Contacts of the helix formed by residues 137 - 159 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F GLU* 4.2 8.5 - - - -
65F HIS* 2.7 53.6 + + + -
68F LYS* 3.3 20.5 - - + +
69F LEU* 3.4 22.2 + - + +
114F LEU* 3.9 37.0 - - + -
132F PHE* 3.4 36.8 - + - -
133F ILE* 2.9 16.2 + - + +
135F THR 3.7 0.4 - - - -
136F HIS* 1.3 99.0 - - + +
138F LEU* 1.3 66.2 + - - +
139F ASN 3.3 2.2 - - - +
140F GLU* 3.2 5.6 + - + +
141F GLN* 3.0 28.1 + - - +
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E PRO* 3.7 38.6 - - + -
128E HIS* 3.8 24.0 - - + +
131E ASP* 6.2 0.7 - - + -
111F ASN* 4.2 8.0 - - - +
114F LEU* 4.0 21.8 - - + +
115F LEU* 4.1 17.0 - - + -
118F HIS* 4.5 0.7 - - + -
133F ILE* 3.0 36.3 + - + +
134F GLU* 3.8 19.4 + - + +
137F TYR* 1.3 75.9 - - - +
139F ASN* 1.3 62.4 + - - +
141F GLN* 3.3 6.4 + - - +
142F VAL* 3.1 25.6 + - - +
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Residues in contact with ASN 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLN* 4.4 7.2 + - - +
128E HIS* 2.8 32.9 + - + +
131E ASP* 4.9 10.1 - - - +
136E HIS* 6.1 0.8 + - - -
134F GLU 4.1 7.7 + - - +
135F THR 5.7 2.7 + - - +
137F TYR 4.8 0.4 - - - +
138F LEU* 1.3 77.0 - - - +
140F GLU* 1.3 66.3 + - - +
142F VAL* 4.0 7.8 - - - +
143F LYS* 2.9 51.1 + - - +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F GLU* 5.6 1.9 - - - +
65F HIS* 4.9 21.2 + - + +
135F THR 5.4 2.4 + - - +
136F HIS* 3.4 24.2 - - - +
137F TYR* 3.2 9.7 + - + +
139F ASN* 1.3 79.9 + - - +
141F GLN* 1.3 58.8 + - - +
143F LYS* 2.9 33.1 + - - +
144F ALA* 3.1 27.7 + - - +
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Residues in contact with GLN 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F HIS* 4.7 6.4 - - - -
107F GLU* 2.7 54.0 + - - +
110F VAL* 3.9 15.8 - - - +
111F ASN* 3.3 31.2 - - + +
114F LEU* 3.5 20.7 - - + +
137F TYR* 3.0 12.7 + - - +
138F LEU 3.6 5.8 - - - +
140F GLU* 1.3 75.2 - - - +
142F VAL* 1.3 64.4 + - - +
144F ALA* 3.2 3.5 + - - +
145F ILE* 2.9 30.8 + - - +
201F FE 4.0 14.6 - - - -
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLN* 3.8 37.5 - - + +
76E ARG* 3.8 18.4 - - - +
128E HIS* 3.7 39.0 - - + +
111F ASN* 5.1 11.0 - - - +
138F LEU 3.1 15.2 + - - +
139F ASN* 3.9 6.7 - - - +
141F GLN* 1.3 78.0 - - - +
143F LYS* 1.3 63.8 + - - +
145F ILE* 3.9 6.9 - - + +
146F LYS* 3.1 22.0 + - - +
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Residues in contact with LYS 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LYS* 6.5 0.2 - - - -
75E GLN* 3.9 22.9 - - - +
139F ASN* 2.9 39.6 + - - +
140F GLU* 2.9 37.8 + - - +
142F VAL* 1.3 76.8 - - - +
144F ALA* 1.3 57.9 + - - +
146F LYS* 3.5 5.4 + - - +
147F GLU* 3.0 29.5 + - - +
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 4.0 28.3 - - + +
140F GLU 3.1 17.7 + - - +
141F GLN* 3.2 5.1 + - - +
143F LYS* 1.3 74.7 - - - +
145F ILE* 1.3 59.8 + - - +
147F GLU* 3.4 6.5 + - - +
148F LEU* 3.0 38.8 + - + +
203F MG 4.7 12.1 - - - -
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Residues in contact with ILE 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 3.7 40.5 - - + +
10E GLN* 3.8 23.3 - - + +
75E GLN 5.7 0.9 - - - +
104F LEU* 3.8 17.9 - - + +
107F GLU* 3.8 28.9 - - + +
108F LYS* 3.8 13.2 - - + -
111F ASN* 3.9 14.8 - - + +
141F GLN 2.9 22.0 + - - +
142F VAL* 3.9 6.7 - - + +
144F ALA* 1.3 71.9 - - - +
146F LYS* 1.3 60.7 + - - +
148F LEU* 3.4 2.0 + - - -
149F GLY 2.9 25.1 + - - -
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Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 4.1 14.1 - - + -
74E ASN* 3.5 42.4 - - - +
75E GLN* 4.1 24.9 + - + +
142F VAL 3.1 17.5 + - - +
143F LYS* 3.8 6.3 - - - +
145F ILE* 1.3 76.6 - - - +
147F GLU* 1.3 58.7 + - - +
149F GLY* 3.3 0.7 + - - -
150F ASP* 2.9 66.7 + - - +
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Residues in contact with GLU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F TYR* 2.6 31.1 + - - +
58F GLN* 4.3 5.4 + - - -
143F LYS 3.0 17.7 + - - +
144F ALA* 3.7 7.9 - - - +
146F LYS* 1.3 78.3 - - - +
148F LEU* 1.3 58.0 + - - +
150F ASP* 3.2 11.8 + - + +
151F HIS* 2.9 54.8 + - + +
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F TYR* 3.8 9.4 - - - +
54F TYR* 3.7 22.7 - - + +
100F MET* 3.7 29.8 - - - +
