Contacts of the helix formed by residues 129 - 150 (chain B) in PDB entry 5LOH
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B TYR* 5.6 3.7 - - - -
127B TYR* 4.3 6.6 + - + -
128B PHE* 1.3 76.8 - - - +
130B GLU* 1.3 65.0 + - - +
131B GLU* 3.1 22.7 + - - +
132B MET* 3.2 24.1 + - - +
133B ALA* 2.9 20.5 + - - +
772B LEU* 4.6 0.2 - - - -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE 4.1 0.2 + - - -
129B ASP* 1.3 75.1 - - - +
131B GLU* 1.3 57.9 + - - +
133B ALA* 3.4 1.6 + - - +
134B VAL* 2.9 37.1 + - + +
772B LEU* 3.8 21.4 - - + +
805B SER* 2.2 33.6 + - - -
807B ASN* 4.7 5.7 + - - +
808B ALA* 4.1 5.4 - - + +
834B LEU* 3.4 30.8 - - + +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ASP* 3.1 10.1 + - - +
130B GLU* 1.3 79.6 - - - +
132B MET* 1.3 63.5 + - - +
134B VAL* 3.1 7.2 + - - +
135B LYS* 2.9 23.1 + - - +
849B PRO* 5.6 0.4 - - - -
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Residues in contact with MET 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 3.8 9.0 - - + -
125B TYR* 4.1 21.5 - - + -
128B PHE* 3.6 35.9 - - + -
129B ASP* 3.2 23.1 + - - +
131B GLU* 1.3 78.2 - - - +
133B ALA* 1.3 57.7 + - - +
135B LYS* 3.3 3.0 + - - +
136B TYR* 3.0 69.2 + - + +
849B PRO* 3.7 33.6 - - + +
850B PHE* 4.1 13.2 - - + -
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE* 4.3 6.2 - - + +
129B ASP 2.9 16.1 + - - +
130B GLU 3.7 4.5 - - - +
132B MET* 1.3 76.2 - - - +
134B VAL* 1.3 58.4 + - + +
136B TYR* 4.0 0.4 - - - +
137B ILE* 2.9 36.1 + - - +
768B LEU* 4.2 8.1 - - + -
771B PHE* 3.9 28.9 - - + -
772B LEU* 3.9 21.5 - - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.9 25.3 + - + +
131B GLU* 3.1 5.8 + - - +
133B ALA* 1.3 75.6 - - + +
135B LYS* 1.3 57.5 + - - +
137B ILE* 4.6 0.7 - - - -
138B SER* 2.1 46.7 + - - +
768B LEU* 5.4 1.8 - - + -
772B LEU* 6.4 0.2 - - + -
834B LEU* 3.6 50.0 - - + +
835B PHE* 3.8 20.0 - - + -
838B VAL* 4.3 11.9 - - + -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLU 2.9 13.3 + - - +
132B MET* 3.7 9.9 - - - +
134B VAL* 1.3 77.3 - - - +
136B TYR* 1.3 63.8 - - + +
138B SER* 3.1 5.8 + - - -
139B GLU* 3.0 28.1 + - - +
846B GLN* 3.9 26.3 + - - +
848B MET* 4.0 13.9 - - + -
849B PRO* 4.9 6.5 - - + -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 3.9 15.5 - - + -
121B LEU* 3.4 15.0 - - + +
128B PHE* 3.6 37.7 - + - -
132B MET* 3.0 49.2 + - + +
133B ALA 4.0 0.9 - - - +
135B LYS* 1.3 76.3 - - + +
137B ILE* 1.3 63.1 + - - +
139B GLU* 3.1 8.0 + - - +
140B VAL* 2.9 29.1 + - + +
162B MET* 6.2 0.2 - - - -
164B ILE* 4.3 5.0 - - + +
168B GLY 4.2 4.5 + - - -
170B ILE* 3.3 33.3 - - + +
771B PHE* 3.7 16.2 - + + -
848B MET* 3.6 21.3 - - + -
849B PRO* 4.5 3.8 - - + -
850B PHE* 3.8 12.5 + - - +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ALA 2.9 25.3 + - - +
134B VAL 4.3 1.6 - - - +
136B TYR* 1.3 72.3 - - - +
138B SER* 1.3 57.5 + - - +
140B VAL* 3.9 5.0 - - + +
141B ALA* 2.9 27.7 + - - +
162B MET* 5.4 0.7 - - + -
764B LEU* 3.6 38.0 - - + +
767B CYS* 4.1 6.7 - - + -
768B LEU* 3.5 49.1 - - + +
771B PHE* 3.9 15.9 - - + -
815B LEU* 5.5 0.9 - - + -
829B LEU* 5.0 0.7 - - + -
835B PHE* 3.7 26.5 - - + -
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 2.1 32.8 + - - +
135B LYS* 3.4 6.6 - - - -
136B TYR 3.1 0.2 - - - -
137B ILE* 1.3 74.5 - - - +
139B GLU* 1.3 65.2 + - - +
141B ALA* 3.1 3.5 + - - +
142B LEU* 2.9 22.5 + - - +
835B PHE* 3.6 16.3 - - - -
838B VAL* 4.4 5.5 - - - +
840B TRP* 3.5 24.4 - - - -
843B LEU* 3.6 24.0 - - - -
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 3.4 33.5 - - + -
135B LYS 3.0 18.0 + - - +
136B TYR* 3.6 6.7 - - - +
138B SER* 1.3 73.7 - - - +
140B VAL* 1.3 62.6 + - - +
142B LEU* 3.1 5.8 + - - +
143B ALA* 3.0 21.8 + - - +
169B HIS* 2.8 30.3 + - - +
170B ILE* 2.9 38.0 + - + +
843B LEU* 3.4 15.0 - - + +
846B GLN* 3.3 17.9 + - - +
848B MET* 3.5 8.0 - - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR* 2.9 22.6 + - + +
137B ILE* 3.9 5.8 - - + +
139B GLU* 1.3 74.8 - - - +
