Contacts of the helix formed by residues 152 - 169 (chain A) in PDB entry 2GAU
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 HIS 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLN 4.6 9.7 + - - -
151A LYS* 1.3 77.3 + - - +
153A VAL* 1.3 68.8 + - - +
154A ARG* 3.3 4.5 - - + +
155A GLY* 3.0 6.1 + - - +
156A ARG* 2.9 22.7 + - - +
232A GLY* 6.0 6.7 - - - -
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Residues in contact with VAL 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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152A HIS* 1.3 74.2 - - - +
154A ARG* 1.3 63.7 + - + +
156A ARG* 3.6 23.9 - - - +
157A LEU* 3.1 21.8 + - - +
192A MET* 3.3 23.7 - - + +
196A ASN* 4.2 25.1 - - + +
200A THR* 2.8 30.7 - - + +
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Residues in contact with ARG 154 (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 HIS* 3.3 3.4 - - + +
153A VAL* 1.3 78.4 - - + +
155A GLY* 1.3 63.7 + - - +
158A ALA* 3.1 26.2 + - - +
200A THR* 4.1 9.6 - - + +
203A THR* 3.5 16.7 - - + +
204A PHE* 3.4 25.6 - - + -
207A GLU* 2.8 42.7 + - - -
209A MET* 5.0 0.2 - - - -
228A THR* 3.9 23.1 + - + +
232A GLY 3.7 26.2 + - - -
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Residues in contact with GLY 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 LYS* 4.0 13.0 - - - -
152A HIS* 3.0 8.3 + - - +
154A ARG* 1.3 76.4 - - - +
156A ARG* 1.3 59.4 + - - +
158A ALA* 3.5 1.7 + - - +
159A GLU* 2.8 32.2 + - - +
228A THR 3.6 20.1 + - - -
229A ALA* 3.8 9.7 - - - +
232A GLY* 4.4 6.8 - - - -
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Residues in contact with ARG 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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147A THR* 3.7 26.8 - - + +
148A LEU* 3.3 23.2 + - + +
151A LYS* 3.5 19.7 + - + +
152A HIS 2.9 17.4 + - - +
153A VAL* 3.6 28.5 - - - +
155A GLY* 1.3 76.6 - - - +
157A LEU* 1.3 58.4 + - - +
159A GLU* 3.4 2.6 + - - +
160A THR* 3.0 32.1 + - - -
190A SER* 3.2 20.6 + - - +
191A ASN* 2.7 52.9 + - - +
192A MET* 3.7 12.4 - - + +
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Residues in contact with LEU 157 (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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153A VAL 3.1 15.2 + - - +
154A ARG 4.3 1.6 - - - +
156A ARG* 1.3 75.7 - - - +
158A ALA* 1.3 66.3 + - - +
160A THR* 3.3 7.5 + - + -
161A LEU* 2.9 39.5 + - + +
186A LEU* 4.7 14.8 - - + +
190A SER* 4.3 17.9 - - - +
192A MET* 3.9 11.8 - - + +
197A ALA* 4.0 9.6 - - + +
200A THR* 3.7 29.8 - - + -
201A LEU* 3.9 29.8 - - + +
204A PHE* 3.9 12.8 - - + -
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Residues in contact with ALA 158 (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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154A ARG 3.1 19.2 + - - +
157A LEU* 1.3 75.3 - - - +
159A GLU* 1.3 63.4 + - - +
161A LEU* 3.3 3.3 + - - +
162A LEU* 3.0 28.1 + - - +
204A PHE* 4.0 3.7 - - + -
225A LEU* 3.7 31.4 - - + +
228A THR* 4.1 5.6 - - + -
229A ALA* 3.6 28.0 - - - +
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Residues in contact with GLU 159 (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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143A ARG* 5.0 10.9 - - - +
144A ARG* 5.6 2.1 - - - -
147A THR* 3.1 34.3 + - + -
151A LYS* 2.6 35.0 + - - +
155A GLY 2.8 19.1 + - - +
156A ARG 3.6 4.5 - - - +
158A ALA* 1.3 76.3 - - - +
160A THR* 1.3 63.8 + - - +
162A LEU* 3.1 5.9 + - - +
163A ILE* 2.9 45.0 + - + +
229A ALA* 3.8 9.4 - - + +
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Residues in contact with THR 160 (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 LEU* 5.5 1.4 - - - +
156A ARG 3.0 10.5 + - - -
157A LEU* 3.3 11.9 + - + +
159A GLU* 1.3 76.4 - - - +
161A LEU* 1.3 63.1 + - - +
163A ILE* 3.2 11.6 + - - +
164A LEU* 3.0 31.0 + - + +
186A LEU* 4.4 12.1 - - + +
189A LEU* 4.0 36.3 + - + +
190A SER* 3.2 31.3 + - - -
