Contacts of the helix formed by residues 143 - 159 (chain Q) in PDB entry 5GJQ
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 143 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138Q PHE* 4.2 28.0 - + - +
141Q LYS* 3.2 25.8 - - + +
142Q ARG* 1.3 72.4 - - - +
144Q GLN* 1.3 67.5 + - - +
145Q GLU 2.8 6.2 + - - -
146Q ALA* 3.0 16.6 + - - +
147Q LEU* 3.3 8.8 + - - +
176Q THR* 4.0 18.0 + - - +
179Q ALA* 4.1 28.8 - - + +
180Q LEU* 4.2 29.6 - - + -
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Residues in contact with GLN 144 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Q TYR* 1.3 77.4 - - + +
145Q GLU* 1.3 63.6 + - - +
147Q LEU* 3.1 48.0 - - - +
148Q HIS* 3.4 8.5 + - - +
180Q LEU* 4.2 24.6 - - + +
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Residues in contact with GLU 145 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q TYR* 2.7 60.1 + - + -
142Q ARG* 3.8 29.1 - - + +
143Q TYR 2.8 0.8 + - - +
144Q GLN* 1.3 82.1 - - - +
146Q ALA* 1.3 64.3 + - - +
148Q HIS* 3.2 5.0 + - - +
149Q LEU* 3.1 19.2 + - - +
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Residues in contact with ALA 146 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Q VAL* 3.9 29.6 - - + +
137Q TYR* 4.3 15.3 - - + +
138Q PHE* 5.0 2.2 - - + +
142Q ARG 5.2 0.2 - - - +
143Q TYR 3.0 11.6 + - - +
145Q GLU* 1.3 72.0 - - - +
147Q LEU* 1.3 70.7 + - - +
149Q LEU* 2.7 21.7 + - - -
150Q GLY* 2.8 14.4 + - - -
173Q GLU* 4.4 4.3 - - - +
176Q THR* 4.2 17.0 - - - +
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Residues in contact with LEU 147 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143Q TYR 3.3 5.8 + - - +
144Q GLN* 3.1 47.3 - - - +
146Q ALA* 1.3 77.9 - - - +
148Q HIS* 1.3 60.4 + - + +
150Q GLY* 4.3 0.2 - - - -
151Q SER* 3.0 39.3 + - - +
173Q GLU* 4.0 13.8 + - - +
176Q THR* 4.7 2.1 + - - +
177Q TYR* 2.8 48.7 - - + +
180Q LEU* 5.8 4.0 - - + -
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Residues in contact with HIS 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Q GLN 3.4 6.5 + - - +
145Q GLU* 3.2 8.3 + - - +
146Q ALA 2.9 1.4 + - - -
147Q LEU* 1.3 80.7 - - + +
149Q LEU* 1.3 65.0 + - - +
151Q SER* 3.8 5.0 - - - -
152Q GLN* 2.6 60.6 + - + +
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Residues in contact with LEU 149 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q GLU* 2.9 22.9 - - + +
133Q LEU* 3.3 35.4 - - + -
134Q VAL* 2.9 35.9 - - + +
137Q TYR* 3.9 10.8 - - + -
145Q GLU 3.1 12.7 + - - +
146Q ALA* 2.7 13.9 + - - +
148Q HIS* 1.3 72.0 - - - +
150Q GLY* 1.3 55.9 + - - +
152Q GLN* 3.3 17.2 + - + +
153Q LEU* 2.9 27.9 + - + +
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Residues in contact with GLY 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Q VAL* 4.4 8.3 - - - +
146Q ALA 2.8 15.9 + - - -
147Q LEU 4.3 0.2 - - - -
149Q LEU* 1.3 69.5 - - - +
151Q SER* 1.3 53.9 + - - +
152Q GLN 3.0 4.5 - - - -
153Q LEU* 2.7 28.1 + - - -
154Q LEU* 2.8 20.3 + - - +
169Q VAL* 4.4 14.8 - - - +
173Q GLU* 4.4 12.8 - - - -
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Residues in contact with SER 151 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Q LEU* 3.0 30.0 + - - +
148Q HIS* 3.8 7.6 - - - -
