Contacts of the helix formed by residues 133 - 156 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 4.2 6.3 - - - -
131B ARG 4.2 0.6 + - - -
132B ARG* 1.3 77.9 - - - +
134B VAL* 1.3 64.6 + - - +
135B GLU* 3.6 9.6 + - - +
136B GLN* 3.1 33.9 + - - +
137B LEU* 3.2 20.1 + - - +
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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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109B GLU* 5.3 3.1 - - - +
112B ARG* 3.9 41.3 - - - +
113B LEU* 3.8 25.8 - - + -
116B VAL* 4.2 23.3 - - + +
133B SER* 1.3 76.4 - - - +
135B GLU* 1.3 57.8 + - - +
137B LEU* 3.4 8.9 + - - +
138B ARG* 2.9 33.5 + - - +
206B PHE 4.1 8.5 - - - +
207B VAL* 4.6 10.1 - - + -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B SER* 3.3 7.6 + - - +
134B VAL* 1.3 76.5 - - - +
136B GLN* 1.3 65.4 + - + +
138B ARG* 3.2 30.6 + - - +
139B GLY* 3.0 22.0 + - - -
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG 4.1 2.1 - - - +
132B ARG* 3.1 37.4 - - - +
133B SER* 3.1 34.0 + - - +
134B VAL 3.3 0.4 - - - -
135B GLU* 1.3 78.1 - - + +
137B LEU* 1.3 65.2 + - - +
139B GLY* 3.1 3.5 + - - +
140B ILE* 3.0 29.1 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.1 16.8 - - + -
116B VAL* 3.8 28.9 - - + +
117B ARG* 4.3 17.5 - - + +
120B PHE* 4.5 16.4 - - + -
128B ALA* 3.6 27.1 - - + -
129B PRO 5.1 0.2 - - - +
132B ARG* 3.7 23.8 - - + +
133B SER 3.2 16.5 + - - +
134B VAL 3.5 7.0 - - - +
136B GLN* 1.3 77.7 - - - +
138B ARG* 1.3 56.6 + - - +
140B ILE* 3.3 14.6 + - + +
141B GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG* 5.0 5.3 - - - +
134B VAL* 2.9 20.6 + - - +
135B GLU* 3.3 38.1 + - - +
136B GLN 3.1 0.2 - - - -
137B LEU* 1.3 78.2 - - - +
139B GLY* 1.3 56.9 + - - +
141B GLU* 3.3 23.1 + - - +
142B GLY* 2.9 24.4 + - - -
207B VAL* 2.5 47.2 + - + +
208B HIS* 4.7 3.8 - - - +
209B THR* 5.5 1.4 + - - +
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Residues in contact with GLY 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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135B GLU 3.0 13.4 + - - -
136B GLN* 3.1 5.1 + - - -
138B ARG* 1.3 74.3 - - - +
140B ILE* 1.3 64.6 + - - +
142B GLY* 3.0 11.9 + - - -
143B SER* 3.1 15.0 + - - -
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Residues in contact with ILE 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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120B PHE* 3.8 22.0 - - + -
129B PRO* 3.6 34.1 - - + -
132B ARG* 3.9 15.9 - - - +
136B GLN 3.0 15.3 + - - +
137B LEU* 3.6 15.0 - - + +
139B GLY* 1.3 74.8 - - - +
141B GLU* 1.3 58.0 + - - +
143B SER* 3.4 6.7 + - - -
144B ARG* 3.0 54.9 + - + +
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Residues in contact with GLU 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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120B PHE* 4.9 1.5 - - + -
123B ARG* 2.6 42.2 + - - +
124B PHE* 4.1 20.6 - - + -
137B LEU 2.9 13.6 + - - +
138B ARG* 3.4 28.5 - - - +
139B GLY 3.1 0.2 - - - -
140B ILE* 1.3 74.2 - - - +
142B GLY* 1.3 59.4 + - - +
144B ARG* 3.9 0.5 - - - +
145B VAL* 2.9 39.5 + - + +
207B VAL* 4.1 10.0 - - - +
208B HIS* 4.8 5.2 + - - -
221B ASP* 3.9 10.2 - - - +
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Residues in contact with GLY 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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138B ARG 2.9 14.8 + - - -
139B GLY* 3.0 4.4 + - - -
141B GLU* 1.3 77.8 - - - +
143B SER* 1.3 62.6 + - - +
145B VAL* 3.2 6.9 + - - +
146B ARG* 3.0 34.5 + - - +
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Residues in contact with SER 143 (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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139B GLY 3.1 10.4 + - - -
140B ILE* 3.6 11.2 - - - -
142B GLY* 1.3 77.5 - - - +
144B ARG* 1.3 64.2 + - - +
146B ARG* 3.2 30.9 + - - +
147B ALA* 3.0 22.1 + - - +
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Residues in contact with ARG 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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120B PHE* 4.1 16.8 - - - -
124B PHE* 3.6 57.6 + - + +
126B GLU* 3.0 30.8 + - - +
129B PRO* 5.6 4.4 - - - +
140B ILE* 3.0 32.3 + - + +
141B GLU 4.0 0.9 - - - +
143B SER* 1.3 77.6 - - - +
145B VAL* 1.3 58.6 + - - +
147B ALA* 3.2 9.9 + - - +
148B THR* 2.9 33.0 + - - +
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Residues in contact with VAL 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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123B ARG* 3.2 31.2 - - - +
124B PHE* 5.1 3.6 - - + -
141B GLU* 2.9 32.8 + - + +
142B GLY* 3.5 7.0 - - - +
144B ARG* 1.3 74.3 - - - +
146B ARG* 1.3 69.6 + - + +
148B THR* 3.0 8.1 + - - -
149B TYR* 3.0 47.6 + - + -
