Contacts of the helix formed by residues 455 - 474 (chain A) in PDB entry 2PKG
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 455 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A TRP* 3.6 20.4 - - + -
420A ARG* 3.2 19.3 - - - +
453A ASP* 2.7 25.7 + - - +
454A HIS* 1.3 76.6 - - + +
456A TYR* 1.3 56.4 + - - +
457A ALA* 3.5 19.7 - - + +
458A ILE* 2.8 43.7 + - + +
459A ARG 3.2 4.2 + - - -
456B TYR* 4.5 27.6 - - + -
457B ALA* 4.6 2.2 - - + +
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Residues in contact with TYR 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A HIS 3.8 1.0 + - - -
455A VAL* 1.3 67.8 - - + +
457A ALA* 1.3 75.7 + - + +
459A ARG* 2.8 46.0 + - - +
460A GLU* 2.8 48.4 + - + +
503A PHE* 6.2 3.6 - + - -
417B TRP* 4.1 18.7 - + - -
455B VAL* 4.8 14.8 - - + -
456B TYR* 6.2 4.2 - - + +
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 4.9 5.8 - - + -
421A LEU* 5.7 0.4 - - + -
455A VAL* 3.4 6.5 - - + +
456A TYR* 1.3 89.6 - - + +
458A ILE* 1.3 62.7 + - - +
460A GLU* 3.5 0.5 + - - +
461A ALA* 3.1 18.9 + - - +
417B TRP* 3.3 40.0 - - + +
455B VAL* 4.9 2.4 - - + +
457B ALA* 3.4 33.6 - - + +
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Residues in contact with ILE 458 (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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417A TRP* 3.2 36.3 - - + +
420A ARG* 3.6 8.5 - - + +
421A LEU* 3.2 27.4 - - + +
424A ILE* 3.7 13.9 - - + +
450A TRP* 4.2 10.8 - - + +
453A ASP* 3.1 40.6 - - + +
455A VAL* 2.8 28.3 + - + +
457A ALA* 1.3 70.0 - - - +
459A ARG* 1.3 64.1 + - - +
461A ALA* 3.2 5.2 + - - +
462A ALA* 2.9 20.3 + - - +
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Residues in contact with ARG 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A TRP 3.4 11.2 - - - +
451A LEU* 3.2 26.9 - - - +
452A VAL* 3.7 3.6 - - - +
453A ASP 3.1 48.1 + - - +
454A HIS 3.9 6.3 + - - -
455A VAL 3.2 0.9 + - - +
456A TYR* 2.8 46.1 + - + +
458A ILE* 1.3 74.1 - - - +
460A GLU* 1.3 65.6 + - - +
462A ALA* 3.0 5.5 + - - +
463A THR* 2.9 26.0 + - - +
496A LEU* 5.6 9.9 - - - +
497A HIS* 5.7 3.3 + - - -
500A THR* 4.0 16.5 + - + +
503A PHE* 6.0 3.8 - - - -
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TYR* 2.8 60.7 + - + +
457A ALA 3.5 5.2 - - - +
459A ARG* 1.3 76.7 - - - +
461A ALA* 1.3 62.1 + - - +
463A THR* 3.2 16.4 + - - +
464A SER* 3.2 18.5 + - - -
503A PHE* 5.2 15.1 - - - +
507A VAL* 6.1 0.7 - - - +
417B TRP* 4.2 13.5 - - + +
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Residues in contact with ALA 461 (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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421A LEU* 3.9 27.1 - - + -
424A ILE* 4.0 13.4 - - + +
425A GLU* 5.6 1.6 - - + -
457A ALA 3.1 11.7 + - - +
458A ILE 3.5 8.1 - - - +
459A ARG 3.2 0.2 - - - -
460A GLU* 1.3 76.3 - - - +
462A ALA* 1.3 66.8 + - - +
464A SER* 2.9 10.3 + - - +
465A ASN* 2.8 21.3 + - - +
417B TRP* 4.7 7.4 - - + -
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 4.1 6.6 - - + +
447A CYS 4.4 2.4 - - - +
450A TRP* 3.2 44.4 - - + -
451A LEU* 3.9 9.9 - - + +
458A ILE 2.9 10.1 + - - +
459A ARG 3.2 9.4 - - - +
461A ALA* 1.3 75.2 - - - +
463A THR* 1.3 58.8 + - - +
465A ASN* 2.9 27.4 - - - +
466A LEU* 3.3 13.2 + - - +
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Residues in contact with THR 463 (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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451A LEU* 3.5 17.0 - - - +
459A ARG* 2.9 16.6 + - - +
460A GLU* 3.2 18.6 + - - +
461A ALA 3.0 0.2 - - - -
462A ALA* 1.3 73.6 - - - +
464A SER* 1.3 67.8 + - - +
466A LEU* 3.0 22.8 + - + +
467A LYS 3.5 2.3 + - - -
500A THR* 5.1 2.8 - - - +
503A PHE* 4.5 8.6 - - + +
504A CYS* 3.9 29.6 - - - +
507A VAL* 3.6 30.1 - - + +
508A LEU* 5.4 0.2 - - + -
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Residues in contact with SER 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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460A GLU 3.2 7.6 + - - -
461A ALA* 2.9 12.0 + - - -
463A THR* 1.3 78.7 - - - +
465A ASN* 1.3 66.5 + - - +
467A LYS* 2.8 31.2 + - - +
468A LYS* 2.9 23.7 + - - +
507A VAL* 4.7 6.3 - - - +
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Residues in contact with ASN 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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424A ILE* 3.9 15.6 + - + -
