Contacts of the helix formed by residues 477 - 498 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B PRO* 5.0 0.2 - - - -
476B SER* 1.3 71.1 - - - +
478B ALA* 1.3 57.7 + - - +
479B SER 3.5 0.9 - - - -
480B LEU* 3.3 8.6 + - + +
481B ILE* 3.0 34.9 + - + +
566B PHE* 4.0 18.1 - - + -
570B ALA* 3.4 43.5 - - + +
573B GLU* 2.9 15.8 + - - +
574B PHE* 5.8 0.4 - - + +
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B SER* 3.3 15.3 + - - +
477B ALA* 1.3 74.7 - - - +
479B SER* 1.3 67.6 + - - +
480B LEU 3.2 0.2 + - - -
481B ILE* 3.4 5.0 + - - +
482B ASP* 3.0 24.9 + - - +
573B GLU* 4.3 5.4 + - - +
577B LYS* 6.3 3.1 - - + -
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B HIS* 3.2 37.0 + - - -
465B PHE* 3.7 19.3 - - - -
467B SER* 4.7 6.7 - - - -
474B PRO* 6.5 0.7 - - - -
476B SER 4.5 5.7 + - - -
477B ALA 3.5 0.4 - - - -
478B ALA* 1.3 77.5 - - - +
480B LEU* 1.3 58.1 + - - +
482B ASP* 3.6 1.5 + - - -
483B PHE* 3.0 22.7 + - - +
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B PHE* 3.9 18.4 - - + -
468B TRP* 3.4 49.4 - - + -
474B PRO* 5.2 4.5 - - + -
476B SER 5.2 0.2 + - - -
477B ALA* 3.3 12.4 + - + +
478B ALA 3.1 0.6 - - - -
479B SER* 1.3 78.3 - - - +
481B ILE* 1.3 61.3 + - + +
483B PHE* 3.2 18.7 + - + +
484B LEU* 2.9 27.8 + - + +
525B PHE* 4.4 11.9 - - + -
528B LEU* 3.9 19.1 - - + -
566B PHE* 3.9 27.1 - - + -
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Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ALA* 3.0 24.9 + - + +
478B ALA* 4.1 4.5 - - - +
480B LEU* 1.3 77.4 - - + +
482B ASP* 1.3 63.3 + - - +
484B LEU* 3.2 11.4 + - + +
485B ARG* 3.1 21.4 + - + +
528B LEU* 4.4 25.8 - - + -
532B LEU* 3.8 28.0 - - + -
570B ALA* 4.9 6.3 - - + +
571B ILE* 6.1 0.4 - - - -
574B PHE* 3.6 45.5 - - + -
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Residues in contact with ASP 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B HIS* 2.7 32.9 + - + +
442B TYR* 4.0 6.8 - - - -
478B ALA 3.0 18.3 + - - +
479B SER* 3.6 4.9 - - - +
481B ILE* 1.3 76.2 - - - +
483B PHE* 1.3 63.0 + - - +
485B ARG* 3.3 8.6 + - - +
486B VAL* 3.0 30.3 + - - +
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Residues in contact with PHE 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B VAL* 3.5 29.2 - - + -
400B MET 4.4 0.2 - - - -
401B THR* 5.0 2.0 - - + -
441B HIS* 4.3 4.0 - - + -
442B TYR* 3.5 39.9 - + + -
463B PHE* 3.7 34.1 - + + -
465B PHE* 3.6 42.2 - + + -
479B SER 3.0 15.0 + - - +
480B LEU* 3.3 13.9 - - + +
482B ASP* 1.3 78.3 - - - +
484B LEU* 1.3 55.1 + - - +
486B VAL* 3.2 8.0 + - + +
487B VAL* 2.9 35.8 + - + +
525B PHE* 3.8 17.9 - + - -
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 2.9 14.2 + - + +
481B ILE* 3.2 15.0 + - + +
483B PHE* 1.3 76.8 - - - +
485B ARG* 1.3 59.1 + - - +
487B VAL* 3.2 3.3 + - - +
488B ARG* 2.9 42.8 + - + +
525B PHE* 4.2 31.0 - - + +
528B LEU* 4.1 12.3 - - + -
529B ASP* 3.3 54.3 - - + +
532B LEU* 4.5 17.5 - - + -
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Residues in contact with ARG 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ILE* 3.1 12.9 + - + +
482B ASP* 3.3 12.3 + - - +
484B LEU* 1.3 81.1 - - - +
486B VAL* 1.3 58.1 - - + +
488B ARG* 3.4 4.6 + - - +
489B ASN* 2.9 30.9 + - - +
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Residues in contact with VAL 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B TYR* 3.6 29.4 - - + +
444B LYS* 6.0 0.7 - - + -
463B PHE* 3.5 28.3 - - + -
482B ASP* 3.0 25.6 + - - +
483B PHE* 3.4 10.3 - - + +
485B ARG* 1.3 77.9 - - + +
487B VAL* 1.3 63.1 + - - +
489B ASN* 3.3 6.9 + - - +
490B GLN* 3.0 22.9 + - + +
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 4.1 7.9 - - + +
399B VAL* 3.6 33.4 - - + -
463B PHE* 4.0 22.2 - - + -
483B PHE* 2.9 37.4 + - + +
484B LEU 3.2 6.7 + - - +
