Contacts of the helix formed by residues 455 - 474 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A TYR* 4.8 20.2 - - + -
457A ALA* 4.9 1.3 - - + +
417B TRP* 3.8 20.9 - - + -
420B ARG* 3.5 16.8 - - - +
453B ASP* 2.7 32.6 + - - +
454B HIS* 1.3 73.9 - - + +
456B TYR* 1.3 71.2 + - - +
457B ALA* 3.8 12.3 - - + +
458B ILE* 2.9 29.0 + - + +
459B ARG 3.1 8.3 + - - -
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 4.3 22.2 - + - -
455A VAL* 4.5 20.6 - - + -
456A TYR* 6.2 4.3 - - + +
454B HIS 3.8 3.4 + - - -
455B VAL* 1.3 70.1 - - + +
457B ALA* 1.3 83.5 + - - +
459B ARG* 2.6 43.3 + - + +
460B GLU* 2.6 39.4 + - + +
503B PHE* 5.6 9.6 - + - -
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 3.3 37.3 - - + -
455A VAL* 4.6 3.1 - - + +
457A ALA* 3.4 33.8 - - + +
417B TRP* 5.2 4.3 - - + -
455B VAL* 3.4 6.3 + - + +
456B TYR* 1.3 88.0 - - - +
458B ILE* 1.3 63.9 + - - +
460B GLU* 3.2 3.4 + - - +
461B ALA* 3.0 20.4 + - - +
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Residues in contact with ILE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B TRP* 3.4 28.5 - - + +
420B ARG* 3.5 10.5 - - + +
421B LEU* 3.2 44.2 - - + +
424B ILE* 3.9 16.6 - - + +
450B TRP* 4.1 9.4 - - + +
453B ASP* 3.3 37.0 - - + +
455B VAL* 2.9 13.6 + - + +
456B TYR 2.6 4.0 + - - -
457B ALA* 1.3 76.4 - - - +
459B ARG* 1.3 64.2 + - - +
461B ALA* 3.2 4.0 + - - +
462B ALA* 2.9 19.2 + - - +
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Residues in contact with ARG 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TRP 3.6 15.0 - - - +
451B LEU* 3.2 29.0 - - + +
452B VAL* 4.2 5.4 + - - +
453B ASP 2.7 46.6 + - - +
454B HIS* 3.6 14.5 + - - +
455B VAL 3.1 2.4 + - - +
456B TYR* 2.6 44.1 + - + +
458B ILE* 1.3 75.0 - - - +
460B GLU* 1.3 49.4 + - - +
462B ALA* 2.7 21.9 + - - +
463B THR* 2.8 24.1 + - - +
496B LEU* 4.7 23.7 + - - +
497B HIS* 5.2 10.9 - - - -
500B THR* 3.8 19.5 + - + +
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Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 3.9 22.2 - - + +
456B TYR* 2.6 47.9 + - + +
457B ALA* 3.2 13.5 - - - +
459B ARG* 1.3 79.2 - - - +
461B ALA* 1.3 60.7 + - - +
463B THR* 3.3 14.5 + - - +
464B SER* 3.2 20.3 + - - -
503B PHE* 5.0 15.6 - - - +
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Residues in contact with ALA 461 (chain B).
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* 4.5 8.5 - - + -
418A ARG* 6.2 1.6 - - + -
421B LEU* 3.8 30.1 - - + -
424B ILE* 3.8 12.1 - - + +
425B GLU* 5.4 3.6 - - + +
457B ALA 3.0 13.9 + - - +
458B ILE 3.9 2.9 - - - +
460B GLU* 1.3 73.4 - - - +
462B ALA* 1.3 59.5 + - - +
464B SER* 3.6 9.9 - - - -
465B ASN* 2.9 27.9 + - - +
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Residues in contact with ALA 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ILE* 4.5 7.2 - - + +
447B CYS 5.1 4.3 - - - +
450B TRP* 3.7 26.7 - - + +
451B LEU* 3.3 18.8 - - + -
458B ILE 2.9 13.7 + - - +
459B ARG* 2.7 19.1 - - - +
461B ALA* 1.3 75.0 - - - +
463B THR* 1.3 65.2 + - - +
465B ASN* 2.9 23.6 + - - +
466B LEU* 3.3 7.4 + - - +
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B LEU* 3.3 13.3 - - - +
459B ARG 2.8 17.2 + - - -
460B GLU* 3.4 16.2 + - - +
462B ALA* 1.3 73.9 - - - +
464B SER* 1.3 64.4 + - - -
466B LEU* 2.8 27.1 + - + +
467B LYS* 3.6 2.3 + - - +
500B THR* 4.6 5.9 - - - +
503B PHE* 3.6 31.9 - - + +
504B CYS* 3.7 24.2 - - - +
507B VAL* 4.9 11.1 - - + +
508B LEU* 5.7 0.6 - - + +
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Residues in contact with SER 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B GLU 3.2 9.6 + - - -
461B ALA* 3.6 12.1 - - - -
463B THR* 1.3 78.9 - - - +
465B ASN* 1.3 65.0 + - - +
467B LYS* 2.9 24.4 + - - +
468B LYS* 3.0 17.1 + - - +
507B VAL* 5.2 6.3 - - - -
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Residues in contact with ASN 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ILE* 3.5 17.4 + - + -
