Contacts of the helix formed by residues 133 - 156 (chain A) in PDB entry 5DQZ
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 SER 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ARG 3.6 2.7 + - - -
132A ARG* 1.3 79.5 - - - +
134A VAL* 1.3 66.1 + - - +
135A GLU* 2.9 18.9 + - - +
136A GLN* 3.4 19.4 + - - +
137A LEU* 3.2 18.9 + - - +
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Residues in contact with VAL 134 (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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112A ARG* 5.3 7.2 - - - +
113A LEU* 3.6 31.0 - - + -
116A VAL* 4.0 26.2 - - + -
117A ARG* 5.9 0.9 - - + -
120A PHE* 4.5 3.4 - - + -
133A SER* 1.3 73.9 - - - +
135A GLU* 1.3 62.9 + - - +
136A GLN 3.1 1.8 - - - -
137A LEU* 3.2 11.5 + - + +
138A ARG* 3.0 37.7 + - + +
207A VAL* 6.2 1.8 - - + -
285B ASP* 3.7 44.0 - - + +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 2.9 21.5 + - - +
134A VAL* 1.3 73.8 + - - +
136A GLN* 1.3 55.5 + - - +
138A ARG* 3.3 33.2 + - - +
139A GLY* 3.0 22.3 + - - -
284B GLU 4.7 4.0 - - - +
285B ASP* 3.0 33.8 - - - +
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Residues in contact with GLN 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 ARG* 2.5 65.6 + - + +
133A SER* 3.6 21.6 + - - +
134A VAL 3.1 0.2 - - - -
135A GLU* 1.3 79.0 - - - +
137A LEU* 1.3 59.6 + - - +
139A GLY* 3.2 2.7 + - - +
140A ILE* 2.9 33.4 + - + +
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Residues in contact with LEU 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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116A VAL* 5.5 0.4 - - + -
117A ARG* 4.8 18.8 - - + +
120A PHE* 3.8 37.7 - - + -
124A PHE* 4.1 20.5 - - + -
128A ALA* 4.2 18.2 - - + -
129A PRO* 4.5 15.7 - - + +
132A ARG* 4.1 17.9 - - + +
133A SER 3.2 14.5 + - - +
134A VAL* 3.2 14.8 + - + +
136A GLN* 1.3 76.5 - - - +
138A ARG* 1.3 64.1 + - - +
140A ILE* 3.3 9.0 + - + +
141A GLU* 3.0 26.5 + - - +
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Residues in contact with ARG 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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120A PHE* 4.1 8.5 - - + -
134A VAL* 3.0 25.7 + - + +
135A GLU* 3.5 30.1 + - - +
136A GLN 3.2 0.2 - - - -
137A LEU* 1.3 75.4 - - - +
139A GLY* 1.3 58.6 + - - +
141A GLU 3.5 0.2 + - - -
142A GLY 2.9 22.7 + - - -
207A VAL* 4.8 5.2 - - - -
284B GLU 4.6 2.0 + - - -
285B ASP 2.7 40.1 + - - -
286B ALA 3.5 8.9 + - - -
287B GLN* 2.7 34.8 + - - +
288B PRO* 3.8 18.8 - - - +
35G T 3.0 37.0 + - - +
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Residues in contact with GLY 139 (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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135A GLU 3.0 13.8 + - - -
136A GLN* 3.2 4.2 + - - -
137A LEU 3.2 0.2 - - - -
138A ARG* 1.3 74.5 - - - +
140A ILE* 1.3 64.6 + - - +
142A GLY* 3.0 12.4 + - - -
143A SER* 3.0 15.4 + - - -
146A ARG* 4.3 5.3 + - - -
35G T 5.3 0.4 - - - -
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Residues in contact with ILE 140 (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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124A PHE* 4.3 16.8 - - + -
129A PRO* 4.7 11.0 - - + -
132A ARG* 3.7 39.0 - - - +
136A GLN* 2.9 22.7 + - + +
137A LEU* 3.3 11.6 + - + +
139A GLY* 1.3 72.9 - - - +
141A GLU* 1.3 59.0 + - - +
143A SER* 3.1 12.4 - - - -
144A ARG* 3.0 23.9 + - + +