103F ALA* 3.7 26.0 - - + +
104F LEU* 3.9 17.0 - - + +
107F GLU* 3.5 31.0 - - + -
144F ALA* 3.0 24.1 + - + +
145F ILE* 3.9 3.6 - - - +
147F GLU* 1.3 74.4 - - - +
149F GLY* 1.3 57.0 + - - +
151F HIS* 3.2 4.6 + - + +
152F VAL* 2.9 34.6 + - - +
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Residues in contact with GLY 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLN* 3.1 35.4 + - - -
8E VAL* 4.1 8.1 - - - -
104F LEU* 4.3 5.9 - - - +
145F ILE 2.9 17.1 + - - -
146F LYS 3.7 1.6 - - - -
147F GLU 3.3 0.2 - - - -
148F LEU* 1.3 75.0 - - - +
150F ASP* 1.3 57.3 + - - +
152F VAL* 3.3 1.4 + - - +
153F THR* 2.9 26.4 + - - -
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Residues in contact with ASP 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F LYS* 2.9 59.8 + - - +
147F GLU* 3.4 10.6 - - - +
149F GLY* 1.3 76.4 - - - +
151F HIS* 1.3 62.5 + - + +
153F THR* 3.3 6.4 + - - -
154F ASN* 2.9 42.7 + - - +
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Residues in contact with HIS 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F TYR* 3.8 21.9 + + - -
100F MET* 3.9 31.4 - - + -
147F GLU* 2.9 39.7 + - + +
148F LEU* 3.2 7.8 + - - +
150F ASP* 1.3 81.5 - - + +
152F VAL* 1.3 62.4 + - - +
154F ASN* 3.3 2.3 + - - +
155F LEU* 3.0 31.1 + - - +
170F PHE* 3.6 21.5 - + + -
174F THR* 3.7 23.6 - - + +
175F LEU* 3.9 11.2 - - + +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLN* 3.6 8.1 - - - +
97F LEU* 3.9 13.2 - - + +
100F MET* 3.7 26.9 - - + +
101F GLU* 3.8 20.2 - - + +
104F LEU* 4.6 7.6 - - + -
148F LEU 2.9 21.0 + - - +
149F GLY 3.7 4.0 - - - +
151F HIS* 1.3 74.5 - - - +
153F THR* 1.3 58.6 + - - +
155F LEU* 3.2 2.1 + - - +
156F ARG* 2.9 73.2 + - - +
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Residues in contact with THR 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLN* 3.1 23.4 + - - -
149F GLY 2.9 11.8 + - - -
150F ASP* 3.6 7.9 - - - +
152F VAL* 1.3 79.1 - - - +
154F ASN* 1.3 62.3 + - - +
156F ARG* 3.7 8.7 + - - +
157F LYS* 2.9 56.1 + - + +
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Residues in contact with ASN 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ASP* 2.9 37.8 + - - +
151F HIS* 4.9 0.8 + - - +
153F THR* 1.3 78.0 - - - +
155F LEU* 1.3 58.0 + - - +
157F LYS* 3.2 7.0 + - - +
158F MET* 2.9 43.7 + - - +
170F PHE* 3.9 24.8 - - + -
174F THR* 5.8 1.3 - - - -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F PHE* 4.1 6.3 - - + -
97F LEU* 3.9 33.9 - - + +
100F MET* 4.0 20.2 - - + -
151F HIS 3.0 21.2 + - - +
152F VAL 3.8 2.7 - - - +
154F ASN* 1.3 77.0 - - - +
156F ARG* 1.3 63.4 + - - +
158F MET* 3.4 5.4 + - - +
159F GLY 3.4 3.6 + - - -
160F ALA* 3.0 31.9 + - + +
166F ALA* 4.4 2.7 - - + +
167F GLU* 4.2 27.4 - - + -
170F PHE* 3.6 44.2 - - + -
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Residues in contact with ARG 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLN* 3.4 25.1 + - - +
97F LEU* 3.9 15.7 - - + -
101F GLU* 2.8 31.7 + - - +
104F LEU* 6.2 0.6 - - - +
152F VAL* 2.9 33.9 + - - +
153F THR* 3.7 7.4 + - - +
155F LEU* 1.3 77.4 - - - +
157F LYS* 1.3 62.5 + - + +
159F GLY* 3.1 15.6 + - - -
160F ALA 4.2 8.4 - - - +
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Residues in contact with LYS 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F THR* 2.9 40.1 + - + +
154F ASN* 3.8 7.4 - - - +
156F ARG* 1.3 77.6 - - + +
158F MET* 1.3 61.2 + - + +
159F GLY 3.4 0.5 + - - -
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Residues in contact with MET 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ASN* 2.9 31.3 + - + +
155F LEU* 3.7 4.7 - - - +
156F ARG 3.2 0.2 - - - -
157F LYS* 1.3 78.0 - - + +
159F GLY* 1.3 57.4 + - - +
163F SER* 4.4 4.5 + - - -
166F ALA* 3.3 46.2 - - + +
169F LEU* 4.0 16.2 - - + -
170F PHE* 3.7 37.9 - - + +
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Residues in contact with GLY 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F ARG 3.1 12.5 + - - -
157F LYS 3.2 1.6 + - - -
158F MET* 1.3 79.5 - - - +
160F ALA* 1.3 63.6 + - - +
162F ARG* 3.6 9.7 + - - +
163F SER* 3.1 26.9 + - - -
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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