Contacts of the helix formed by residues 462 - 476 (chain A) in PDB entry 1PJR
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 ALA 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A LEU* 5.1 0.2 - - - -
448A LEU* 4.1 18.9 - - + +
458A ALA 4.0 14.6 - - - +
459A GLY* 2.9 11.1 + - - +
461A LEU* 1.3 76.3 - - - +
463A ALA* 1.3 58.5 - - - +
465A ARG* 3.1 9.2 + - - +
466A SER* 2.9 30.5 + - - -
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A GLY 4.0 8.7 - - - +
424A ALA* 4.0 20.2 - - + -
459A GLY 3.0 14.4 + - - +
462A ALA* 1.3 75.6 - - - +
464A PHE* 1.3 63.2 + - - +
466A SER* 3.0 11.9 + - - -
467A GLN* 2.9 26.7 + - + +
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Residues in contact with PHE 464 (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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398A TYR* 5.1 3.4 - + - -
411A LEU* 3.9 20.6 - - + -
414A ILE* 4.3 19.3 - - + -
415A ILE* 4.1 26.9 - - + -
420A ARG* 3.7 40.6 - - - +
424A ALA* 5.1 3.0 - - + +
425A SER* 5.9 1.3 - - - -
427A ILE* 5.2 3.6 - - + -
445A LEU* 4.8 13.2 - - + -
460A ALA 4.4 6.0 - - - +
461A LEU* 3.1 22.0 + - + +
463A ALA* 1.3 79.1 - - - +
465A ARG* 1.3 66.2 + - - +
467A GLN* 3.3 10.3 + - + +
468A LEU* 3.1 50.8 + - + +
471A TRP* 5.6 4.3 - + - -
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Residues in contact with ARG 465 (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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442A PHE* 2.9 70.0 + - + -
443A GLU* 4.3 5.3 - - - +
445A LEU* 3.7 25.3 - - + +
446A GLY* 3.5 20.5 - - - +
461A LEU 2.8 16.0 + - - +
462A ALA* 3.1 11.2 + - - +
464A PHE* 1.3 76.7 - - - +
466A SER* 1.3 57.3 + - - +
468A LEU* 3.3 7.5 - - - +
469A GLU* 2.7 62.6 + - - +
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Residues in contact with SER 466 (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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462A ALA 2.9 16.0 + - - -
463A ALA* 3.5 9.6 + - - -
465A ARG* 1.3 74.3 - - - +
467A GLN* 1.4 64.6 + - - +
469A GLU* 3.2 14.5 + - - +
470A GLN* 3.0 32.4 + - - +
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Residues in contact with GLN 467 (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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420A ARG* 5.7 9.2 - - - +
423A GLY* 5.8 5.9 - - - -
463A ALA* 2.9 20.8 + - + +
464A PHE* 3.3 14.6 + - + +
466A SER* 1.4 70.3 + - - +
468A LEU* 1.3 58.6 + - - +
470A GLN* 3.2 25.0 + - - +
471A TRP* 2.9 65.4 + - + -
490A LYS* 3.1 41.3 + - - +
491A SER* 4.9 0.8 - - - +
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Residues in contact with LEU 468 (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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401A VAL* 3.9 35.0 - - + +
402A ILE* 4.7 3.6 - - + -
405A PRO* 4.5 6.3 - - + -
411A LEU* 3.9 16.2 - - + -
442A PHE* 4.0 26.2 - - + -
464A PHE* 3.1 43.6 + - + +
465A ARG 3.3 9.6 - - - +
467A GLN* 1.3 79.5 - - - +
469A GLU* 1.4 60.0 + - - +
471A TRP* 3.3 15.7 + - + +
472A THR* 2.8 37.7 + - - +
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Residues in contact with GLU 469 (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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442A PHE* 4.2 10.0 - - + -
465A ARG* 2.7 55.6 + - - +
466A SER* 3.5 14.8 - - - +
468A LEU* 1.4 69.6 - - - +
470A GLN* 1.3 63.4 + - + +
472A THR* 3.3 9.8 + - - -
473A GLN* 3.1 35.3 + - - +
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Residues in contact with GLN 470 (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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466A SER* 3.0 22.4 + - - +
467A GLN* 3.2 27.5 + - - +
469A GLU* 1.3 75.3 - - + +
471A TRP* 1.3 62.4 + - + +
473A GLN* 2.9 13.9 + - - +
474A LEU* 2.9 29.5 + - + +
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Residues in contact with TRP 471 (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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398A TYR* 3.8 26.2 - + - -
401A VAL* 6.3 0.7 - - + -
402A ILE* 3.7 40.9 - - + +
420A ARG* 5.2 4.3 - - - -
464A PHE* 5.6 3.8 - + - -
467A GLN* 2.9 56.9 + - + +
468A LEU* 3.8 15.3 - - + +
470A GLN* 1.3 74.9 - - + +
472A THR* 1.3 63.2 + - - +
474A LEU* 3.0 34.8 + - + +
475A GLN 3.2 11.3 + - - -
483A LEU* 4.2 3.9 - - + +
486A GLU* 4.4 14.0 + - + +
487A VAL* 3.9 27.9 - - + +
490A LYS* 4.1 14.1 - - + +
491A SER* 4.0 24.7 - - - -
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Residues in contact with THR 472 (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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402A ILE* 3.8 27.1 + - - +
405A PRO* 4.5 14.0 - - + +
442A PHE* 5.7 1.0 - - - -
468A LEU* 2.8 28.2 + - - +
469A GLU* 3.5 11.5 - - - -
471A TRP* 1.3 75.9 - - - +
473A GLN* 1.3 67.8 + - - +
475A GLN* 3.4 19.4 + - - +
476A GLU* 5.1 2.6 - - - +
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Residues in contact with GLN 473 (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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469A GLU* 3.1 31.5 + - - +
470A GLN* 2.9 14.1 + - - +
472A THR* 1.3 79.7 - - - +
474A LEU* 1.3 66.1 + - - +
475A GLN 3.1 1.4 + - - -
476A GLU* 3.1 20.8 + - - +
477A TYR* 4.4 10.7 - - + -
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Residues in contact with LEU 474 (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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470A GLN* 2.9 13.2 + - + +
471A TRP* 3.0 28.2 + - + +
473A GLN* 1.3 76.7 - - - +
475A GLN* 1.3 57.6 + - - +
476A GLU 2.8 7.6 + - - -
477A TYR* 3.2 50.2 + - + +
478A VAL* 3.4 29.4 + - + +
483A LEU* 4.3 10.3 - - + -
486A GLU* 3.7 37.2 - - + +
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Residues in contact with GLN 475 (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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402A ILE* 3.4 24.7 + - + -
403A ALA* 4.2 11.5 + - - +
471A TRP 3.2 5.9 + - - +
472A THR* 3.4 24.6 + - - +
474A LEU* 1.3 74.5 - - - +
476A GLU* 1.3 65.1 + - + +
477A TYR 3.5 0.8 + - - -
478A VAL* 4.0 14.5 - - - +
483A LEU* 3.9 27.5 - - + +
530A SER* 5.7 1.4 - - - -
531A LEU* 4.0 17.9 + - + +
532A ILE* 3.7 25.9 - - - +
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Residues in contact with GLU 476 (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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472A THR 5.1 2.5 - - - +
473A GLN* 3.1 12.9 + - - +
474A LEU 2.8 4.9 + - - -
475A GLN* 1.3 82.6 - - + +
477A TYR* 1.3 64.2 + - + +
478A VAL 5.1 0.2 - - - -
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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