Contacts of the helix formed by residues 481 - 497 (chain A) in PDB entry 4P5O
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 SER 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A LEU* 4.4 3.1 + - - +
439A GLU* 5.3 8.3 + - - +
442A LEU* 3.5 27.4 - - - +
479A SER* 4.8 0.4 - - - -
480A ALA* 1.3 82.5 - - - +
482A ASP* 1.3 65.1 + - - +
483A ASP* 3.7 5.7 + - - +
484A ALA* 3.1 22.7 + - - +
485A GLU* 3.3 23.2 + - - +
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Residues in contact with ASP 482 (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* 4.2 17.2 + - - +
480A ALA 4.4 0.2 - - - -
481A SER* 1.3 71.7 + - - +
483A ASP* 1.3 68.1 + - - +
485A GLU* 3.2 9.6 + - - +
486A ALA* 2.9 28.7 + - - +
508A PHE* 4.4 15.6 - - + -
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLU* 5.4 10.0 - - - +
481A SER* 3.4 4.5 + - - +
482A ASP* 1.3 82.2 + - - +
484A ALA* 1.3 57.7 + - - +
486A ALA* 3.6 8.6 + - - +
487A SER* 2.9 27.5 + - - -
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Residues in contact with ALA 484 (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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430A LEU* 4.6 11.4 - - + -
442A LEU* 3.8 24.7 - - + -
443A GLU* 5.6 1.6 - - - -
446A LEU* 3.9 10.4 - - + +
481A SER* 3.1 29.9 + - - +
482A ASP 3.1 0.2 - - - -
483A ASP* 1.3 75.4 - - - +
485A GLU* 1.3 56.9 + - - +
487A SER* 2.8 27.8 + - - -
488A MET* 2.9 12.3 + - - +
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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
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430A LEU* 3.2 17.3 - - + +
466A TYR* 4.0 1.7 + - - -
470A LEU* 3.2 19.8 - - + +
473A ARG* 2.7 36.9 + - - -
474A LEU* 4.1 5.4 - - + +
479A SER* 2.0 38.5 + - - +
481A SER 3.3 16.4 - - - +
482A ASP* 3.4 9.9 - - - +
484A ALA* 1.3 74.7 - - - +
486A ALA* 1.3 63.7 + - - +
488A MET* 3.0 5.7 + - - +
489A ILE* 2.9 31.2 + - + +
508A PHE* 4.7 11.9 - - + -
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Residues in contact with ALA 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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482A ASP 2.9 15.3 + - - +
483A ASP* 3.6 10.1 - - - +
485A GLU* 1.3 75.6 - - - +
487A SER* 1.3 61.6 + - - +
489A ILE* 3.5 6.5 + - - +
490A SER* 3.0 22.7 + - - -
508A PHE* 4.1 25.5 - - + -
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Residues in contact with SER 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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443A GLU* 3.1 33.1 + - - -
446A LEU* 5.1 1.3 - - - -
483A ASP 2.9 14.1 + - - -
484A ALA* 2.8 17.2 + - - -
486A ALA* 1.3 72.7 - - - +
488A MET* 1.3 61.4 + - - -
490A SER* 3.1 10.7 - - - -
491A LYS* 2.9 31.8 + - - +
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Residues in contact with MET 488 (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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426A CYS* 4.0 25.4 - - - -
430A LEU* 4.7 0.7 - - + -
446A LEU* 3.7 32.0 - - + +
449A VAL* 4.0 8.5 - - + -
450A MET* 3.5 32.1 - - + +
462A PHE* 4.5 6.3 - - + -
466A TYR* 3.0 30.7 - - + +
484A ALA 2.9 6.7 + - - +
485A GLU* 3.0 9.8 + - - +
487A SER* 1.3 76.0 - - - +
489A ILE* 1.3 55.4 + - - +
491A LYS* 2.7 32.7 + - - +
492A LEU* 2.8 29.8 + - + +
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Residues in contact with ILE 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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466A TYR* 5.0 5.6 - - + +
470A LEU* 3.9 26.0 - - + -
