Contacts of the helix formed by residues 174 - 182 (chain B) in PDB entry 3PU3
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 LEU 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B VAL* 4.5 8.1 - - + -
150B GLU* 3.5 29.8 - - + +
153B VAL* 3.9 21.3 - - + -
154B GLY 3.6 21.3 - - - +
155B PRO 3.7 1.0 + - - +
157B ARG* 2.9 18.3 + - + +
159B VAL* 3.8 27.6 - - + -
172B MET 3.4 0.8 + - - -
173B LYS* 1.3 72.0 - - - +
175B LYS* 1.3 58.1 + - - +
177B PHE* 3.0 17.6 + - + +
178B VAL* 2.8 38.8 + - + +
192B VAL* 5.3 3.1 - - + -
195B LEU* 4.7 10.1 - - + -
239B ILE* 5.6 3.4 - - + -
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Residues in contact with LYS 175 (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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309A GLN 5.8 2.2 + - - -
150B GLU* 3.3 25.8 - - - +
155B PRO* 3.1 24.6 + - + +
156B GLU* 3.1 32.7 + - - +
173B LYS* 3.1 14.8 - - + +
174B LEU* 1.3 77.0 - - - +
176B GLU* 1.3 62.3 + - + +
178B VAL* 3.4 2.8 + - - +
179B ASP* 2.9 27.9 + - - +
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Residues in contact with GLU 176 (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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131A LYS* 5.1 15.4 + - + +
172B MET* 3.8 28.5 - - - +
173B LYS* 3.1 17.9 + - + +
175B LYS* 1.3 81.7 - - + +
177B PHE* 1.3 65.5 + - - +
179B ASP* 3.5 8.1 + - + +
180B TYR* 3.1 20.6 + - - +
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Residues in contact with PHE 177 (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 VAL* 5.6 2.2 - - + -
159B VAL* 4.8 1.1 - - + -
161B VAL* 4.0 19.5 - - + -
172B MET* 3.7 18.9 - - + -
173B LYS 3.3 4.8 + - - +
174B LEU* 3.0 21.5 + - + +
176B GLU* 1.3 77.0 - - - +
178B VAL* 1.3 59.2 + - + +
180B TYR* 3.1 25.9 + + - +
181B TYR* 2.7 42.4 + + + +
190B LEU* 3.6 33.2 - - + -
191B ASN 4.3 1.1 - - - -
192B VAL* 3.6 27.8 - - + -
239B ILE* 3.9 37.2 - - + -
241B VAL* 5.2 0.7 - - + -
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Residues in contact with VAL 178 (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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107A ARG* 4.0 15.9 - - - +
146B VAL* 4.3 15.7 - - + +
147B SER* 4.9 1.3 - - - -
149B VAL* 6.5 0.2 - - + -
150B GLU* 3.7 39.5 - - + +
174B LEU* 2.8 27.4 + - + +
175B LYS 3.6 7.2 - - - +
177B PHE* 1.3 78.0 - - + +
179B ASP* 1.3 63.1 + - - +
181B TYR* 3.0 7.0 + - - +
182B TYR* 2.9 49.8 + - + -
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Residues in contact with ASP 179 (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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107A ARG* 5.3 0.6 + - - +
130A PRO* 3.4 16.8 - - - +
131A LYS* 3.5 37.1 + - + +
7B EDO 2.6 65.2 + - - -
175B LYS 2.9 14.2 + - - +
176B GLU* 3.6 12.8 - - + +
177B PHE 3.3 0.2 - - - -
178B VAL* 1.3 76.7 - - - +
180B TYR* 1.3 62.1 + - - +
183B SER* 3.2 8.7 + - - -
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Residues in contact with TYR 180 (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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172B MET* 5.9 0.9 - - - -
176B GLU 3.1 14.1 + - - +
177B PHE* 3.3 26.0 - + - +
179B ASP* 1.3 76.3 - - - +
181B TYR* 1.3 70.2 + - - +
183B SER* 2.9 24.2 + - - -
186B ARG* 3.7 28.0 - - + +
187B LYS 4.9 0.9 - - - -
188B ARG* 2.5 36.1 + - + -
189B VAL* 3.4 1.6 - - - -
190B LEU* 2.8 51.1 + - + -
241B VAL* 3.7 28.5 - - + +
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Residues in contact with TYR 181 (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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21B EDO 3.2 28.4 + - - -
146B VAL* 3.9 22.5 - - + +
177B PHE* 2.7 23.9 + + + +
178B VAL* 3.0 11.6 + - - +
180B TYR* 1.3 81.8 - - + +
182B TYR* 1.3 76.7 + + - +
183B SER 3.2 2.9 + - - +
186B ARG* 2.9 52.5 + - - +
239B ILE* 3.9 24.7 - - + -
240B CYS 4.9 2.0 - - - -
241B VAL* 3.9 14.6 - - + -
328B ASP* 3.4 29.8 + - + +
329B CYS 5.0 2.3 + - - -
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Residues in contact with TYR 182 (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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18A EDO 5.2 1.1 - - - -
102A GLU* 2.5 43.2 + - - -
107A ARG* 3.6 40.5 - - + +
7B EDO 3.5 16.8 - - - +
21B EDO 3.2 20.9 + - - -
146B VAL* 4.2 1.3 - - + -
147B SER* 3.1 23.8 + - - -
178B VAL* 2.9 38.1 + - + +
181B TYR* 1.3 95.0 - + - +
183B SER* 1.3 65.1 + - - +
184B THR* 3.9 2.6 + - - -
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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