225B PHE* 3.8 12.7 - - + -
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Residues in contact with ARG 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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142B GLY 3.0 15.4 + - - +
143B SER* 3.4 35.0 + - - +
145B VAL* 1.3 78.7 - - + +
147B ALA* 1.3 64.0 + - - +
149B TYR* 3.3 11.8 + - + +
150B ALA* 3.0 23.8 + - - +
160B TRP* 5.4 0.3 + - - -
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Residues in contact with ALA 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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143B SER 3.0 12.6 + - - +
144B ARG* 3.4 13.7 - - - +
145B VAL 3.2 0.2 - - - -
146B ARG* 1.3 77.3 - - - +
148B THR* 1.3 56.4 + - - +
150B ALA* 3.3 7.3 + - - +
151B LEU* 2.9 28.9 + - - +
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Residues in contact with THR 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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124B PHE* 5.6 3.3 - - - -
144B ARG* 2.9 16.0 + - - +
145B VAL* 3.0 10.3 + - - -
147B ALA* 1.3 74.1 - - - +
149B TYR* 1.3 64.8 + - - +
151B LEU* 3.2 10.6 + - + +
152B LEU* 2.9 35.1 + - + +
225B PHE* 3.7 36.9 - - + +
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Residues in contact with TYR 149 (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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145B VAL* 3.0 41.4 + - + -
146B ARG* 3.7 10.1 - - + +
148B THR* 1.3 75.6 - - - +
150B ALA* 1.3 58.1 + - - +
152B LEU* 3.5 4.3 + - + +
153B ALA* 2.9 31.3 + - - +
160B TRP* 3.5 44.4 - + + +
163B ARG* 4.2 23.0 + - + +
180B ILE* 3.9 27.8 - - + +
224B LYS* 5.0 7.1 + - - +
225B PHE* 3.7 27.0 - + - -
229B VAL* 4.1 10.4 - - + +
233B PHE* 4.1 15.9 - + - -
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Residues in contact with ALA 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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146B ARG 3.0 14.0 + - - +
147B ALA* 3.6 10.8 - - - +
148B THR 3.2 0.2 - - - -
149B TYR* 1.3 75.4 - - - +
151B LEU* 1.3 63.1 + - - +
153B ALA* 3.3 8.2 + - - +
154B LYS* 3.0 48.1 + - - +
160B TRP* 4.6 7.1 - - + -
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Residues in contact with LEU 151 (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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147B ALA 2.9 17.2 + - - +
148B THR* 3.2 11.0 + - + +
150B ALA* 1.3 76.3 - - - +
152B LEU* 1.3 59.1 + - + +
154B LYS* 3.1 10.8 + - + +
155B GLN* 2.9 59.6 + - + +
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Residues in contact with LEU 152 (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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148B THR* 2.9 34.9 + - + +
149B TYR* 4.0 4.0 - - - +
151B LEU* 1.3 78.5 - - + +
153B ALA* 1.3 63.0 + - - +
155B GLN* 4.0 13.5 - - - +
156B TYR* 3.0 53.4 + - + +
225B PHE* 4.5 4.7 - - + +
229B VAL* 3.7 29.6 - - + -
230B PRO* 4.1 25.6 - - + -
233B PHE* 3.9 18.1 - - + -
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Residues in contact with ALA 153 (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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149B TYR 2.9 19.5 + - - +
150B ALA* 3.4 8.1 - - - +
152B LEU* 1.3 77.9 - - - +
154B LYS* 1.3 60.3 + - + +
157B GLY* 3.1 6.4 + - - -
158B VAL 2.8 42.4 + - - +
160B TRP* 3.6 21.5 - - + -
233B PHE* 3.7 13.6 - - + -
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Residues in contact with LYS 154 (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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150B ALA* 3.0 37.9 + - - +
151B LEU* 3.1 9.6 + - + +
153B ALA* 1.3 79.5 - - + +
155B GLN* 1.3 64.7 + - + +
156B TYR 3.4 0.2 - - - -
157B GLY* 3.6 8.4 + - - -
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Residues in contact with GLN 155 (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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151B LEU* 2.9 49.8 + - + +
152B LEU* 3.3 21.1 + - - +
154B LYS* 1.3 79.1 - - + +
156B TYR* 1.3 69.5 + - + +
157B GLY 3.8 0.2 + - - -
237B ARG* 4.4 5.4 + - - -
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Residues in contact with TYR 156 (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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152B LEU* 3.0 42.5 + - + +
155B GLN* 1.3 89.3 - - + +
157B GLY* 1.3 63.0 + - - +
158B VAL* 4.3 3.8 - - + -
230B PRO* 3.5 25.9 + - - +
231B LYS* 6.1 0.5 - - - +
233B PHE* 3.9 23.6 - - + +
234B GLU* 3.6 39.1 + - + +
237B ARG* 3.0 49.0 - - + +
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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
------------------------------------------------------------
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