Contacts of the helix formed by residues 457 - 472 (chain B) in PDB entry 1JPP
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 ARG 457 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B ILE* 4.2 25.2 - - - +
453B ARG 4.8 4.5 + - - -
454B ALA* 3.2 25.9 + - - +
455B GLY* 3.3 4.9 - - - -
456B ASP* 1.3 91.4 + - - +
458B GLU* 1.3 58.7 + - - +
459B ASP* 3.1 21.8 + - - +
460B ILE* 3.2 23.0 + - + +
461B THR* 3.4 15.0 + - - +
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Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ASP 3.0 17.6 + - - +
457B ARG* 1.3 69.9 - - - +
459B ASP* 1.3 58.5 + - - +
460B ILE 3.2 2.9 - - - -
461B THR* 3.5 9.0 - - - +
462B GLU* 3.4 30.7 - - - +
501B PRO* 3.5 21.7 - - - +
502B SER* 3.7 2.9 - - - +
503B HIS* 3.5 40.8 + - - +
506B LEU* 3.7 32.6 - - + +
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Residues in contact with ASP 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B THR* 3.4 30.3 + - + +
457B ARG* 3.9 15.1 - - - +
458B GLU* 1.3 73.8 + - - +
460B ILE* 1.3 68.3 + - - +
462B GLU* 5.5 1.1 - - - -
463B PRO* 3.9 15.7 - - - +
1031D TYR* 4.6 15.9 + - - +
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ILE* 3.9 29.6 - - + -
417B VAL* 4.3 14.8 - - + -
418B THR* 3.5 26.9 - - - +
421B ALA* 4.6 7.5 - - + +
450B THR* 4.1 20.9 - - + -
451B VAL* 6.1 0.2 - - - -
454B ALA* 4.0 23.1 - - + -
457B ARG* 3.2 22.1 + - + +
459B ASP* 1.3 91.3 - - - +
461B THR* 1.3 65.6 + - - +
462B GLU 3.4 1.1 - - - -
463B PRO* 3.5 10.7 - - - +
464B ALA* 3.5 15.4 + - - +
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Residues in contact with THR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B VAL* 4.1 19.7 - - + +
454B ALA* 3.8 16.2 - - + -
455B GLY 3.8 20.4 - - - +
456B ASP 5.4 0.2 - - - -
457B ARG 3.4 11.0 + - - +
458B GLU* 3.5 18.0 - - - +
460B ILE* 1.3 75.2 - - - +
462B GLU* 1.3 67.0 + - - +
464B ALA* 3.5 4.4 + - - +
465B ILE* 3.1 30.4 + - - +
497B LEU* 4.5 19.9 - - + +
506B LEU* 3.9 14.9 - - - +
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 3.4 17.4 + - - +
459B ASP* 5.5 0.9 - - - -
460B ILE 3.4 0.2 - - - -
461B THR* 1.3 83.4 + - - +
463B PRO* 1.3 75.0 - - + +
465B ILE* 3.3 2.6 + - - +
466B CYS* 3.2 34.0 + - - -
505B PRO* 4.0 28.1 - - - +
506B LEU* 3.8 25.7 - - + +
509B ALA* 5.3 2.1 - - + +
1025D ILE* 5.1 11.4 - - + +
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Residues in contact with PRO 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B THR 5.4 2.0 - - - +
421B ALA* 4.1 8.3 - - + -
422B GLY* 3.9 29.6 - - - +
425B SER* 3.6 10.5 + - - +
459B ASP* 3.9 17.5 - - - +
460B ILE 3.5 13.7 - - - +
462B GLU* 1.3 97.3 - - + +
464B ALA* 1.3 61.2 + - - +
466B CYS* 3.1 11.7 + - + +
467B ALA* 3.0 19.1 + - - +
1025D ILE* 6.3 1.6 - - + -
1027D TYR* 4.0 19.7 - - + +
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Residues in contact with ALA 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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421B ALA* 4.8 8.4 - - + +
447B LEU* 4.9 16.7 - - + +
450B THR* 4.9 10.8 - - + -
451B VAL* 3.8 24.5 - - + -
460B ILE 3.5 16.3 + - - +
461B THR 3.8 0.9 - - - +
462B GLU 3.3 1.0 - - - -
463B PRO* 1.3 78.1 - - - +
465B ILE* 1.3 59.1 + - - +
467B ALA* 2.9 24.5 + - - +
468B LEU* 3.1 17.7 + - - +
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Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B VAL* 4.2 17.7 - - + -
461B THR 3.1 20.9 + - - +
462B GLU* 3.8 4.5 - - - +
464B ALA* 1.3 75.7 - - - +
466B CYS* 1.3 61.8 + - - +
468B LEU* 3.3 9.3 + - + +
469B ARG* 3.2 21.3 + - - +
493B VAL* 6.5 0.4 - - + -
494B VAL* 5.3 10.1 - - + -
