Contacts of the helix formed by residues 231 - 239 (chain A) in PDB entry 1PQA
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 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A HIS* 3.7 23.8 - - + +
98A ASN* 3.2 39.9 - - - +
100A LEU* 3.5 38.6 - - + -
177A GLN* 4.0 27.6 - - + +
226A ALA* 4.3 3.4 - - + -
227A SER 3.1 18.6 + - - +
228A VAL 3.1 4.9 + - - +
230A ALA* 1.4 76.8 - - - +
232A ARG* 1.3 62.8 - - - +
233A SER 3.2 3.1 - - - -
234A PHE* 3.2 7.9 + - + +
235A ILE* 3.2 22.2 + - + +
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Residues in contact with ARG 232 (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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120A LEU* 3.7 26.6 + - - +
121A ALA 2.9 36.7 + - - +
122A ALA* 4.1 2.4 - - - +
123A SER* 3.8 43.7 - - - +
228A VAL* 3.1 28.9 + - - +
229A GLY 4.1 2.0 + - - +
230A ALA 3.5 3.0 - - - -
231A LEU* 1.3 75.2 - - - +
233A SER* 1.4 68.7 + - - +
235A ILE* 3.7 5.2 - - - -
236A ASP* 2.8 68.9 + - - +
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Residues in contact with SER 233 (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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230A ALA 5.2 0.8 + - - -
231A LEU 3.2 1.4 - - - -
232A ARG* 1.4 82.5 - - - +
234A PHE* 1.3 58.8 + - - +
236A ASP* 4.2 4.4 - - - +
237A THR* 2.8 29.2 + - - -
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Residues in contact with PHE 234 (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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52A LEU* 5.0 0.9 - - + -
88A ARG* 3.3 34.5 - - + -
89A VAL 3.9 0.2 - - - -
90A HIS* 3.3 49.8 + + + +
91A PRO* 3.4 22.7 - - + -
100A LEU* 3.9 28.7 - - + -
101A ALA* 4.2 0.2 - - - -
102A ILE* 3.9 19.9 - - + +
231A LEU 3.2 7.2 + - - +
233A SER* 1.3 72.1 - - - +
235A ILE* 1.3 78.6 - - + +
237A THR* 4.6 2.0 - - - -
238A TYR* 3.3 48.5 + + - +
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Residues in contact with ILE 235 (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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46A LEU* 3.9 22.4 - - + -
52A LEU* 4.0 22.7 - - + -
100A LEU* 3.9 26.9 - - + -
102A ILE* 4.7 5.8 - - + +
120A LEU* 3.7 24.2 - - + -
228A VAL* 4.0 26.7 - - + +
231A LEU 3.2 21.1 + - - +
232A ARG* 3.4 6.5 + - - +
233A SER 3.3 0.2 - - - -
234A PHE* 1.3 82.1 - - + +
236A ASP* 1.3 58.3 + - - +
237A THR 3.2 0.3 + - - -
238A TYR* 3.2 0.5 + - - +
239A ALA* 2.9 34.5 + - + +
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Residues in contact with ASP 236 (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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120A LEU* 4.0 8.0 - - - +
123A SER* 5.9 0.2 - - - -
232A ARG* 2.8 64.9 + - - +
233A SER* 4.2 5.0 - - - +
235A ILE* 1.3 72.0 - - - +
237A THR* 1.3 66.5 - - - +
239A ALA* 4.2 11.9 + - - +
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Residues in contact with THR 237 (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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233A SER* 2.8 21.4 + - - -
234A PHE* 3.8 4.0 - - - -
235A ILE 3.2 0.6 - - - -
236A ASP* 1.3 84.9 - - - +
238A TYR* 1.3 96.0 - - + +
239A ALA* 4.8 1.4 - - - +
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Residues in contact with TYR 238 (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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88A ARG* 3.1 63.2 + - - +
91A PRO* 5.4 6.6 - - + +
102A ILE* 4.0 19.2 - - + +
104A LYS* 3.0 28.6 + - - -
234A PHE* 3.3 38.1 + + - +
235A ILE 3.2 2.8 + - - -
237A THR* 1.3 103.4 - - + +
239A ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 239 (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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46A LEU* 3.9 25.6 - - + -
47A ASN* 2.8 30.8 + - - +
49A ASN* 4.7 0.9 - - - +
50A THR* 3.3 18.1 + - - -
102A ILE* 4.8 1.9 - - + +
104A LYS* 3.3 7.7 + - - -
120A LEU* 6.2 1.1 - - + -
235A ILE* 2.9 20.8 + - + +
236A ASP* 4.4 10.7 - - - +
237A THR 3.6 2.2 - - - +
238A TYR* 1.3 83.0 - - - +
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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