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Residues in contact with LEU 161 (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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157A LEU* 2.9 39.4 + - + +
158A ALA 3.8 4.0 - - - +
160A THR* 1.3 75.0 - - - +
162A LEU* 1.3 58.6 + - - +
164A LEU* 3.3 7.2 + - + +
165A LYS* 2.9 27.4 + - - +
177A LEU* 4.1 19.9 - - + +
186A LEU* 4.1 17.7 - - + -
201A LEU* 4.4 2.7 - - + -
204A PHE* 4.5 7.9 - - + -
210A LEU* 3.7 35.9 - - + -
217A ILE* 3.8 27.6 - - + -
219A ILE* 4.5 3.5 - - + +
225A LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 162 (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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158A ALA 3.0 14.9 + - - +
159A GLU* 3.7 3.8 - - - +
161A LEU* 1.3 75.7 - - - +
163A ILE* 1.3 58.6 + - + +
165A LYS* 3.4 20.5 + - + +
166A GLU* 2.9 28.2 + - - +
219A ILE* 4.8 0.4 - - + -
222A CYS* 4.0 16.2 - - - -
225A LEU* 3.8 24.0 - - + +
226A GLN* 3.5 50.0 - - + +
229A ALA* 3.6 21.5 - - + -
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Residues in contact with ILE 163 (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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144A ARG* 5.6 11.4 - - + +
159A GLU* 2.9 45.0 + - + +
160A THR* 3.5 10.8 - - - +
162A LEU* 1.3 75.6 - - + +
164A LEU* 1.3 64.4 + - + +
166A GLU* 3.3 5.7 + - + +
167A ASN* 2.9 48.6 + - - +
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Residues in contact with LEU 164 (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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78A ILE* 4.2 20.0 - - + -
160A THR* 3.0 24.2 + - + +
161A LEU* 3.6 14.8 - - + +
163A ILE* 1.3 76.7 - - + +
165A LYS* 1.3 59.5 + - - +
168A PHE* 2.8 61.9 + - + +
169A GLY 3.6 0.9 + - - +
177A LEU* 4.3 9.6 - - + -
179A ILE* 4.0 22.9 - - + -
181A LEU* 4.1 8.1 - - + -
186A LEU* 3.8 29.4 - - + -
189A LEU* 4.3 6.3 - - + -
217A ILE* 6.2 0.2 - - + -
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Residues in contact with LYS 165 (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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161A LEU 2.9 14.5 + - - +
162A LEU* 3.4 24.0 - - + +
164A LEU* 1.3 75.8 - - - +
166A GLU* 1.3 67.1 + - - +
169A GLY* 2.8 30.7 + - - +
170A PHE* 3.6 41.3 - - + -
177A LEU* 3.6 17.6 - - + +
219A ILE* 4.1 7.2 - - + -
222A CYS* 3.8 30.1 - - - -
226A GLN* 5.1 3.9 - - - +
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Residues in contact with GLU 166 (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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80A LYS* 5.0 6.0 + - - +
162A LEU 2.9 17.6 + - - +
163A ILE* 3.7 7.9 - - + +
164A LEU 3.3 0.2 - - - -
165A LYS* 1.3 88.8 + - - +
167A ASN* 1.3 68.7 + - - +
169A GLY* 4.6 1.2 + - - -
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Residues in contact with ASN 167 (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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78A ILE 4.8 7.5 + - - -
80A LYS* 3.6 44.5 + - + +
81A PRO* 5.5 0.9 - - - +
163A ILE* 2.9 38.7 + - - +
164A LEU* 5.9 0.6 - - - +
166A GLU* 1.3 87.0 - - - +
168A PHE* 1.3 87.2 + - + +
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Residues in contact with PHE 168 (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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61A LYS* 3.9 31.4 - - + +
78A ILE* 3.5 39.3 - - + -
79A VAL 3.9 4.0 - - - -
80A LYS* 3.7 26.7 - - + -
81A PRO* 4.7 4.9 - - + -
164A LEU* 2.8 38.0 + - + +
167A ASN* 1.3 91.4 - - + +
169A GLY* 1.3 63.6 + - - +
170A PHE 5.1 0.2 - - - +
178A SER* 3.5 19.3 + - - +
179A ILE* 3.7 34.5 - - + -
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Residues in contact with GLY 169 (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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164A LEU 3.6 1.4 + - - +
165A LYS* 2.8 22.1 + - - -
166A GLU 4.6 0.8 + - - -
167A ASN 3.9 0.2 - - - -
168A PHE* 1.3 80.2 - - - +
170A PHE* 1.3 67.4 + - - -
177A LEU* 3.6 11.1 - - - +
178A SER* 3.1 20.1 + - - -
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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