Contacts of the helix formed by residues 379 - 389 (chain A) in PDB entry 2PU1
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 THR 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A GLU 3.6 11.4 + - - +
378A ASP* 1.3 78.7 + - - +
380A TYR* 1.3 66.0 + - - +
381A ILE* 3.2 3.4 - - - -
382A ALA* 3.0 19.6 + - - +
383A ASP* 3.8 5.5 + - - +
405A ALA* 3.4 34.3 - - + +
406A LYS* 4.3 8.1 - - - -
409A GLN* 3.9 28.4 + - + +
412A ARG* 5.4 2.9 - - - +
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Residues in contact with TYR 380 (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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114A MET* 3.5 35.2 - - + -
117A SER* 2.7 29.8 + - - -
118A LYS* 4.4 9.6 - - + -
128A LEU* 3.8 24.2 - - + -
132A LEU* 3.4 33.2 - - + +
344A ILE* 4.2 14.4 - - + -
350A ILE* 3.4 33.4 - - + +
378A ASP* 2.9 20.5 + - - +
379A THR* 1.3 75.8 + - - +
381A ILE* 1.3 60.3 + - + +
382A ALA 3.1 0.7 + - - -
383A ASP* 3.2 6.9 + - - +
384A LEU* 2.9 37.9 + - + -
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Residues in contact with ILE 381 (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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342A LEU 5.8 0.2 - - - +
344A ILE* 4.7 23.3 - - + +
369A VAL* 3.7 14.8 - - + +
370A SER* 3.8 15.0 - - - +
371A HIS* 3.5 33.2 - - + +
375A GLU* 4.8 2.9 - - - +
378A ASP* 4.7 1.1 + - - +
380A TYR* 1.3 77.6 - - + +
382A ALA* 1.3 60.2 + - - +
384A LEU* 3.7 11.2 - - + -
385A VAL* 2.9 32.7 + - - +
393A ILE* 3.9 7.6 - - + +
395A THR* 3.6 27.4 - - - +
406A LYS* 3.6 22.4 - - + -
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR 3.0 12.8 + - - +
381A ILE* 1.3 77.4 - - - +
383A ASP* 1.3 65.7 + - - +
385A VAL* 3.3 19.2 - - - +
386A VAL* 3.4 14.4 + - - +
393A ILE* 4.5 3.1 - - - -
406A LYS* 3.6 24.9 - - - +
409A GLN* 3.5 24.0 - - + -
410A LEU* 3.8 15.9 - - + -
413A ILE* 3.9 3.1 - - - -
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Residues in contact with ASP 383 (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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128A LEU* 3.3 33.3 + - + +
129A TYR* 3.1 43.9 + - - +
132A LEU* 4.6 0.7 - - - -
379A THR* 3.8 6.3 + - - +
380A TYR* 3.2 8.3 + - - +
382A ALA* 1.3 80.3 - - - +
384A LEU* 1.3 56.9 + - - +
387A ALA* 2.9 30.5 + - - +
409A GLN* 2.8 34.4 + - - +
413A ILE* 3.8 8.5 - - - -
700A EDO 4.5 1.7 + - - -
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Residues in contact with LEU 384 (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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132A LEU* 4.1 24.1 - - + +
342A LEU* 3.9 17.7 - - + -
344A ILE* 3.6 30.7 - - + -
350A ILE* 5.5 2.9 - - + -
353A ALA* 5.4 2.7 - - + -
354A ILE* 4.8 14.4 - - + -
369A VAL* 4.4 11.2 - - + -
380A TYR* 2.9 31.3 + - + +
381A ILE* 3.8 9.2 - - + +
382A ALA 3.3 0.2 - - - -
383A ASP* 1.3 76.7 - - - +
385A VAL* 1.3 57.5 + - - +
387A ALA* 3.1 2.5 + - - +
388A LEU* 2.9 57.6 + - + +
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Residues in contact with VAL 385 (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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142A ARG 4.3 2.2 - - - +
144A PRO* 3.6 29.8 - - + -
369A VAL* 3.7 22.4 - - + +
381A ILE 2.9 17.1 + - - +
382A ALA 3.3 13.9 - - - +
384A LEU* 1.3 75.6 - - - +
386A VAL* 1.3 65.4 + - - +
388A LEU* 3.5 1.9 + - - +
389A GLY* 3.1 17.3 + - - -
390A SER* 3.4 18.1 + - - +
391A GLY 4.8 0.6 + - - +
392A GLN 3.2 33.7 - - - +
393A ILE* 3.7 12.6 - - + -
410A LEU* 4.1 3.4 - - + -
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Residues in contact with VAL 386 (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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129A TYR* 4.2 12.8 - - + -
141A LEU* 3.5 26.5 - - + +
142A ARG 3.5 26.0 + - - +
143A LEU* 4.1 13.5 - - + -
144A PRO* 4.2 2.5 - - + -
382A ALA 3.4 17.1 + - - +
383A ASP 3.9 2.9 - - - +
384A LEU 3.3 0.4 - - - -
385A VAL* 1.3 75.9 - - - +
387A ALA* 1.3 62.7 + - - +
389A GLY* 3.1 14.0 + - - -
410A LEU* 3.7 20.4 - - + -
413A ILE* 3.9 23.3 - - + -
417A LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 387 (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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129A TYR* 3.3 27.7 - - - +
132A LEU* 3.4 25.1 - - + -
133A ALA* 3.5 12.7 - - - +
138A THR* 2.6 36.4 + - - +
141A LEU* 4.0 1.6 - - - -
383A ASP 2.9 17.6 + - - +
384A LEU* 3.4 6.5 - - + +
386A VAL* 1.3 77.2 - - - +
388A LEU* 1.3 53.5 + - + +
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Residues in contact with LEU 388 (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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132A LEU 5.5 0.2 - - - +
136A ALA* 3.8 26.0 - - + -
138A THR* 3.7 13.0 + - - +
342A LEU* 3.5 33.0 - - + -
354A ILE* 4.7 9.9 - - + -
357A SER* 3.6 23.6 - - - +
358A LYS* 6.1 0.9 - - + -
361A MET* 3.5 19.5 - - + +
367A VAL* 4.7 2.2 - - + -
369A VAL* 4.0 16.8 - - + -
384A LEU* 2.9 34.6 + - + +
385A VAL* 4.0 3.8 - - - +
386A VAL 3.3 0.2 - - - -
387A ALA* 1.3 76.9 - - + +
389A GLY* 1.3 62.0 + - - +
390A SER* 3.2 6.8 + - - +
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Residues in contact with GLY 389 (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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138A THR* 4.3 0.4 - - - -
140A GLU 3.6 22.5 - - - +
142A ARG* 3.5 24.6 + - - +
361A MET* 4.9 0.6 - - - +
385A VAL 3.1 4.0 + - - -
386A VAL 3.1 17.0 + - - -
387A ALA 3.3 0.4 - - - -
388A LEU* 1.3 78.4 - - - +
390A SER* 1.3 63.3 + - - +
391A GLY 3.3 3.0 + - - -
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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