485A GLU* 2.9 22.4 + - + +
486A ALA* 3.8 4.9 - - - +
488A MET* 1.3 76.0 - - + +
490A SER* 1.3 64.4 + - - +
492A LEU* 3.7 7.7 - - - +
493A LYS* 2.9 24.7 + - + +
501A THR* 3.9 17.4 - - - +
504A LEU* 4.3 25.1 - - + -
505A GLN* 4.3 21.3 - - - +
508A PHE* 4.5 30.3 - - + -
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Residues in contact with SER 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA 3.0 15.6 + - - -
487A SER* 3.1 14.8 - - - -
489A ILE* 1.3 78.0 - - - +
491A LYS* 1.3 57.9 + - - +
493A LYS* 3.3 6.5 + - - +
494A GLN* 3.0 27.5 + - - +
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Residues in contact with LYS 491 (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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443A GLU* 3.4 27.5 + - - -
446A LEU* 4.4 11.9 - - + -
447A ASN* 2.6 30.0 + - - +
450A MET* 3.8 33.9 - - + +
487A SER* 2.9 25.6 + - - +
488A MET* 2.7 22.5 + - - +
490A SER* 1.3 72.0 - - - +
492A LEU* 1.3 64.3 + - - +
494A GLN* 3.2 11.6 + - - +
495A ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 492 (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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450A MET* 3.8 27.6 - - + -
453A PHE* 5.5 1.1 - - + -
462A PHE* 4.2 15.7 - - + -
466A TYR* 3.5 39.9 - - + -
488A MET* 2.8 33.9 + - + +
489A ILE* 3.7 7.2 - - - +
491A LYS* 1.3 69.4 - - - +
493A LYS* 1.3 57.6 + - - +
495A ALA* 2.8 4.5 + - - +
496A CYS* 2.7 44.3 + - - -
500A TYR* 4.2 11.4 - - + -
501A THR* 3.8 11.9 - - + -
504A LEU* 4.1 13.0 - - + -
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Residues in contact with LYS 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 2.9 19.5 + - + +
490A SER* 3.6 6.7 - - - +
492A LEU* 1.3 73.9 - - - +
494A GLN* 1.3 64.5 + - - +
497A GLY* 3.0 31.3 + - - +
498A PHE* 3.8 30.9 - - + +
501A THR* 3.2 31.5 - - - +
505A GLN* 5.6 7.0 + - - +
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Residues in contact with GLN 494 (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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490A SER* 3.0 13.5 + - - +
491A LYS* 3.3 14.4 - - - +
493A LYS* 1.3 78.7 - - - +
495A ALA* 1.3 61.3 + - + +
497A GLY* 4.7 0.9 + - - -
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Residues in contact with ALA 495 (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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450A MET* 4.1 17.7 - - + -
453A PHE* 4.2 17.0 - - + -
454A LYS* 6.3 2.0 - - + -
491A LYS 3.0 10.7 + - - +
492A LEU 2.8 12.6 + - - +
494A GLN* 1.3 74.7 - - + +
496A CYS* 1.3 59.3 + - - +
497A GLY* 3.1 8.4 + - - -
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Residues in contact with CYS 496 (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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453A PHE* 3.8 20.6 - - - -
463A GLN* 3.2 37.0 - - - +
492A LEU* 2.7 23.5 + - - +
495A ALA* 1.3 75.4 - - - +
497A GLY* 1.3 59.9 + - - +
499A GLU* 5.0 0.9 + - - +
500A TYR* 3.5 38.3 + - + +
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Residues in contact with GLY 497 (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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493A LYS* 3.0 25.6 + - - +
494A GLN 5.2 0.7 - - - -
495A ALA 3.1 4.4 + - - -
496A CYS* 1.3 81.7 - - - +
498A PHE* 1.3 65.2 + - - -
499A GLU 3.4 2.0 + - - -
500A TYR* 3.7 4.7 + - - +
501A THR* 3.4 13.0 + - - +
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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