Contacts of the helix formed by residues 158 - 167 (chain F) 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 ASN 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F GLY 3.4 12.8 - - - +
37F GLN* 3.6 12.6 - - - +
38F LYS* 3.2 42.7 - - - +
87F VAL* 4.1 7.1 - - - +
154F THR* 4.5 1.2 + - - -
156F SER* 3.2 30.9 + - - +
157F GLY* 1.3 77.1 - - - +
159F LEU* 1.3 63.5 + - - +
160F HIS* 3.3 18.9 + - + -
161F GLY* 3.6 8.5 + - - -
162F GLN* 2.9 12.0 + - - +
556F S2C 4.6 3.0 + - - +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLY* 3.1 12.7 + - - +
86F ILE* 4.2 7.2 - - + -
87F VAL 3.7 20.2 + - - +
89F PRO* 4.1 10.5 - - + -
92F VAL* 3.5 40.4 - - + -
121F SER* 4.1 5.8 - - - -
124F ILE* 5.4 2.3 - - + +
157F GLY 3.4 0.6 + - - -
158F ASN* 1.3 68.2 - - - +
160F HIS* 1.3 58.4 + - - +
161F GLY 3.0 10.4 + - - -
162F GLN* 3.1 31.5 + - - +
163F PRO* 3.3 11.3 - - - +
166F PHE* 3.7 32.6 - - + -
178F LEU* 3.8 11.9 - - + -
181F PHE* 3.8 11.2 - - + -
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Residues in contact with HIS 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLY* 2.8 24.5 + - - +
37F GLN* 3.3 30.6 - - + +
119F ASP* 3.8 17.9 - - - +
120F HIS* 4.0 1.3 - - - +
121F SER 3.9 13.2 - - - +
147F ASP* 3.3 6.4 - - - +
158F ASN* 3.8 17.9 + - + +
159F LEU* 1.3 71.6 - - - +
161F GLY* 1.3 58.9 + - - +
162F GLN 3.4 1.6 - - - -
163F PRO* 3.3 11.6 - - - +
264F GLY* 6.4 0.7 - - - -
265F THR* 4.8 11.6 - - + +
296F GLU* 2.9 30.1 + - - +
556F S2C 3.1 47.5 + - + +
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Residues in contact with GLY 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ASP* 3.0 32.0 - - - -
149F ASN* 3.1 18.2 + - - +
158F ASN 3.6 3.1 + - - -
159F LEU 3.0 1.4 - - - -
160F HIS* 1.3 82.7 - - - +
162F GLN* 1.3 62.5 + - - +
163F PRO* 3.4 3.8 - - - -
205F GLU* 4.1 1.4 - - - +
556F S2C 3.7 24.7 - - - -
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Residues in contact with GLN 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ILE* 4.2 3.0 - - - +
147F ASP 3.4 2.9 - - - -
149F ASN* 2.9 30.3 - - + +
150F THR 4.2 0.2 - - - -
151F PRO* 3.3 35.4 - - - +
154F THR* 4.1 16.3 - - - +
157F GLY 3.6 11.7 + - - -
158F ASN 2.9 29.6 + - - +
159F LEU* 3.1 20.9 + - - +
161F GLY* 1.3 80.8 - - - +
163F PRO* 1.3 70.5 - - - +
164F VAL 3.3 2.0 - - - -
165F SER* 2.9 19.2 + - - -
166F PHE* 3.4 17.2 - - + -
556F S2C 5.7 0.4 - - - +
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Residues in contact with PRO 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F HIS* 3.3 27.4 - - + +
121F SER* 3.9 4.9 - - - -
123F ALA* 4.4 4.3 - - + -
124F ILE* 4.0 20.6 - - + +
141F TRP* 3.8 17.7 - - + -
147F ASP* 3.4 11.9 - - + +
159F LEU 3.3 10.2 - - - +
160F HIS 3.3 18.8 - - - +
161F GLY 3.4 2.2 - - - -
162F GLN* 1.3 91.3 - - - +
164F VAL* 1.3 62.2 + - - +
165F SER 3.1 1.2 + - - -
166F PHE* 3.3 14.1 + - + +
167F LEU* 3.5 17.6 - - + +
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Residues in contact with VAL 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F TRP* 3.8 33.7 - - + -
146F ALA 3.8 3.8 - - - +
147F ASP 3.2 15.9 + - - +
148F ILE* 3.7 8.5 - - + -
162F GLN 3.1 0.2 + - - -
163F PRO* 1.3 75.0 - - - +
165F SER* 1.3 61.6 + - - +
167F LEU* 3.2 9.3 + - + -
168F LEU* 3.1 50.9 + - + +
193F ILE* 4.1 13.5 - - + -
195F TYR* 3.4 26.2 - - - +
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Residues in contact with SER 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ASP 4.4 0.2 + - - -
148F ILE* 3.2 11.1 + - - +
149F ASN 2.9 21.3 + - - -
150F THR* 3.1 29.1 - - - +
162F GLN 2.9 14.6 + - - -
164F VAL* 1.3 80.1 - - - +
166F PHE* 1.3 63.4 + - - -
167F LEU 3.1 1.3 + - - -
168F LEU 3.9 11.4 + - - +
171F LEU* 4.0 12.3 - - - +
172F GLN* 4.8 1.0 + - - -
175F VAL* 3.6 24.7 - - - +
186F PRO* 5.8 0.3 - - - +
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Residues in contact with PHE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ILE* 3.7 22.7 - - + -
151F PRO* 3.8 30.3 - - + -
159F LEU* 3.7 20.4 - - + -
162F GLN* 3.4 32.1 - - + -
163F PRO 3.3 4.2 + - - +
165F SER* 1.3 75.7 - - - +
167F LEU* 1.3 59.1 + - - +
168F LEU 3.8 0.2 - - - -
175F VAL* 3.7 17.9 - - + -
176F PRO 4.6 2.0 - - - -
178F LEU* 3.8 9.0 - - + -
181F PHE* 3.7 33.4 - + + -
184F ILE* 3.6 34.0 - - + +
186F PRO* 3.9 17.9 - - - +
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Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F ALA 4.0 9.0 - - - +
124F ILE* 4.1 17.3 - - + +
127F ILE* 3.5 39.3 - - + -
128F SER* 3.9 21.5 - - - +
141F TRP* 5.0 4.5 - - + -
163F PRO 3.5 20.6 - - - +
164F VAL* 3.2 10.5 + - + +
165F SER 3.1 0.6 - - - -
166F PHE* 1.3 86.9 - - - +
168F LEU* 1.3 64.6 + - + +
184F ILE* 5.1 1.6 - - + -
185F LYS 6.0 0.2 - - - +
186F PRO* 4.3 1.8 - - - -
187F CYS* 3.2 32.6 + - - -
188F ILE* 3.0 28.7 - - + +
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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