427A MET* 4.0 3.9 - - - +
428A PRO* 3.4 35.6 - - - +
447A CYS* 3.7 20.3 - - - +
450A TRP* 4.0 6.6 - - - -
461A ALA 2.8 11.8 + - - +
462A ALA* 2.9 20.9 - - - +
464A SER* 1.3 76.2 - - - +
466A LEU* 1.3 50.4 + - - +
468A LYS* 3.2 7.3 + - - +
469A LEU* 2.7 57.3 + - - +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A CYS* 4.2 7.6 - - + +
448A MET* 3.2 37.0 - - + -
451A LEU* 4.4 1.8 - - + -
462A ALA 3.5 12.3 - - - +
463A THR* 3.0 16.6 + - - +
465A ASN* 1.3 80.9 - - - +
467A LYS* 1.3 68.1 + - - +
469A LEU* 2.6 28.5 + - + +
470A VAL* 2.7 18.0 + - + +
477A TRP* 6.0 0.2 - - - -
482A ILE* 3.6 26.2 - - + -
486A VAL* 4.4 2.7 - - + -
504A CYS* 4.2 15.9 - - - -
508A LEU* 4.1 24.9 - - + -
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Residues in contact with LYS 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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463A THR 3.5 1.4 + - - -
464A SER* 2.8 22.2 + - - +
466A LEU* 1.3 75.1 - - - +
468A LYS* 1.3 71.1 + - + +
470A VAL* 3.2 7.7 + - - +
471A GLU* 2.9 50.7 + - - +
507A VAL* 3.2 25.4 - - + +
508A LEU* 4.8 2.6 - - - +
510A GLU* 4.0 24.3 + - - +
511A VAL* 3.9 25.1 - - + -
340B HIS* 6.1 0.2 + - - -
379B GLU* 6.3 1.4 - - - +
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Residues in contact with LYS 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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428A PRO* 4.0 31.6 - - + +
464A SER* 2.9 29.2 + - - +
465A ASN* 3.4 9.0 - - - +
467A LYS* 1.3 83.5 - - - +
469A LEU* 1.3 63.3 + - - +
471A GLU* 3.1 33.4 + - - +
472A LYS* 3.1 14.2 + - - +
340B HIS* 6.5 0.9 - - - -
379B GLU* 3.7 34.4 + - - -
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Residues in contact with LEU 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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427A MET* 4.8 0.7 - - + +
428A PRO* 4.4 13.0 - - + +
431A ALA* 3.8 10.3 - - + -
439A PHE* 3.3 44.2 - - + -
447A CYS* 3.8 7.9 - - + -
465A ASN* 2.7 42.2 + - - +
466A LEU* 2.6 22.1 + - + +
468A LYS* 1.3 69.2 - - - +
470A VAL* 1.3 57.0 + - - +
472A LYS* 3.3 6.0 + - + +
473A PHE* 2.9 53.2 + - + -
477A TRP* 3.7 13.2 - - + -
482A ILE* 5.6 1.8 - - + -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 2.7 20.6 + - - +
467A LYS 3.5 7.0 - - - +
469A LEU* 1.3 67.8 - - - +
471A GLU* 1.3 60.4 + - - +
472A LYS 2.9 1.6 - - - -
473A PHE 2.6 6.4 + - - -
474A GLY* 2.6 30.7 + - - -
475A LYS* 4.2 17.3 - - - +
477A TRP* 3.9 16.2 - - + -
478A ALA* 3.9 27.1 - - + -
482A ILE* 5.0 2.0 - - + -
508A LEU* 4.0 19.5 - - + -
511A VAL* 3.5 31.9 - - + +
512A CYS* 4.7 1.1 - - - -
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Residues in contact with GLU 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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467A LYS* 2.9 45.0 + - - +
468A LYS* 3.1 24.6 + - - +
470A VAL* 1.3 76.5 - - - +
472A LYS* 1.3 57.3 + - - +
474A GLY 4.6 1.9 + - - -
511A VAL* 3.6 25.4 - - + +
340B HIS* 3.5 35.2 + - + +
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Residues in contact with LYS 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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428A PRO* 3.7 26.0 - - + +
429A LEU* 4.3 23.0 - - - +
432A GLY* 4.0 26.4 - - - +
468A LYS 3.1 10.2 + - - +
469A LEU* 3.6 11.9 - - + +
470A VAL 2.9 0.6 - - - -
471A GLU* 1.3 80.2 - - - +
473A PHE* 1.3 71.7 + - + +
474A GLY 3.8 0.2 - - - -
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Residues in contact with PHE 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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431A ALA* 3.6 37.9 - - + -
432A GLY* 4.1 8.7 - - - -
435A GLY 4.3 0.9 - - - -
436A VAL* 3.6 41.4 - - + +
439A PHE* 4.0 15.5 - + + -
469A LEU* 2.9 27.4 + - + +
470A VAL 2.6 10.5 + - - -
472A LYS* 1.3 93.6 - - + +
474A GLY* 1.3 56.7 + - - -
476A GLU* 5.3 1.0 - - - +
477A TRP* 3.2 51.2 + + + +
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Residues in contact with GLY 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 VAL* 2.6 20.7 + - - -
471A GLU 4.6 2.4 + - - -
472A LYS 3.8 0.2 - - - -
473A PHE* 1.3 72.2 - - - +
475A LYS* 1.3 60.2 + - - -
476A GLU* 3.1 11.4 - - - -
477A TRP* 2.9 30.5 + - - +
478A ALA* 3.1 4.7 + - - +
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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