Contacts of the helix formed by residues 162 - 168 (chain D) in PDB entry 1PQ3
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 GLN 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ILE* 4.4 3.2 - - - +
147D ASP 3.4 5.2 - - - -
149D ASN* 3.0 25.8 - - + +
150D THR 3.9 6.5 - - - -
151D PRO* 3.0 38.1 - - - +
154D THR* 3.9 15.6 - - - +
157D GLY 3.9 6.9 + - - -
158D ASN 2.9 28.3 + - - +
159D LEU* 2.9 21.3 + - - +
161D GLY* 1.3 81.9 - - - +
163D PRO* 1.4 69.8 - - - +
165D SER* 3.0 19.6 + - - -
166D PHE* 3.1 16.8 - - + -
554D S2C 5.7 0.4 - - - +
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Residues in contact with PRO 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D HIS 3.3 25.4 - - - +
121D SER* 3.9 9.2 - - - -
123D ALA* 4.3 6.5 - - + -
124D ILE* 4.0 17.7 - - + +
141D TRP* 3.8 20.6 - - + -
147D ASP* 3.3 15.7 - - + +
159D LEU 3.4 5.2 - - - +
160D HIS 3.5 13.5 - - - +
161D GLY 3.3 2.9 - - - -
162D GLN 1.4 89.0 - - - +
164D VAL* 1.3 63.3 + - - +
165D SER 2.9 1.7 + - - -
166D PHE* 3.1 15.6 + - + +
167D LEU* 3.6 16.1 + - + +
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TRP* 3.8 34.3 - - + -
146D ALA 3.6 9.4 - - - +
147D ASP 3.3 9.0 + - - +
148D ILE* 3.7 19.1 - - + -
163D PRO* 1.3 74.5 - - - +
165D SER* 1.3 62.0 + - - +
166D PHE 3.4 0.2 - - - -
167D LEU* 3.8 9.4 - - + -
168D LEU* 3.1 39.5 + - + +
193D ILE* 4.1 11.9 - - + -
195D TYR* 3.2 29.4 - - + +
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Residues in contact with SER 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ASP 4.3 0.8 + - - -
148D ILE* 3.2 9.4 + - - +
149D ASN 2.7 30.0 + - - -
150D THR* 3.3 19.8 - - - +
162D GLN 3.0 13.9 + - - -
163D PRO 2.9 0.4 + - - -
164D VAL* 1.3 79.6 - - - +
166D PHE* 1.3 67.1 + - - +
167D LEU 3.1 1.3 + - - -
168D LEU 3.8 12.0 + - - +
171D LEU* 4.0 12.8 - - - +
172D GLN* 5.1 0.7 + - - -
175D VAL* 3.8 21.2 - - - +
186D PRO* 5.8 0.2 - - - +
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ILE* 3.7 24.2 - - + -
151D PRO* 3.8 26.2 - - + -
159D LEU* 4.0 14.4 - - + -
162D GLN* 3.1 42.0 - - + -
163D PRO 3.1 5.0 + - - +
165D SER* 1.3 75.7 - - - +
167D LEU* 1.3 62.0 + - - +
175D VAL* 3.9 24.7 - - + -
176D PRO 4.7 3.6 - - - -
178D LEU* 4.0 4.5 - - + -
181D PHE* 3.5 37.5 - + + -
184D ILE* 3.7 29.8 - - + +
186D PRO* 3.8 18.8 - - - +
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ALA* 4.2 6.7 - - + +
124D ILE* 4.0 29.2 - - + +
127D ILE* 3.5 41.3 - - + -
128D SER* 4.2 6.3 - - - +
141D TRP* 5.1 3.4 - - + -
163D PRO 3.6 19.3 - - - +
164D VAL* 3.3 10.3 + - + +
165D SER 3.1 1.0 - - - -
166D PHE* 1.3 83.0 - - - +
168D LEU* 1.3 63.6 + - + +
184D ILE* 5.1 2.9 - - + -
185D LYS 5.6 0.7 - - - +
186D PRO* 4.1 1.8 - - - -
187D CYS* 3.0 41.7 + - - +
188D ILE* 3.2 23.4 - - + +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ILE* 3.8 6.7 - - + -
164D VAL* 3.1 33.8 + - + +
165D SER 3.8 6.8 + - - +
167D LEU* 1.3 77.5 - - + +
169D ARG* 1.3 64.4 + - - +
170D GLU* 4.5 4.3 - - - +
171D LEU* 3.5 26.6 + - + -
172D GLN* 3.5 8.0 + - - -
186D PRO* 3.8 6.0 - - - +
188D ILE* 3.6 27.6 - - + -
189D SER 3.9 15.3 - - - +
190D SER* 4.1 8.7 - - - -
193D ILE* 4.2 13.2 - - + -
214D ILE* 3.6 31.0 - - + -
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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
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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