Contacts of the helix formed by residues 477 - 499 (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 ALA 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A PRO* 5.0 0.2 - - - -
476A SER* 1.3 69.8 - - - +
478A ALA* 1.3 58.1 + - - +
479A SER 3.3 2.0 - - - -
480A LEU* 3.2 7.4 + - - +
481A ILE* 2.8 42.6 + - + +
528A LEU* 5.0 1.3 - - + -
566A PHE* 4.0 16.2 - - + -
570A ALA* 3.5 33.9 - - + -
573A GLU* 2.7 18.0 + - - +
601A SCN 4.1 3.4 - - - -
704A EDO 4.1 1.4 - - - -
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A SER* 3.3 16.6 + - - +
477A ALA* 1.3 76.2 - - - +
479A SER* 1.3 59.4 + - - +
481A ILE* 3.4 0.9 + - - +
482A ASP* 2.9 29.5 + - - +
573A GLU* 4.6 0.7 - - - +
577A LYS* 4.8 8.7 - - + -
601A SCN 3.7 26.0 + - - +
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A HIS* 2.9 56.2 + - - +
465A PHE* 3.8 11.2 - - - -
467A SER* 4.6 2.7 - - - -
476A SER* 4.5 4.9 + - - -
477A ALA 3.3 0.6 - - - -
478A ALA* 1.3 78.9 - - - +
480A LEU* 1.3 59.0 + - - +
482A ASP* 3.3 6.6 + - - +
483A PHE* 2.9 29.6 + - - +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A THR* 5.9 2.9 - - + -
465A PHE* 3.7 36.1 - - + -
468A TRP* 4.1 19.5 - - + -
474A PRO* 5.0 4.0 - - + +
476A SER 5.1 1.0 + - - +
477A ALA* 3.2 13.0 + - - +
479A SER* 1.3 80.7 - - - +
481A ILE* 1.3 58.3 + - + +
483A PHE* 3.3 8.6 + - + +
484A LEU* 2.9 27.4 + - + +
524A THR* 4.8 4.3 - - + -
525A PHE* 4.2 28.5 - - + -
528A LEU* 4.0 17.3 - - + -
566A PHE* 3.9 30.3 - - + -
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ALA* 2.8 29.2 + - + +
478A ALA 4.0 0.2 - - - +
480A LEU* 1.3 70.2 - - - +
482A ASP* 1.3 63.6 + - - +
484A LEU* 3.2 9.1 + - + +
485A ARG* 3.0 39.8 + - + +
528A LEU* 4.0 23.8 - - + -
532A LEU* 4.1 24.7 - - + -
570A ALA 4.2 3.8 - - - +
574A PHE* 3.8 28.0 - - + -
601A SCN 3.6 39.0 - - - +
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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
----------------------------------------------------------
442A TYR* 4.9 6.9 - - - -
478A ALA 2.9 18.4 + - - +
479A SER* 3.7 7.4 - - - +
481A ILE* 1.3 75.6 - - - +
483A PHE* 1.3 59.4 + - - +
485A ARG* 3.1 20.6 + - - +
486A VAL* 3.0 36.4 + - - +
601A SCN 5.5 0.2 + - - -
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Residues in contact with PHE 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL* 3.7 26.2 - - + -
401A THR* 5.3 0.9 - - + -
441A HIS* 6.1 0.4 - - + -
442A TYR* 3.6 44.0 - + + -
463A PHE* 3.7 32.3 - + + -
465A PHE* 3.6 42.2 - + + -
479A SER 2.9 18.4 + - - +
480A LEU* 3.3 9.6 - - + +
482A ASP* 1.3 74.1 + - - +
484A LEU* 1.3 62.1 + - - +
486A VAL* 3.1 10.8 + - + +
487A VAL* 2.8 40.2 + - + +
525A PHE* 3.9 17.0 - + - -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 2.9 14.2 + - + +
481A ILE* 3.4 12.1 - - + +
483A PHE* 1.3 75.3 - - - +
485A ARG* 1.3 59.7 + - + +
487A VAL* 3.3 3.4 + - + +
488A ARG* 2.8 49.1 + - + +
525A PHE* 3.6 37.0 - - + +
528A LEU* 4.5 4.9 - - + -
529A ASP* 3.4 55.0 - - + +
532A LEU* 3.8 24.2 - - + -
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Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 3.0 33.9 + - + +
482A ASP* 3.1 19.8 + - - +
484A LEU* 1.3 79.3 - - + +
486A VAL* 1.3 61.9 + - + +
488A ARG* 3.8 19.0 - - - +
489A ASN* 3.0 37.3 + - - +
574A PHE* 3.3 30.9 - - - -
578A GLU* 3.4 14.6 + - - -
601A SCN 4.8 5.5 + - - -
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 3.6 37.0 - - + +
444A LYS* 6.0 0.7 - - + -
463A PHE* 3.6 29.4 - - + -
482A ASP* 3.0 26.8 + - - +
483A PHE* 3.1 9.8 + - + +
485A ARG* 1.3 78.5 - - + +
487A VAL* 1.3 63.3 + - - +
489A ASN* 3.4 5.7 + - - +
490A GLN* 3.0 22.7 + - + +
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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
----------------------------------------------------------
397A VAL* 4.0 12.4 - - + +
399A VAL* 3.7 33.0 - - + -
463A PHE* 3.9 22.7 - - + -
483A PHE* 2.8 36.0 + - + +
484A LEU* 3.6 10.1 - - + +
486A VAL* 1.3 76.1 - - - +
488A ARG* 1.3 64.0 + - + +
490A GLN* 3.2 2.1 + - - +
491A GLN* 2.9 22.9 + - - +
