Contacts of the helix formed by residues 147 - 162 (chain B) in PDB entry 5GPY
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 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.5 6.5 - - - +
146B ARG* 1.3 101.4 - - + +
148B LYS* 1.3 65.2 + - - +
149B LYS* 3.4 20.4 + - - +
150B ALA* 2.8 34.2 + - - +
151B LEU* 3.0 18.7 + - - +
175B LEU* 3.7 12.3 - - - +
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Residues in contact with LYS 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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147B ASP* 1.3 75.9 - - - +
149B LYS* 1.3 63.1 + - - +
151B LEU* 3.0 7.8 + - - +
152B LEU* 3.0 25.5 + - - +
181B ALA* 3.9 24.6 - - + +
184B ALA* 3.7 30.3 + - + +
185B LEU* 3.6 30.1 - - + +
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Residues in contact with LYS 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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147B ASP* 3.3 18.1 + - - +
148B LYS* 1.3 84.8 - - - +
150B ALA* 1.3 56.7 + - - +
152B LEU* 3.2 9.9 + - + +
153B ARG* 2.9 29.6 + - + +
185B LEU* 5.9 0.2 - - - -
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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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144B ASN 4.9 3.7 - - - +
145B VAL* 4.0 8.2 - - + +
146B ARG* 3.7 23.6 - - + +
147B ASP* 2.8 26.2 + - - +
149B LYS* 1.3 70.3 - - - +
151B LEU* 1.3 65.5 + - - +
153B ARG* 4.1 6.0 - - - +
154B LEU* 3.0 24.9 + - - +
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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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145B VAL* 3.6 12.7 - - + +
147B ASP 3.0 12.1 + - - +
148B LYS* 3.0 12.2 + - - +
150B ALA* 1.3 76.8 - - - +
152B LEU* 1.3 63.9 + - - +
154B LEU* 3.4 5.5 + - + +
155B LEU* 3.1 37.5 + - + +
171B ILE* 4.0 38.4 - - + -
175B LEU* 4.5 8.7 - - + -
181B ALA* 4.7 1.3 - - + -
182B VAL* 3.8 31.4 - - + +
185B LEU* 3.8 20.9 - - + -
189B ILE* 4.4 5.2 - - + -
201B LEU* 4.9 2.7 - - + -
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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 LYS 3.0 11.8 + - - +
149B LYS* 3.2 10.7 + - + +
151B LEU* 1.3 78.3 - - - +
153B ARG* 1.3 60.3 + - - +
155B LEU* 3.2 7.0 + - + +
156B ASP* 2.9 31.9 + - + +
185B LEU* 4.1 22.4 - - + +
188B GLN* 3.8 39.3 - - + +
189B ILE* 5.7 0.2 - - + -
203B PHE* 3.9 28.0 - - + -
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Residues in contact with ARG 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 LYS* 2.9 18.7 + - + +
150B ALA* 4.1 6.3 - - - +
152B LEU* 1.3 77.3 - - - +
154B LEU* 1.3 58.9 + - - +
156B ASP* 3.3 11.0 + - + +
157B GLN* 2.8 56.2 + - + +
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Residues in contact with LEU 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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143B TYR* 3.8 27.6 - - + -
144B ASN 5.5 1.3 - - - +
145B VAL* 3.7 26.5 - - + -
150B ALA 3.0 18.6 + - - +
151B LEU* 3.6 5.8 - - + +
152B LEU 3.3 0.2 - - - -
153B ARG* 1.3 77.8 - - - +
155B LEU* 1.3 60.1 + - + +
157B GLN* 3.4 5.4 + - + +
158B HIS* 3.1 45.4 + - + +
166B ILE* 3.8 17.9 - - + -
171B ILE* 4.3 7.2 - - + -
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Residues in contact with LEU 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* 3.1 35.9 + - + +
152B LEU* 3.7 10.8 - - + +
154B LEU* 1.3 74.8 - - - +
156B ASP* 1.3 64.1 + - - +
158B HIS* 3.3 7.1 + - + +
159B ASP 3.1 17.8 + - - -
166B ILE* 4.0 19.3 - - + -
185B LEU* 5.2 0.2 - - + -
188B GLN 5.3 0.7 - - - +
189B ILE* 3.6 40.4 - - + -
201B LEU* 3.9 35.4 - - + +
202B PHE 4.8 2.0 - - - +
203B PHE* 3.3 29.6 + - + +
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Residues in contact with ASP 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* 2.9 19.6 + - + +
153B ARG* 3.5 12.9 + - + +
155B LEU* 1.3 77.4 - - - +
157B GLN* 1.3 58.0 + - + +
159B ASP* 3.2 4.2 + - - +
160B GLN* 2.8 57.9 + - - +
203B PHE* 3.9 35.2 - - + -
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Residues in contact with GLN 157 (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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153B ARG* 2.8 54.7 + - + +
154B LEU* 3.8 7.2 - - + +
156B ASP* 1.3 74.8 - - + +
158B HIS* 1.3 60.4 - - + +
160B GLN* 3.7 23.5 + - - +
161B ARG* 2.8 72.4 + - - +
163B LEU* 5.2 1.1 - - + -
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Residues in contact with HIS 158 (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 TYR* 4.3 15.0 - + - -
154B LEU* 3.1 38.1 + - + +
155B LEU* 3.5 12.1 - - + +
157B GLN* 1.3 79.1 - - + +
159B ASP* 1.3 56.6 + - - +
162B GLY* 2.9 10.4 + - - -
163B LEU* 2.8 64.5 + - + +
164B GLY 3.0 28.5 + - - +
165B GLY 4.7 1.8 - - - -
166B ILE* 3.5 28.8 - - + +
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Residues in contact with ASP 159 (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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35A ASP* 5.4 3.6 - - - +
39A ARG* 4.1 9.9 + - - -
155B LEU 3.1 12.6 + - - +
156B ASP* 3.4 8.4 - - - +
158B HIS* 1.3 77.1 - - - +
160B GLN* 1.3 69.8 + - - +
161B ARG 3.3 0.5 + - - -
162B GLY* 3.5 6.9 + - - -
203B PHE* 3.8 39.4 - - + +
205B ASP* 4.5 14.0 - - - +
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Residues in contact with GLN 160 (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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39A ARG* 3.3 15.2 + - - -
156B ASP* 2.8 46.7 + - - +
157B GLN* 3.7 24.2 + - - +
159B ASP* 1.3 81.3 - - - +
161B ARG* 1.3 63.7 + - + +
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Residues in contact with ARG 161 (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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39A ARG* 3.7 12.1 + - - +
157B GLN* 2.8 50.0 + - - +
160B GLN* 1.3 78.7 - - + +
162B GLY* 1.3 64.2 + - - +
163B LEU* 3.3 41.5 + - + +
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Residues in contact with GLY 162 (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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39A ARG* 3.6 26.6 - - - -
51A LEU* 3.3 23.0 - - - +
158B HIS 2.9 6.5 + - - -
159B ASP 3.5 4.9 + - - -
160B GLN 3.4 3.4 + - - -
161B ARG* 1.3 79.3 - - - +
163B LEU* 1.3 60.9 + - - +
164B GLY 3.4 2.7 - - - -
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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