1.3 77.9 - - - +
144D ALA* 1.3 57.3 + - - +
146D LYS* 3.4 5.5 + - - +
147D GLU* 3.0 29.3 + - - +
75F GLN* 4.0 20.4 - - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 4.1 28.5 - - + +
140D GLU 3.0 17.6 + - - +
141D GLN* 3.7 4.3 - - - +
143D LYS* 1.3 76.3 - - - +
145D ILE* 1.3 58.2 + - - +
147D GLU* 3.4 7.7 + - - +
148D LEU* 3.0 37.5 + - + +
204D MG 4.7 11.2 - - - -
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 3.7 21.3 - - + +
107D GLU* 3.9 32.1 - - + +
108D LYS* 4.0 11.0 - - + -
111D ASN* 3.9 15.0 - - + +
141D GLN 2.8 23.5 + - - +
142D VAL* 3.9 7.2 - - + +
144D ALA* 1.3 72.8 - - - +
146D LYS* 1.3 59.9 + - - +
148D LEU* 3.4 2.5 + - - -
149D GLY* 2.9 24.8 + - - -
8F VAL* 3.6 38.4 - - + +
10F GLN* 3.9 21.8 - - + +
75F GLN 5.8 0.7 - - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D VAL 3.0 18.5 + - - +
143D LYS* 3.8 5.8 - - - +
144D ALA 3.3 0.2 - - - -
145D ILE* 1.3 76.7 - - - +
147D GLU* 1.3 58.8 + - - +
149D GLY* 3.8 0.9 - - - -
150D ASP* 2.9 68.2 + - - +
8F VAL* 4.1 14.0 - - + +
74F ASN* 3.5 40.4 - - - +
75F GLN* 4.1 24.9 - - + +
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D TYR* 2.6 32.6 + - - +
58D GLN* 4.4 4.9 + - - -
143D LYS 3.0 16.8 + - - +
144D ALA* 3.7 7.5 - - - +
145D ILE 3.3 0.2 - - - -
146D LYS* 1.3 77.4 - - - +
148D LEU* 1.3 56.9 + - - +
150D ASP* 3.2 11.2 + - - +
151D HIS* 3.0 51.2 + - + +
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 4.0 6.3 - - + +
54D TYR* 3.7 21.3 - - + +
55D PHE* 5.0 0.2 - - + -
100D MET* 3.7 31.9 - - - +
103D ALA* 3.8 28.5 - - + +
104D LEU* 3.8 15.7 - - + +
107D GLU* 3.5 31.6 - - + +
144D ALA* 3.0 23.0 + - + +
145D ILE* 4.0 3.6 - - - +
147D GLU* 1.3 72.4 - - - +
149D GLY* 1.3 61.2 + - - +
151D HIS* 3.2 4.8 + - + +
152D VAL* 2.9 33.7 + - - +
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 4.3 6.4 - - - +
145D ILE 2.9 17.1 + - - -
146D LYS 3.8 1.1 - - - -
148D LEU* 1.3 74.7 - - - +
150D ASP* 1.3 59.0 + - - +
152D VAL* 3.4 1.3 + - - +
153D THR* 2.9 26.2 + - - -
7F GLN* 3.0 35.3 + - - -
8F VAL* 4.2 7.2 - - - -
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 2.9 56.9 + - - +
147D GLU* 3.2 10.8 + - - +
149D GLY* 1.3 77.5 - - - +
151D HIS* 1.3 62.3 + - + +
153D THR* 3.3 5.8 + - - -
154D ASN* 2.9 41.5 + - - +
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Residues in contact with HIS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D TYR* 3.8 22.0 + + - -
100D MET* 3.9 31.9 - - + -
147D GLU* 3.0 40.5 + - + +
148D LEU* 3.6 7.4 - - - +
150D ASP* 1.3 79.6 - - + +
152D VAL* 1.3 63.3 - - - +
154D ASN* 3.3 3.4 + - - +
155D LEU* 3.0 31.5 + - - +
170D PHE* 3.6 22.1 - + + -
174D THR* 3.8 22.9 - - + +
175D LEU* 3.9 11.2 - - + +
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.9 12.3 - - + +
100D MET* 3.8 33.7 - - + +
101D GLU* 3.9 12.1 - - + +
104D LEU* 4.7 5.8 - - + -
148D LEU 2.9 21.2 + - - +
149D GLY 3.7 4.3 - - - +
151D HIS* 1.3 73.7 - - - +
153D THR* 1.3 64.1 + - - +
155D LEU* 3.3 2.5 + - - +
156D ARG* 2.9 69.2 + - - +
7F GLN* 3.6 10.3 - - - +
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Residues in contact with THR 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLY 2.9 11.3 + - - -
150D ASP* 3.6 7.6 - - - +
152D VAL* 1.3 78.9 - - - +
154D ASN* 1.3 61.9 + - - +
156D ARG* 3.3 9.5 + - - +
157D LYS* 2.9 59.6 + - + +
7F GLN* 3.1 23.4 + - - -
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Residues in contact with ASN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ASP* 2.9 34.8 + - - +
151D HIS* 4.9 1.2 + - - +
153D THR* 1.3 78.3 - - - +
155D LEU* 1.3 63.2 + - - +
157D LYS* 3.2 5.9 + - - +
158D MET* 3.0 37.2 + - - +
170D PHE* 3.8 24.0 - - + -
174D THR* 5.8 1.5 - - - +
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PHE* 4.1 14.8 - - + -
97D LEU* 3.9 33.7 - - + +
100D MET* 4.1 16.2 - - + -
151D HIS 3.0 21.4 + - - +
152D VAL 3.8 2.7 - - - +
154D ASN* 1.3 75.0 - - - +
156D ARG* 1.3 64.5 + - - +
158D MET* 3.3 5.6 + - - +
159D GLY 3.3 5.0 + - - -
160D ALA* 3.0 32.3 + - + +
166D ALA 4.3 2.7 - - - +
167D GLU* 4.1 26.9 - - + -
170D PHE* 3.6 40.4 - - + -
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Residues in contact with ARG 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 4.1 15.0 - - + +
101D GLU* 2.8 30.5 + - - +
104D LEU* 6.3 0.4 - - - +
152D VAL* 2.9 43.6 + - - +
153D THR* 3.6 8.6 + - - +
155D LEU* 1.3 77.2 - - - +
157D LYS* 1.3 66.2 + - + +
159D GLY* 3.1 13.9 + - - -
160D ALA 4.4 8.0 - - - +
7F GLN* 3.5 18.6 + - - +
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Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D THR* 2.9 38.5 + - + +
154D ASN* 3.9 6.3 - - - +
156D ARG* 1.3 81.5 - - + +
158D MET* 1.3 60.3 + - + +
159D GLY* 3.4 1.0 + - - -
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Residues in contact with MET 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASN* 3.0 31.4 + - + +
155D LEU* 3.6 5.2 - - - +
156D ARG 3.2 0.2 - - - -
157D LYS* 1.3 77.5 - - + +
159D GLY* 1.3 56.4 + - - +
160D ALA 3.8 0.2 - - - -
163D SER* 4.5 4.0 + - - -
166D ALA* 3.4 44.5 - - + +
169D LEU* 4.0 15.9 - - + -
170D PHE* 3.9 38.8 - - + +
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Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ARG 3.1 12.7 + - - -
157D LYS 3.1 1.9 + - - -
158D MET* 1.3 77.4 - - - +
160D ALA* 1.3 65.4 + - - +
162D ARG* 3.7 8.0 + - - +
163D SER* 3.1 26.6 + - - -
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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