141B ALA* 1.3 57.5 + - - +
143B ALA* 3.2 7.8 + - - +
144B LEU* 2.9 29.5 + - + +
157B LEU* 3.7 28.5 - - + -
162B MET* 3.6 24.0 - - + -
170B ILE* 3.6 25.6 - - + -
172B LEU* 4.1 7.9 - - + -
764B LEU* 3.6 23.3 - - + -
771B PHE* 5.7 0.2 - - + -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE 2.9 19.8 + - - +
138B SER* 3.1 7.6 + - - +
140B VAL* 1.3 78.1 - - - +
142B LEU* 1.3 56.9 + - - +
144B LEU* 3.4 2.8 + - - +
145B ASP* 2.9 29.5 + - - +
761B TRP* 3.8 18.8 - - + -
764B LEU* 4.2 4.2 - - + +
826B MET* 4.0 9.1 - - - +
829B LEU* 3.7 27.8 - - + -
840B TRP* 4.4 3.8 - - + -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 3.8 30.3 - - + -
138B SER 2.9 16.5 + - - +
139B GLU 3.1 5.4 + - - +
141B ALA* 1.3 75.3 - - - +
143B ALA* 1.3 58.5 + - - +
145B ASP* 3.3 7.5 + - + +
146B TYR* 2.9 28.8 + - - +
826B MET* 3.7 12.6 - - + -
830B LYS* 6.0 1.1 - - - +
840B TRP* 3.6 37.2 - - + +
843B LEU* 3.7 33.4 - - + -
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Residues in contact with ALA 143 (chain B).
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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90B SER* 5.5 0.4 - - - -
92B PHE* 3.4 38.0 - - + +
93B ILE* 4.1 6.6 - - + +
139B GLU 3.0 8.6 + - - +
140B VAL* 3.2 8.0 + - - +
142B LEU* 1.3 77.4 - - - +
144B LEU* 1.3 62.0 + - - +
146B TYR* 3.0 8.5 + - - +
147B LEU* 2.9 28.3 + - - +
172B LEU* 3.6 19.5 - - + -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 2.9 22.1 + - + +
141B ALA 3.7 4.3 - - - +
143B ALA* 1.3 76.0 - - - +
145B ASP* 1.3 56.7 + - - +
147B LEU* 3.4 5.3 + - + +
148B HIS* 2.9 42.3 + - + +
154B HIS* 4.0 23.1 - - + -
157B LEU* 3.7 20.0 - - + -
172B LEU* 3.8 21.3 - - + -
760B ASP* 3.4 39.0 - - + +
761B TRP* 4.3 22.0 - - + -
764B LEU* 4.4 4.9 - - + -
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Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA 2.9 18.2 + - - +
142B LEU* 3.7 9.2 - - + +
144B LEU* 1.3 75.5 - - - +
146B TYR* 1.3 57.4 + - - +
148B HIS* 3.8 8.5 + - - +
149B ARG* 2.6 62.7 + - - +
761B TRP* 4.5 3.9 - - + -
826B MET* 3.5 39.4 - - + +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B SER* 3.1 31.6 - - - -
89B LYS 3.8 11.1 + - - -
90B SER* 3.9 29.6 - - - +
93B ILE* 4.0 23.6 - - + -
142B LEU 2.9 14.3 + - - +
143B ALA* 3.0 10.3 + - - +
145B ASP* 1.3 73.1 - - - +
147B LEU* 1.3 74.0 + - + +
149B ARG* 3.0 8.9 + - + +
150B HIS* 3.0 64.2 + + + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.7 26.7 - - + -
143B ALA 2.9 18.8 + - - +
144B LEU* 3.9 7.4 - - + +
146B TYR* 1.3 81.7 - - + +
148B HIS* 1.3 62.7 + - + +
150B HIS* 2.9 14.1 + - + -
151B GLY 3.0 0.5 + - - -
152B ILE* 2.9 49.8 + - + +
154B HIS* 4.0 35.2 - - + +
172B LEU* 4.2 10.5 - - + -
175B PHE* 3.9 27.6 - - + -
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Residues in contact with HIS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A ARG* 3.2 17.3 - - - +
754A ALA* 3.3 12.9 + - - +
144B LEU* 2.9 26.3 + - + +
145B ASP* 3.8 8.5 - - - +
147B LEU* 1.3 78.9 - - + +
149B ARG* 1.3 62.7 + - - +
151B GLY 3.1 9.0 + - - -
152B ILE 3.0 22.0 - - - +
757B PRO* 3.5 30.8 - - + +
760B ASP* 2.8 31.4 + - + +
761B TRP* 3.5 36.7 + + - -
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Residues in contact with ARG 149 (chain B).
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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751A LEU 4.5 4.3 - - - +
752A GLY 4.1 3.8 - - - +
753A ARG* 3.9 41.2 - - - +
145B ASP* 2.6 64.2 + - - +
146B TYR* 3.0 9.4 + - + +
148B HIS* 1.3 76.4 - - - +
150B HIS* 1.3 68.5 + - + +
151B GLY 3.3 0.9 + - - -
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Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A GLY 3.6 7.0 - - - +
88B SER* 4.8 10.3 + - - -
146B TYR* 3.0 60.4 + + - +
147B LEU* 2.9 12.7 + - - +
149B ARG* 1.3 83.3 - - + +
151B GLY* 1.3 60.8 + - - +
152B ILE* 3.5 13.2 - - + +
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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