Contacts of the helix formed by residues 480 - 490 (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 VAL 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A LEU* 5.3 0.4 - - + -
479A SER* 1.4 71.3 - - - +
481A THR* 1.3 56.6 + - - +
483A LEU* 3.7 8.4 - - - +
484A VAL* 2.9 41.6 + - + +
519A THR* 3.8 19.5 - - + -
522A PHE* 4.3 8.7 - - + -
523A GLU* 3.6 9.2 + - - +
529A LYS 3.9 21.5 + - - +
531A LEU* 3.9 32.1 - - + +
534A PHE* 3.7 37.2 - - + -
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Residues in contact with THR 481 (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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479A SER* 3.2 1.7 - - - -
480A VAL* 1.3 75.6 - - - +
482A GLU* 1.3 63.1 + - + +
484A VAL* 3.2 4.3 + - - +
485A GLU* 3.0 28.1 + - + +
516A LEU* 4.4 11.9 - - + -
519A THR* 2.9 25.0 + - - +
520A LYS* 3.2 39.9 + - + -
523A GLU* 2.9 27.9 + - - -
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Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TYR 4.8 1.2 - - - +
478A VAL* 3.6 25.5 - - + +
479A SER* 2.9 46.1 + - - +
481A THR* 1.3 75.4 - - + +
483A LEU* 1.3 56.3 + - - +
485A GLU* 3.2 7.7 + - - +
486A GLU* 2.8 29.6 + - - +
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Residues in contact with LEU 483 (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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399A LEU* 4.5 12.1 - - + -
402A ILE* 4.3 18.6 - - + -
471A TRP* 4.2 20.0 - - + +
474A LEU* 4.3 20.6 - - + -
475A GLN* 3.9 20.0 - - + +
478A VAL* 3.6 10.4 - - + +
479A SER 2.8 20.4 + - - +
480A VAL* 3.7 6.7 - - - +
482A GLU* 1.3 70.3 - - - +
484A VAL* 1.3 57.4 + - - +
486A GLU* 3.0 7.2 + - - +
487A VAL* 2.9 35.2 + - + +
531A LEU* 3.7 34.8 - - + -
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 4.2 13.4 - - + +
399A LEU* 3.9 35.2 - - + -
480A VAL* 2.9 31.4 + - + +
481A THR* 3.6 4.5 - - - +
483A LEU* 1.3 73.3 - - - +
485A GLU* 1.3 61.2 + - - +
487A VAL* 4.0 5.6 - - - +
488A LEU* 3.1 38.0 + - + +
515A PHE* 4.2 10.1 - - + -
516A LEU* 3.5 24.0 - - + -
519A THR* 4.2 8.7 - - + -
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A THR* 3.0 21.8 + - + +
482A GLU* 3.8 8.1 - - - +
484A VAL* 1.3 74.6 - - - +
486A GLU* 1.3 61.7 + - - +
488A LEU* 3.5 4.8 + - - +
489A ASP* 3.1 26.9 + - - +
494A ARG* 2.7 34.2 + - - +
516A LEU* 3.7 27.1 - - + +
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Residues in contact with GLU 486 (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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471A TRP* 4.4 10.1 - - + +
474A LEU* 3.7 32.6 - - + +
478A VAL* 6.2 0.7 - - + -
482A GLU 2.8 14.7 + - - +
483A LEU* 3.0 9.4 + - + +
485A GLU* 1.3 75.2 - - - +
487A VAL* 1.3 61.5 + - - +
489A ASP* 3.8 4.3 - - - +
490A LYS* 2.9 61.5 + - + +
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Residues in contact with VAL 487 (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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395A ILE* 3.9 14.8 - - + -
398A TYR* 3.7 37.9 - - + -
399A LEU* 4.9 4.5 - - + -
402A ILE* 3.5 29.2 - - + -
471A TRP* 3.9 24.7 - - + +
483A LEU* 2.9 28.8 + - + +
484A VAL* 4.0 4.5 - - - +
486A GLU* 1.3 71.1 - - - +
488A LEU* 1.3 58.4 + - + +
491A SER* 2.8 37.8 + - - +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 3.9 25.4 - - + -
398A TYR* 6.4 0.4 - - + -
484A VAL* 3.1 38.7 + - + +
485A GLU* 3.9 4.9 - - - +
487A VAL* 1.3 76.2 - - + +
489A ASP* 1.3 61.0 + - - +
491A SER* 4.1 3.4 - - - +
493A TYR* 3.5 32.2 + - + -
494A ARG* 3.1 60.9 + - + +
512A LEU* 4.1 28.9 - - + +
515A PHE* 6.1 0.4 - - + -
516A LEU* 5.1 3.6 - - + -
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Residues in contact with ASP 489 (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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485A GLU 3.1 17.4 + - - +
486A GLU* 3.8 5.8 - - - +
488A LEU* 1.3 77.7 - - - +
490A LYS* 1.3 96.4 + - - +
492A GLY* 3.0 16.5 + - - -
494A ARG* 5.2 7.2 - - - +
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Residues in contact with LYS 490 (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* 5.5 1.4 - - - -
422A ILE* 5.2 6.2 - - - +
467A GLN* 3.1 34.4 + - - +
471A TRP* 4.1 11.9 - - + +
486A GLU* 2.9 43.0 + - + +
489A ASP* 1.3 106.0 + - - +
491A SER* 1.3 56.4 + - - +
492A GLY 3.1 1.5 + - - -
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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