Contacts of the helix formed by residues 382 - 393 (chain A) in PDB entry 2PA5
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A LYS* 4.0 32.1 - - + +
358A ILE* 5.6 6.9 - - - +
376A GLN* 4.4 5.1 + - - +
378A PRO* 3.7 7.0 - - - +
379A LEU* 2.8 31.9 + - + +
381A ASN* 1.3 101.0 - - - +
383A TYR* 1.3 63.7 + - - +
384A ARG 3.2 2.0 - - - -
385A ASP* 3.0 19.1 + - - +
386A PHE* 2.9 24.3 + - - +
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Residues in contact with TYR 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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378A PRO* 3.7 17.5 - - + -
379A LEU 2.9 33.4 + - - -
380A GLU* 3.4 40.7 + - + +
382A THR* 1.3 76.8 - - - +
384A ARG* 1.3 63.8 + - - +
386A PHE* 3.3 6.6 + - - +
387A TRP* 3.0 31.2 + - - -
413A GLY* 3.2 9.1 - - - -
414A GLN* 3.1 35.3 + - - +
415A TYR* 3.5 26.2 - - + -
424A ILE* 6.4 0.2 - - + -
426A PHE* 3.6 27.6 - + + -
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Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLU 5.3 0.2 + - - -
381A ASN 4.8 10.8 - - - +
383A TYR* 1.3 78.6 - - - +
385A ASP* 1.3 72.2 + - - +
387A TRP* 3.4 2.2 + - - +
388A LEU* 2.9 31.3 + - - +
426A PHE* 4.3 29.7 - - + +
429A LEU* 4.7 2.3 - - - +
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Residues in contact with ASP 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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330A LYS* 4.1 13.0 - - - +
346A LEU* 3.7 30.7 - - + +
355A THR 5.6 1.3 - - - +
357A TYR 4.1 9.3 - - - +
358A ILE* 4.0 12.5 - - + +
381A ASN 4.0 5.2 - - - +
382A THR* 3.0 25.8 + - - +
384A ARG* 1.3 86.3 - - - +
386A PHE* 1.3 60.8 + - - +
388A LEU* 3.4 8.1 + - - +
389A MET* 2.9 29.5 + - - +
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Residues in contact with PHE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 3.8 14.3 - - + +
375A THR* 4.3 11.2 - - + -
376A GLN 5.4 0.2 - - - -
378A PRO* 3.5 29.6 - - + -
382A THR* 2.9 12.9 + - - +
383A TYR 3.5 8.3 - - - +
385A ASP* 1.3 76.3 - - - +
387A TRP* 1.3 76.4 + + - +
389A MET* 3.2 16.3 + - + +
390A VAL* 2.9 47.3 + - + +
398A ILE* 3.8 20.4 - - + -
415A TYR* 3.5 36.6 - + - -
512A VAL* 3.9 25.4 - - + -
514A HIS* 4.5 4.9 - + - -
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Residues in contact with TRP 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR 3.0 27.2 + - - +
384A ARG* 4.1 2.9 - - - +
386A PHE* 1.3 76.0 - + - +
388A LEU* 1.3 61.5 + - - +
390A VAL* 3.3 12.2 + - + +
391A TRP* 2.9 29.3 + - - +
398A ILE* 3.8 25.6 - - + -
415A TYR* 2.8 50.4 + + - +
416A TRP* 4.0 9.2 - - + -
426A PHE* 3.3 29.0 - + + -
429A LEU* 3.6 17.6 - - + +
431A VAL* 3.9 22.7 - - + -
447A LEU* 3.6 24.9 - - + -
449A ILE* 3.7 36.9 - - + +
460A VAL* 4.9 2.5 - - + -
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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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346A LEU* 4.2 22.7 - - + -
347A THR 4.1 9.9 - - - +
348A LYS* 4.9 9.4 - - + -
384A ARG 2.9 19.1 + - - +
385A ASP* 3.6 8.3 - - - +
387A TRP* 1.3 77.0 - - - +
389A MET* 1.3 55.8 + - - +
391A TRP* 3.1 6.9 + - + +
392A GLU* 2.8 66.0 + - + +
428A PHE* 4.1 31.0 - - + -
429A LEU* 3.5 10.8 - - + +
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Residues in contact with MET 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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344A VAL* 3.8 28.0 - - + -
346A LEU* 3.8 13.8 - - + +
358A ILE* 4.0 18.8 - - + -
360A ALA* 3.7 25.4 - - + -
373A ILE* 4.0 24.2 - - + -
375A THR* 4.4 5.4 - - + -
385A ASP 2.9 14.4 + - - +
386A PHE* 3.2 26.4 + - + +
388A LEU* 1.3 76.8 - - - +
390A VAL* 1.3 62.1 + - + +
392A GLU* 4.5 3.4 - - - +
393A GLN* 2.9 37.1 + - + +
512A VAL* 4.3 14.6 - - + -
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Residues in contact with VAL 390 (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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386A PHE* 2.9 46.6 + - + +
387A TRP* 3.3 17.5 + - + +
389A MET* 1.3 75.8 - - + +
391A TRP* 1.3 60.7 + - - +
394A LYS* 3.2 2.3 + - - -
395A VAL* 3.1 53.5 + - + +
398A ILE* 4.2 6.5 - - + -
449A ILE* 3.4 27.1 - - + -
458A ARG* 4.3 0.9 + - - -
460A VAL* 4.1 5.6 - - + -
512A VAL* 4.6 14.4 - - + -
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Residues in contact with TRP 391 (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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387A TRP 2.9 17.7 + - - +
388A LEU* 3.6 9.2 - - + +
390A VAL* 1.3 75.5 - - - +
392A GLU* 1.3 76.2 + - + +
394A LYS* 3.1 4.7 + - - +
429A LEU* 4.3 9.0 - - + -
449A ILE* 3.7 38.8 - - + -
451A ASN* 3.3 34.1 - - + +
454A GLU* 3.1 35.2 + - - -
456A GLN* 3.6 32.5 - - + -
458A ARG* 2.8 77.1 + - + +
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Residues in contact with GLU 392 (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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345A LYS 4.0 4.9 - - - +
346A LEU* 3.6 10.6 - - - +
347A THR* 2.6 61.1 + - - +
388A LEU* 2.8 47.4 + - + +
389A MET* 4.1 3.1 - - - +
391A TRP* 1.3 79.9 - - + +
393A GLN* 1.3 72.0 + - - +
394A LYS* 3.3 9.4 + - - +
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Residues in contact with GLN 393 (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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344A VAL* 4.0 18.9 - - + +
345A LYS 4.3 10.9 + - - +
362A PHE* 3.5 26.5 - - - -
373A ILE* 4.0 20.0 - - + -
389A MET* 2.9 20.7 + - + +
392A GLU* 1.3 88.1 + - + +
394A LYS* 1.3 69.8 + - - +
395A VAL* 3.2 15.2 + - + -
509A PRO* 3.7 11.4 - - - +
510A PRO* 3.7 10.5 - - + +
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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