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Residues in contact with GLU 141 (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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120A PHE* 3.7 14.6 - - + -
123A ARG* 2.9 38.5 + - - -
124A PHE* 3.5 26.5 - - + -
137A LEU 3.0 15.4 + - - +
138A ARG 4.1 2.2 - - - +
140A ILE* 1.3 75.5 - - - +
142A GLY* 1.3 67.2 + - - +
144A ARG* 3.3 19.4 + - - -
145A VAL* 2.8 36.8 + - + +
221A ASP* 4.9 3.8 - - - +
225A PHE* 5.5 0.5 - - - -
35G T 3.8 21.3 - - - -
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Residues in contact with GLY 142 (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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138A ARG 2.9 12.1 + - - -
139A GLY* 3.0 4.7 + - - -
141A GLU* 1.3 75.1 - - - +
143A SER* 1.3 63.4 + - - +
145A VAL* 3.2 5.6 + - - +
146A ARG* 3.0 42.7 + - - +
35G T 3.2 27.1 + - - -
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Residues in contact with SER 143 (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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139A GLY 3.0 11.6 + - - -
140A ILE* 3.1 14.4 - - - -
142A GLY* 1.3 75.0 - - - +
144A ARG* 1.3 63.8 + - - +
146A ARG* 3.2 20.9 + - - +
147A ALA* 2.9 23.2 + - - +
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Residues in contact with ARG 144 (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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123A ARG* 3.1 44.6 + - - +
124A PHE* 4.3 16.2 - - + +
140A ILE* 3.0 14.6 + - + +
141A GLU* 3.1 27.8 + - - +
143A SER* 1.3 75.4 - - - +
145A VAL* 1.3 57.0 + - - +
147A ALA* 3.3 9.0 + - + +
148A THR* 2.8 44.1 + - - +
221A ASP 4.7 2.4 + - - -
222A ILE 5.3 5.7 + - - -
225A PHE* 3.7 38.1 - - - +
226A ASP* 5.6 2.2 + - - -
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Residues in contact with VAL 145 (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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141A GLU* 2.8 41.3 + - + +
142A GLY 3.6 4.7 - - - +
144A ARG* 1.3 76.2 - - - +
146A ARG* 1.3 65.6 + - - +
148A THR* 3.1 8.3 + - - -
149A TYR* 2.9 47.9 + - + +
224A LYS* 6.1 1.8 - - - +
225A PHE* 3.9 25.9 - - + -
35G T 4.2 18.2 - - + +
36G T 3.9 15.3 - - - +
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Residues in contact with ARG 146 (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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139A GLY* 4.3 5.1 + - - -
142A GLY* 3.0 25.1 + - - +
143A SER* 3.6 30.1 + - - +
145A VAL* 1.3 74.6 - - - +
147A ALA* 1.3 62.5 + - - +
149A TYR* 3.3 11.5 + - + +
150A ALA* 3.0 23.2 + - - +
160A TRP* 5.2 1.2 + - - -
35G T 5.4 0.8 + - - -
36G T 4.4 10.8 + - - +
37G T 3.5 32.2 + - - +
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Residues in contact with ALA 147 (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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143A SER 2.9 13.8 + - - +
144A ARG* 3.4 13.2 - - + +
146A ARG* 1.3 76.0 - - - +
148A THR* 1.3 58.0 + - - +
150A ALA* 3.3 6.9 + - - +
151A LEU* 2.9 29.0 + - - +
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Residues in contact with THR 148 (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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144A ARG* 2.8 38.8 + - - +
145A VAL* 3.1 6.5 + - - -
147A ALA* 1.3 72.8 - - - +
149A TYR* 1.3 66.6 + - - +
151A LEU* 3.3 9.0 + - + +
152A LEU* 2.9 35.8 + - + +
225A PHE* 3.4 38.8 - - + -
