Contacts of the helix formed by residues 457 - 472 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A ILE* 4.3 24.5 - - - +
453A ARG 4.7 3.4 + - - -
454A ALA* 3.1 25.1 + - - +
455A GLY* 3.3 4.4 - - - -
456A ASP* 1.3 90.7 + - - +
458A GLU* 1.3 57.5 + - - +
459A ASP* 3.2 21.2 + - - +
460A ILE* 3.3 23.0 + - + +
461A THR* 3.4 15.8 + - - +
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Residues in contact with GLU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ASP 3.0 18.0 + - - +
457A ARG* 1.3 68.5 - - - +
459A ASP* 1.3 56.6 + - - +
460A ILE 3.2 4.3 - - - -
461A THR* 3.4 9.0 - - - +
462A GLU* 3.4 31.0 - - - +
501A PRO* 4.6 4.0 - - - +
502A SER* 3.8 14.2 + - - -
503A HIS* 3.5 45.6 + - - +
506A LEU* 3.7 32.7 - - + +
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Residues in contact with ASP 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A THR* 3.5 29.0 + - + +
457A ARG* 3.2 8.7 + - - +
458A GLU* 1.3 79.1 + - - +
460A ILE* 1.3 71.2 + - - +
462A GLU* 5.3 0.9 - - - -
463A PRO* 3.8 16.9 - - - +
1031C TYR* 4.5 15.9 + - - +
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Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 3.7 33.0 - - + -
417A VAL* 4.4 12.8 - - + -
418A THR* 3.3 27.8 - - - +
421A ALA* 4.5 6.2 - - + +
450A THR* 4.1 22.0 - - + -
454A ALA* 4.0 21.8 - - + -
457A ARG* 3.3 23.3 + - + +
459A ASP* 1.3 90.0 - - - +
461A THR* 1.3 65.5 + - - +
462A GLU 3.4 1.3 - - - -
463A PRO* 3.3 11.2 - - - +
464A ALA* 3.5 14.6 + - - +
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Residues in contact with THR 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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451A VAL* 4.5 17.3 - - + +
454A ALA* 3.8 20.4 - - + -
455A GLY 3.8 17.0 - - - +
456A ASP 5.3 0.2 - - - -
457A ARG 3.5 12.1 - - - +
458A GLU* 3.4 17.8 - - - +
460A ILE* 1.3 76.8 - - - +
462A GLU* 1.3 68.0 + - - +
464A ALA* 3.4 5.6 + - - +
465A ILE* 3.0 30.4 + - - +
497A LEU* 4.6 15.7 - - + -
506A LEU* 3.9 18.6 - - - +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU* 3.4 17.7 + - - +
459A ASP* 5.4 0.7 - - - -
461A THR* 1.3 82.7 + - - +
463A PRO* 1.3 72.4 - - + +
465A ILE* 3.4 2.6 + - - +
466A CYS* 3.3 34.7 + - - -
505A PRO* 4.0 28.8 - - - +
506A LEU* 3.8 26.1 - - + +
509A ALA* 5.2 2.1 - - + +
1025C ILE* 5.0 12.9 - - + +
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Residues in contact with PRO 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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418A THR 5.4 1.3 - - - +
421A ALA* 4.1 7.9 - - + -
422A GLY* 3.9 29.8 - - - +
425A SER* 3.5 17.9 + - - +
459A ASP* 3.8 17.5 - - - +
460A ILE 3.3 14.4 - - - +
462A GLU* 1.3 98.5 - - + +
464A ALA* 1.3 60.5 + - - +
466A CYS* 3.4 4.9 + - + -
467A ALA* 3.1 16.9 + - - +
1027C TYR* 4.0 20.0 - - + +
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Residues in contact with ALA 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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421A ALA* 4.7 8.0 - - + +
447A LEU* 5.0 15.2 - - + +
450A THR* 4.9 12.8 - - + -
451A VAL* 3.8 22.2 - - + -
460A ILE 3.5 14.8 + - - +
461A THR 3.4 4.0 + - - +
462A GLU 3.3 0.6 - - - -
463A PRO* 1.3 76.8 - - - +
465A ILE* 1.3 61.4 + - - +
467A ALA* 2.9 23.8 + - - +
468A LEU* 3.2 16.9 + - - +
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Residues in contact with ILE 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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451A VAL* 4.3 17.3 - - + -
461A THR 3.0 23.2 + - - +
462A GLU* 3.9 4.9 - - - +
464A ALA* 1.3 75.2 - - - +
466A CYS* 1.3 61.9 + - - +
468A LEU* 3.3 10.7 + - + +
469A ARG* 3.1 21.0 + - - +
494A VAL* 5.3 9.0 - - + -
497A LEU* 4.2 25.6 - - + -
506A LEU* 4.8 5.2 - - + +
509A ALA* 3.8 33.4 - - + +
510A THR* 4.1 12.3 - - + +
513A LEU* 3.9 24.4 - - + +