511A ILE* 4.1 17.0 - - + -
525A PHE* 4.3 9.4 - - + -
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU* 2.8 42.9 + - + +
485A ARG* 3.8 17.8 - - - +
487A VAL* 1.3 74.0 - - + +
489A ASN* 1.3 68.9 + - - +
491A GLN* 3.4 6.5 + - - +
492A SER* 3.0 24.3 + - - -
511A ILE* 5.6 2.0 - - - -
529A ASP* 2.7 46.6 + - - +
532A LEU* 3.9 8.1 - - - +
533A ALA* 3.6 11.8 - - - +
536A GLU* 2.8 36.1 + - - -
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Residues in contact with ASN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ARG* 3.0 27.6 + - - +
486A VAL* 3.8 5.8 - - - +
488A ARG* 1.3 83.4 - - - +
490A GLN* 1.3 57.0 + - - +
492A SER* 3.3 7.6 + - - -
493A LEU* 3.0 29.9 + - - +
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Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 4.1 6.0 - - + +
444A LYS* 3.9 16.9 + - - -
461A THR* 3.4 30.5 + - - +
463A PHE* 3.7 28.3 - - + -
486A VAL* 3.0 17.1 + - + +
487A VAL 3.8 1.1 - - - +
489A ASN* 1.3 76.3 - - - +
491A GLN* 1.3 53.5 + - - +
493A LEU* 3.2 27.2 + - - +
494A ALA* 2.8 47.7 + - - +
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Residues in contact with GLN 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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368A GLN* 5.6 0.6 - - - +
371A ALA 5.7 0.2 + - - -
396A LEU* 4.3 9.6 + - - +
397A VAL* 3.7 21.8 + - + +
487A VAL 2.9 17.0 + - - +
488A ARG* 3.7 6.3 - - - +
490A GLN* 1.3 77.5 - - - +
492A SER* 1.3 57.5 + - - +
494A ALA* 3.9 1.1 - - - +
495A VAL* 2.8 50.3 + - - +
508A GLU* 3.0 26.2 + - - +
509A PRO* 3.0 28.1 + - - +
510A PRO 4.8 1.2 - - - +
511A ILE* 3.4 36.1 - - + +
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ARG 3.0 17.4 + - - -
489A ASN* 3.6 9.4 - - - -
491A GLN* 1.3 77.9 - - - +
493A LEU* 1.3 58.2 + - - +
495A VAL* 3.9 4.6 - - - +
496A SER* 2.9 31.6 + - - -
508A GLU* 5.5 3.1 - - - -
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ASN 3.0 17.3 + - - +
490A GLN* 3.7 26.7 - - - +
492A SER* 1.3 76.3 - - - +
494A ALA* 1.3 65.6 + - - +
496A SER* 2.8 24.4 + - - +
497A ASN* 3.0 29.4 + - - +
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.8 34.1 - - + +
397A VAL* 4.9 2.2 - - + -
490A GLN* 2.8 33.8 + - - +
491A GLN* 3.9 2.7 - - - +
493A LEU* 1.3 79.7 - - - +
495A VAL* 1.3 62.0 + - - +
497A ASN* 3.2 6.4 + - - +
498A MET* 2.9 24.3 + - - +
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Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.6 18.2 - - + -
491A GLN* 2.8 48.5 + - - +
492A SER* 3.9 3.8 - - - +
494A ALA* 1.3 71.0 - - - +
496A SER* 1.3 64.0 + - - +
498A MET* 3.2 28.0 + - + +
499A GLY 4.1 1.6 + - - -
508A GLU* 3.9 26.7 - - + +
509A PRO* 3.9 10.1 - - + -
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Residues in contact with SER 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A SER* 2.9 15.1 + - - -
493A LEU* 2.8 22.2 + - - +
495A VAL* 1.3 79.4 - - - +
497A ASN* 1.3 67.3 + - - +
499A GLY* 4.5 3.5 + - - -
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Residues in contact with ASN 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 3.0 37.6 + - - +
494A ALA* 3.2 5.1 + - - +
496A SER* 1.3 87.6 + - - +
498A MET* 1.3 62.8 + - - +
499A GLY* 3.4 2.0 + - - -
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Residues in contact with MET 498 (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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394A LYS* 4.1 21.8 - - + +
396A LEU* 3.9 24.7 - - + -
494A ALA 2.9 12.7 + - - +
495A VAL* 3.2 24.0 + - + +
497A ASN* 1.3 78.2 - - - +
499A GLY* 1.3 77.8 + - - +
509A PRO* 3.5 40.6 - - + -
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Residues in contact with GLY 499 (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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495A VAL 4.1 2.6 + - - -
496A SER 4.5 3.9 + - - -
497A ASN 3.4 4.0 - - - -
498A MET* 1.3 98.3 - - - +
500A ALA* 1.3 67.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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