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Residues in contact with TYR 149 (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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145A VAL* 2.9 32.3 + - + +
146A ARG* 3.5 10.1 - - + +
148A THR* 1.3 76.0 - - - +
150A ALA* 1.3 57.5 + - - +
152A LEU* 4.9 0.9 - - + -
153A ALA* 2.9 30.4 + - - +
160A TRP* 3.6 35.1 + + + +
163A ARG* 3.9 22.9 + - + -
180A ILE* 4.0 25.4 - - + +
184A THR* 6.0 0.5 - - - +
224A LYS* 5.0 7.6 + - - +
225A PHE* 4.0 23.0 - + - -
229A VAL* 4.5 7.5 - - + +
233A PHE* 3.8 16.0 - + - -
34G C 4.9 3.3 + - - -
36G T 3.1 39.8 + - - -
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Residues in contact with ALA 150 (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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146A ARG 3.0 14.0 + - - +
147A ALA* 3.6 10.3 - - - +
148A THR 3.2 0.2 - - - -
149A TYR* 1.3 77.9 - - - +
151A LEU* 1.3 56.9 + - - +
153A ALA* 3.2 8.5 + - - +
154A LYS* 3.0 28.4 + - - +
160A TRP* 4.4 10.7 - - + +
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Residues in contact with LEU 151 (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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147A ALA 2.9 17.8 + - - +
148A THR* 3.7 9.6 - - + +
150A ALA* 1.3 76.5 - - - +
152A LEU* 1.3 60.6 + - + +
154A LYS* 3.1 24.9 + - - +
155A GLN* 2.9 36.7 + - + +
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Residues in contact with LEU 152 (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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148A THR* 2.9 37.8 + - + +
149A TYR* 4.0 0.4 - - - +
151A LEU* 1.3 79.0 - - + +
153A ALA* 1.3 56.6 + - - +
155A GLN* 4.2 13.9 - - - +
156A TYR* 2.9 52.6 + - + +
225A PHE* 4.2 7.4 - - + +
229A VAL* 4.0 26.9 - - + -
230A PRO* 4.0 27.6 - - + -
233A PHE* 3.9 21.0 - - + -
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Residues in contact with ALA 153 (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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149A TYR 2.9 19.8 + - - +
150A ALA* 3.2 8.9 + - - +
152A LEU* 1.3 77.0 - - - +
154A LYS* 1.3 56.6 + - - +
157A GLY* 2.9 4.2 + - - -
158A VAL 2.7 34.7 + - - +
160A TRP* 3.6 30.5 - - + -
233A PHE* 3.6 16.7 - - + -
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Residues in contact with LYS 154 (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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150A ALA 3.0 15.4 + - - +
151A LEU* 3.1 23.4 + - - +
153A ALA* 1.3 75.9 - - - +
155A GLN* 1.3 69.4 + - - +
156A TYR 3.3 0.4 - - - -
157A GLY* 3.3 10.5 + - - -
237A ARG* 5.2 0.3 + - - -
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Residues in contact with GLN 155 (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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151A LEU* 2.9 25.5 + - + +
152A LEU* 3.9 15.7 - - - +
154A LYS* 1.3 83.6 - - - +
156A TYR* 1.3 88.1 + - + +
157A GLY 3.3 0.2 - - - -
237A ARG* 4.5 5.9 + - - -
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Residues in contact with TYR 156 (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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152A LEU* 2.9 26.3 + - + +
155A GLN* 1.3 103.6 + - + +
157A GLY* 1.3 58.4 + - - +
158A VAL* 3.6 6.6 - - + +
230A PRO* 3.6 35.3 + - + +
233A PHE* 3.9 27.4 - - + +
234A GLU* 3.5 42.6 + - + -
237A ARG* 2.4 43.0 + - + +
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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