497B LEU* 4.2 24.5 - - + -
506B LEU* 4.8 4.0 - - + -
509B ALA* 3.9 30.1 - - + +
510B THR* 4.1 14.8 - - + +
513B LEU* 3.7 28.1 - - + +
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Residues in contact with CYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B SER* 3.7 11.9 - - - +
462B GLU* 3.2 28.0 + - - -
463B PRO* 3.1 10.5 + - - +
465B ILE* 1.3 77.1 - - - +
467B ALA* 1.3 60.6 + - - +
469B ARG* 3.4 9.2 + - - +
470B HIS* 3.1 41.5 + - + +
509B ALA* 4.1 22.2 - - - -
1025D ILE* 4.9 14.4 - - - -
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ALA 5.2 2.0 - - - +
424B LEU* 4.8 5.4 - - + +
425B SER* 4.1 24.2 + - - +
428B THR* 4.4 2.9 + - - +
447B LEU* 4.4 18.2 - - + -
463B PRO 3.0 11.2 + - - +
464B ALA* 2.9 16.0 + - - +
466B CYS* 1.3 75.8 - - - +
468B LEU* 1.3 61.8 + - - +
470B HIS* 3.8 6.2 + - - +
471B LEU* 3.4 29.9 + - + +
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ILE* 4.5 27.6 - - + +
447B LEU* 3.6 39.3 - - + +
448B VAL* 4.6 19.5 - - + +
451B VAL* 5.3 3.1 - - + -
464B ALA 3.1 14.1 + - - +
465B ILE* 3.3 14.3 + - + +
467B ALA* 1.3 75.6 - - - +
469B ARG* 1.3 62.0 + - - +
471B LEU* 3.5 4.0 + - + +
472B THR* 3.0 31.6 + - - +
485B VAL* 5.3 13.9 - - + -
494B VAL* 6.0 2.9 - - + -
513B LEU* 4.3 25.2 - - + +
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Residues in contact with ARG 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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465B ILE 3.2 12.8 + - - +
466B CYS* 3.5 15.8 - - - +
467B ALA 3.3 0.2 - - - -
468B LEU* 1.3 76.4 - - - +
470B HIS* 1.3 70.5 + - + +
472B THR* 3.5 14.5 + - - -
473B SER* 4.1 6.2 - - - -
508B LYS* 4.9 13.5 + - - +
509B ALA* 4.2 30.6 - - - +
512B GLY* 3.8 28.4 + - - +
513B LEU* 4.4 10.3 - - + +
516B ASN* 3.5 21.2 + - - +
1021D LEU* 4.3 21.4 - - - +
1022D ASP* 5.0 0.8 - - - +
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Residues in contact with HIS 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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425B SER* 3.1 35.1 + - - -
428B THR* 3.2 29.6 - - + +
429B CYS* 3.3 23.0 - - - -
435B LYS* 3.0 23.3 + - - -
466B CYS* 3.1 28.9 + - + +
467B ALA* 4.1 1.9 - - - +
468B LEU 3.4 0.4 - - - -
469B ARG* 1.3 86.3 - - + +
471B LEU* 1.3 62.8 + - - +
472B THR 3.5 0.3 + - - -
473B SER* 3.5 11.0 + - - +
1022D ASP* 3.3 32.3 + - - +
1023D THR 4.6 8.4 + - - -
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Residues in contact with LEU 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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428B THR* 4.2 11.0 - - + +
435B LYS* 3.5 45.8 - - + +
438B VAL* 4.2 18.4 - - + -
439B CYS* 4.3 8.7 - - - -
444B ILE* 3.9 28.5 - - + -
447B LEU* 4.2 18.8 - - + -
467B ALA* 3.4 20.1 + - + +
468B LEU* 3.5 6.7 + - - +
469B ARG 3.3 0.6 - - - -
470B HIS* 1.3 75.4 - - - +
472B THR* 1.3 58.5 + - + +
473B SER 3.1 7.0 + - - -
475B HIS* 3.0 24.8 + - - +
478B ALA* 4.2 0.2 - - - -
481B ALA* 3.7 9.3 - - + +
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Residues in contact with THR 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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444B ILE* 5.8 1.6 - - + -
468B LEU 3.0 17.9 + - - +
469B ARG* 3.5 8.3 + - - -
470B HIS 3.4 0.6 - - - -
471B LEU* 1.3 75.5 - - + +
473B SER* 1.3 62.1 + - - +
478B ALA* 4.3 7.6 - - - -
481B ALA* 3.7 27.1 - - + +
482B GLN* 3.7 34.2 - - + +
485B VAL* 4.4 7.0 - - + -
513B LEU* 4.3 4.8 - - + +
516B ASN* 3.6 27.9 + - - +
517B LEU* 4.4 12.1 - - + -
519B LEU* 6.0 0.9 - - - +
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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