486B VAL* 1.3 75.7 - - - +
488B ARG* 1.3 65.2 + - + +
490B GLN* 3.3 2.9 + - - +
491B GLN* 3.0 22.0 + - - +
511B ILE* 4.1 19.7 - - + -
525B PHE* 4.1 13.9 - - + -
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Residues in contact with ARG 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 2.9 45.6 + - + +
485B ARG* 3.9 5.4 - - - +
487B VAL* 1.3 75.9 - - + +
489B ASN* 1.3 63.3 + - - +
491B GLN* 3.3 7.9 + - - +
492B SER* 2.9 25.1 + - - -
511B ILE* 5.4 4.9 - - + -
525B PHE* 6.3 0.2 - - + -
529B ASP* 3.7 14.6 - - - +
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Residues in contact with ASN 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ARG 2.9 19.4 + - - +
486B VAL* 3.6 7.4 - - - +
487B VAL 3.3 0.2 - - - -
488B ARG* 1.3 76.3 - - - +
490B GLN* 1.3 57.4 + - - +
492B SER* 3.3 6.9 + - - -
493B LEU* 2.9 39.4 + - + +
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Residues in contact with GLN 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 4.0 7.2 - - + -
444B LYS* 3.5 24.7 + - - -
461B THR* 3.6 29.1 + - - +
463B PHE* 3.7 27.0 - - + -
486B VAL 3.0 16.4 + - - +
487B VAL 3.3 2.2 + - - +
489B ASN* 1.3 76.4 - - - +
491B GLN* 1.3 56.8 + - - +
493B LEU* 3.3 19.7 + - - +
494B ALA* 2.9 35.6 + - - +
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Residues in contact with GLN 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLN* 5.4 0.4 - - - +
396B LEU* 4.3 7.1 + - - +
397B VAL* 3.6 22.8 + - + +
487B VAL 3.0 13.4 + - - +
488B ARG* 3.3 8.9 + - - +
490B GLN* 1.3 74.9 - - - +
492B SER* 1.3 58.2 + - - +
494B ALA* 3.2 2.7 + - - +
495B VAL* 2.9 43.5 + - - +
508B GLU* 3.0 32.2 + - - +
509B PRO* 2.9 31.2 + - - +
510B PRO 4.9 1.0 - - - +
511B ILE* 3.5 35.1 - - + +
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ARG 2.9 17.3 + - - -
489B ASN* 3.5 8.1 - - - -
491B GLN* 1.3 78.2 - - - +
493B LEU* 1.3 58.7 + - - +
495B VAL* 3.4 5.0 + - - +
496B SER* 2.9 34.1 + - - -
508B GLU* 5.7 0.9 - - - -
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ASN* 2.9 24.8 + - + +
490B GLN* 3.6 23.3 - - - +
492B SER* 1.3 80.3 + - - +
494B ALA* 1.3 62.6 + - - +
496B SER* 2.9 20.9 + - - +
497B ASN* 3.1 13.0 + - - +
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Residues in contact with ALA 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 3.8 36.8 - - + +
397B VAL* 5.1 2.0 - - + -
459B GLN 5.9 0.7 - - - +
490B GLN* 2.9 26.8 + - - +
491B GLN* 3.7 4.3 - - - +
493B LEU* 1.3 76.5 - - - +
495B VAL* 1.3 59.2 + - - +
497B ASN* 3.4 8.1 + - - +
498B MET* 3.1 26.0 + - - +
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 3.9 13.2 - - + -
491B GLN* 2.9 45.3 + - - +
492B SER* 3.9 4.3 - - - +
494B ALA* 1.3 74.2 - - - +
496B SER* 1.3 65.3 + - - +
498B MET* 3.0 30.6 + - - +
508B GLU* 3.9 29.8 - - + +
509B PRO* 4.1 4.3 - - + -
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Residues in contact with SER 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B SER* 2.9 17.4 + - - -
493B LEU* 2.9 27.4 + - - +
495B VAL* 1.3 78.3 - - - +
497B ASN* 1.3 58.8 + - - +
498B MET 3.6 2.8 + - - -
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Residues in contact with ASN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU 3.1 16.6 + - - +
494B ALA* 3.6 8.3 - - - +
496B SER* 1.3 77.4 + - - +
498B MET* 1.3 64.4 + - - +
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Residues in contact with MET 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LYS* 4.8 20.4 - - + +
396B LEU* 4.0 19.1 - - + -
494B ALA 3.1 13.4 + - - +
495B VAL* 3.0 25.8 + - - +
496B SER 4.6 2.9 - - - -
497B ASN* 1.3 82.3 - - - +
507B PRO* 4.8 7.6 - - + +
508B GLU* 5.7 0.2 - - - -
509B PRO* 3.9 36.3 - - + -
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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