150Q GLY* 1.3 75.1 - - - +
152Q GLN* 1.3 56.5 + - - +
154Q LEU* 4.2 12.8 + - - +
155Q ARG* 3.6 21.5 + - - -
173Q GLU* 5.3 3.4 - - - +
177Q TYR* 5.4 2.4 + - - -
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Residues in contact with GLN 152 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148Q HIS* 2.6 56.4 + - + +
149Q LEU* 3.4 15.9 - - + +
150Q GLY 3.0 0.6 - - - -
151Q SER* 1.3 75.0 - - - +
153Q LEU* 1.3 60.0 + - - +
154Q LEU 3.3 1.3 + - - -
155Q ARG* 4.2 19.6 + - - +
156Q GLU* 2.9 27.6 - - - +
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Residues in contact with LEU 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q GLN* 4.8 7.0 - - + +
130Q GLU* 3.9 41.5 - - + +
131Q ALA* 4.6 1.3 - - - +
134Q VAL* 4.0 17.7 - - + -
149Q LEU* 2.9 14.8 + - + +
150Q GLY* 2.7 15.4 + - - +
152Q GLN* 1.3 71.6 - - - +
154Q LEU* 1.3 64.1 + - - +
155Q ARG 3.3 1.6 - - - -
156Q GLU* 3.3 33.5 + - + +
157Q LEU* 3.7 20.4 + - + +
166Q LEU* 5.3 0.3 - - - +
169Q VAL* 3.3 34.2 - - + +
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Residues in contact with LEU 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Q GLY 2.8 14.5 + - - +
151Q SER* 4.3 13.7 - - - +
152Q GLN 3.3 1.4 - - - -
153Q LEU* 1.3 80.4 - - - +
155Q ARG* 1.3 60.2 + - - +
157Q LEU 3.9 0.2 + - - -
158Q LYS* 2.1 53.5 + - - +
166Q LEU* 4.0 11.2 - - + +
169Q VAL* 4.1 18.8 - - + -
170Q GLN* 4.7 26.9 - - + +
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Residues in contact with ARG 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151Q SER 3.6 25.0 + - - -
152Q GLN* 4.2 17.5 + - - +
154Q LEU* 1.3 77.2 - - - +
156Q GLU* 1.3 70.9 + - - +
157Q LEU 3.3 2.2 - - - -
158Q LYS* 2.9 25.1 - - + +
159Q LYS* 2.8 35.5 - - - +
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Residues in contact with GLU 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q ARG* 5.3 14.6 + - - +
127Q GLN* 2.2 44.5 + - + +
152Q GLN* 2.9 29.8 - - - +
153Q LEU* 3.3 29.1 + - + -
155Q ARG* 1.3 89.6 + - - +
157Q LEU* 1.3 57.8 + - - +
159Q LYS* 3.6 22.1 + - - +
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Residues in contact with LEU 157 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q GLN* 4.6 9.6 - - + +
153Q LEU* 3.7 27.4 + - + +
156Q GLU* 1.3 82.3 - - - +
158Q LYS* 1.3 58.6 + - - +
159Q LYS 3.3 1.3 - - - -
160Q MET* 3.3 5.8 + - - +
161Q ASP 2.9 7.4 + - - -
162Q ASP* 2.8 36.3 + - + +
165Q LEU* 3.8 34.3 - - + +
166Q LEU* 2.8 24.0 - - + +
169Q VAL* 5.3 1.6 - - + -
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Residues in contact with LYS 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q LEU* 2.1 58.4 + - - +
155Q ARG* 2.9 35.0 - - + +
157Q LEU* 1.3 72.9 - - - +
159Q LYS* 1.3 61.0 + - - +
160Q MET 3.0 2.2 - - - -
161Q ASP* 2.7 37.1 + - - +
166Q LEU* 3.1 27.8 - - + +
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Residues in contact with LYS 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q GLN* 4.2 4.9 - - - +
155Q ARG* 2.8 26.9 - - + +
156Q GLU* 3.6 30.3 + - - +
158Q LYS* 1.3 83.8 - - + +
160Q MET* 1.3 76.2 + - + +
161Q ASP* 4.5 0.3 - - - +
175i LYS* 3.1 24.6 - - - +
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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