427B MET* 4.0 11.5 - - - +
428B PRO* 2.9 41.4 - - - +
447B CYS* 4.2 8.6 - - - +
450B TRP* 4.2 5.2 - - + -
461B ALA 2.9 15.1 + - - +
462B ALA* 2.9 16.8 + - - +
464B SER* 1.3 76.6 - - - +
466B LEU* 1.3 50.3 + - + +
468B LYS* 3.0 9.2 + - - +
469B LEU* 2.5 53.5 + - - +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B CYS* 5.0 6.7 - - + +
448B MET* 3.7 23.6 - - + -
451B LEU* 3.7 14.6 - - + -
462B ALA 3.9 6.3 - - - +
463B THR* 2.8 15.6 + - - +
465B ASN* 1.3 75.2 - - + +
467B LYS* 1.3 65.3 + - - +
469B LEU* 2.6 29.9 + - + +
470B VAL* 2.7 17.7 + - + +
482B ILE* 3.8 25.8 - - + -
486B VAL* 4.4 1.3 - - + -
504B CYS* 3.6 31.6 - - - -
508B LEU* 4.2 22.4 - - + -
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Residues in contact with LYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A HIS* 5.6 2.0 + - - -
463B THR 3.6 1.6 + - - -
464B SER* 2.9 16.7 + - - +
466B LEU* 1.3 74.8 - - - +
468B LYS* 1.3 67.0 + - + +
470B VAL* 3.0 9.7 + - - +
471B GLU* 2.9 55.1 + - + +
507B VAL* 3.5 32.1 - - + +
508B LEU* 4.9 2.8 - - - +
510B GLU* 4.5 11.2 + - - +
511B VAL* 4.1 25.4 - - + -
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Residues in contact with LYS 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A HIS* 6.0 4.2 - - - -
379A GLU* 3.9 35.8 + - - +
428B PRO* 4.0 31.4 - - + -
464B SER* 3.0 14.1 + - - +
465B ASN* 3.0 15.6 + - - +
467B LYS* 1.3 81.4 - - + +
469B LEU* 1.3 64.1 + - - +
471B GLU* 3.0 35.9 + - + +
472B LYS* 3.1 13.3 + - - +
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B MET* 4.9 1.6 - - + -
428B PRO* 4.6 11.2 - - + +
431B ALA* 3.9 14.4 - - + -
439B PHE* 3.3 33.0 - - + -
447B CYS* 4.1 10.1 - - + -
465B ASN* 2.5 38.2 + - - +
466B LEU* 2.6 24.2 + - + +
468B LYS* 1.3 71.6 - - - +
470B VAL* 1.3 55.1 + - - +
472B LYS* 3.3 4.6 + - + +
473B PHE* 2.8 58.6 + - + +
477B TRP* 3.8 15.3 - - + -
482B ILE* 5.4 1.6 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B LEU* 2.7 23.4 + - - +
467B LYS* 3.3 8.1 - - - +
469B LEU* 1.3 70.1 - - - +
471B GLU* 1.3 69.2 + - - +
472B LYS 2.7 1.0 + - - -
473B PHE 2.7 0.5 + - - -
474B GLY* 2.7 26.5 + - - +
475B LYS* 3.9 25.6 - - + +
477B TRP* 4.0 11.9 - - + -
478B ALA* 4.1 18.2 - - + -
482B ILE* 5.5 2.0 - - + -
508B LEU* 3.9 27.1 - - + -
511B VAL* 3.9 23.6 - - + +
512B CYS* 5.1 1.1 - - - -
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Residues in contact with GLU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A HIS* 3.7 29.3 + - + -
467B LYS* 2.9 50.8 + - + +
468B LYS* 3.3 34.9 + - + +
470B VAL* 1.3 76.6 - - - +
472B LYS* 1.3 58.6 + - - +
474B GLY* 4.8 1.2 + - - -
511B VAL* 4.7 12.2 - - + +
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Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B PRO* 3.2 32.5 + - + +
429B LEU* 4.1 16.6 - - - +
432B GLY* 4.1 24.7 - - - +
468B LYS 3.1 9.7 + - - +
469B LEU* 3.9 8.7 - - + +
470B VAL 2.7 4.8 + - - -
471B GLU* 1.3 78.0 - - + +
473B PHE* 1.3 70.6 + - + +
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Residues in contact with PHE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B ALA* 3.6 30.3 - - + -
432B GLY* 4.4 6.7 - - - -
435B GLY* 4.1 2.5 - - - -
436B VAL* 3.6 32.9 - - + +
439B PHE* 3.5 37.0 - + + -
469B LEU* 2.8 31.2 + - + +
470B VAL 2.7 9.1 + - - -
472B LYS* 1.3 84.9 - - + +
474B GLY* 1.3 58.7 + - - +
477B TRP* 3.4 44.5 - + + +
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Residues in contact with GLY 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B VAL* 2.7 22.0 + - - +
471B GLU 4.7 1.2 + - - -
472B LYS 3.8 0.2 - - - -
473B PHE* 1.3 72.1 - - - +
475B LYS* 1.3 52.4 + - - -
476B GLU* 2.7 12.2 + - - +
477B TRP* 2.6 39.9 + - - +
478B ALA 3.2 2.4 + - - -
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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
------------------------------------------------------------
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