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Residues in contact with CYS 466 (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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425A SER* 3.8 11.7 - - - +
462A GLU* 3.3 23.6 + - - -
463A PRO* 3.6 9.4 - - - +
464A ALA 3.2 0.6 - - - -
465A ILE* 1.3 79.4 - - - +
467A ALA* 1.3 57.0 + - - +
469A ARG* 3.5 11.4 + - - +
470A HIS* 3.1 45.6 + - + +
509A ALA* 3.9 21.8 - - - -
1025C ILE* 5.9 7.6 - - - -
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Residues in contact with ALA 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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421A ALA 5.1 2.0 - - - +
424A LEU* 4.7 6.1 - - + +
425A SER* 4.0 23.8 + - - +
428A THR* 4.4 2.9 - - - +
447A LEU* 4.5 17.9 - - + -
463A PRO 3.1 12.4 + - - +
464A ALA* 2.9 15.4 + - - +
466A CYS* 1.3 77.2 - - - +
468A LEU* 1.3 61.0 + - - +
470A HIS* 4.0 5.9 + - - +
471A LEU* 3.2 30.8 + - + +
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Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ILE* 4.5 25.8 - - + +
447A LEU* 3.6 39.5 - - + +
448A VAL* 4.7 18.6 - - + +
451A VAL* 5.3 4.3 - - + -
464A ALA 3.2 13.9 + - - +
465A ILE* 3.3 15.0 + - + +
467A ALA* 1.3 76.3 - - - +
469A ARG* 1.3 63.1 + - - +
471A LEU* 3.5 4.5 + - + +
472A THR* 2.9 32.4 + - + +
485A VAL* 5.3 13.7 - - + -
494A VAL* 5.9 3.1 - - + -
513A LEU* 4.2 24.7 - - + -
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Residues in contact with ARG 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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465A ILE 3.1 15.9 + - - +
466A CYS* 3.6 13.1 - - - +
468A LEU* 1.3 76.1 - - - +
470A HIS* 1.3 71.9 + - + +
472A THR* 3.3 16.8 + - - -
473A SER* 4.1 3.8 - - - -
508A LYS* 4.5 13.7 + - - +
509A ALA* 4.1 27.5 - - - +
512A GLY* 3.8 32.9 + - - +
513A LEU* 4.2 11.4 - - + +
516A ASN* 3.5 22.1 + - - +
1021C LEU* 6.1 3.4 - - - +
1022C ASP* 4.9 1.0 - - - +
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Residues in contact with HIS 470 (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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425A SER* 3.1 35.5 + - - -
426A ASN* 5.9 0.2 - - - -
428A THR* 3.2 27.2 - - + +
429A CYS* 3.4 23.6 - - - -
435A LYS* 3.3 23.2 + - - -
466A CYS* 3.1 28.3 + - + +
467A ALA* 4.2 1.7 - - - +
468A LEU 3.3 0.2 - - - -
469A ARG* 1.3 85.3 - - + +
471A LEU* 1.3 62.3 + - - +
472A THR 3.4 0.7 + - - -
473A SER* 3.4 10.0 + - - +
1022C ASP* 3.3 29.8 - - + +
1023C THR 4.4 14.2 + - - -
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Residues in contact with LEU 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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428A THR* 4.1 11.4 - - + +
435A LYS* 3.4 44.4 - - + +
438A VAL* 4.3 18.2 - - + -
439A CYS* 4.4 8.3 - - - -
444A ILE* 3.9 29.8 - - + -
447A LEU* 4.1 17.5 - - + -
467A ALA* 3.2 21.3 + - + +
468A LEU* 3.5 6.7 + - - +
469A ARG 3.3 0.6 - - - -
470A HIS* 1.3 76.5 - - - +
472A THR* 1.3 58.6 + - + +
473A SER 3.1 7.3 + - - -
475A HIS* 3.0 25.5 + - - +
478A ALA* 4.2 0.5 - - - -
481A ALA* 3.7 9.4 - - + +
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Residues in contact with THR 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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444A ILE* 5.9 1.6 - - + -
468A LEU 2.9 18.3 + - - +
469A ARG* 3.3 10.2 + - - -
470A HIS 3.3 0.8 - - - -
471A LEU* 1.3 74.8 - - + +
473A SER* 1.3 62.0 + - - +
478A ALA* 4.4 7.9 - - - -
481A ALA* 3.8 26.7 - - + +
482A GLN* 3.8 33.4 - - + +
485A VAL* 4.5 11.4 - - + -
513A LEU* 4.1 5.3 - - + +
516A ASN* 3.6 27.4 - - - +
517A LEU* 4.5 7.2 - - + -
519A LEU* 6.0 0.5 - - - +
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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
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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