Contacts of the helix formed by residues 413 - 427 (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 ASP 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLN* 4.6 13.7 + - - -
379A GLN* 5.1 1.7 - - - +
411A SER* 2.9 9.8 + - - +
412A ASP* 1.3 85.6 - - - +
414A ILE* 1.3 60.5 + - - +
415A ASN* 3.1 39.5 + - - +
416A VAL* 3.2 28.0 + - + +
417A VAL* 3.3 25.9 + - - +
453A ARG* 5.7 0.2 - - - -
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Residues in contact with ILE 414 (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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412A ASP 3.5 5.5 + - - +
413A ASP* 1.3 73.2 + - - +
415A ASN* 1.3 70.1 + - - +
416A VAL 3.3 0.4 - - - -
417A VAL* 3.9 12.1 - - + -
418A THR* 3.0 20.1 + - - -
453A ARG* 5.0 15.5 - - - +
454A ALA* 6.1 1.6 - - - -
457A ARG* 4.3 19.3 - - - +
460A ILE* 3.7 29.2 - - + -
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Residues in contact with ASN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLN* 3.8 21.7 + - - +
413A ASP* 3.1 16.7 + - - +
414A ILE* 1.3 89.8 - - - +
416A VAL* 1.3 63.7 + - - +
417A VAL 3.3 0.4 - - - -
418A THR* 4.0 5.8 - - - -
419A CYS* 3.3 29.8 + - - +
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Residues in contact with VAL 416 (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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378A VAL* 5.3 10.1 - - + -
379A GLN* 4.3 7.6 - - - +
382A LEU* 3.8 28.2 - - + +
408A LEU* 4.1 29.6 - - + +
411A SER* 4.1 9.9 - - - +
413A ASP* 3.2 37.9 - - + +
415A ASN* 1.3 79.6 - - - +
417A VAL* 1.3 58.2 + - - +
419A CYS 4.2 0.2 - - - -
420A ALA* 3.2 26.4 + - + +
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Residues in contact with VAL 417 (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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408A LEU 4.4 4.5 - - - -
409A LEU* 3.5 30.3 - - + +
411A SER* 4.2 16.2 - - - +
413A ASP 3.3 16.8 - - - +
414A ILE* 3.9 12.8 - - + +
415A ASN 3.3 0.2 - - - -
416A VAL* 1.3 76.9 - - - +
418A THR* 1.3 59.9 + - - +
420A ALA* 3.3 3.6 + - - +
421A ALA* 2.9 28.2 + - - +
450A THR* 4.1 26.2 - - + -
453A ARG* 4.2 14.4 - - - +
460A ILE* 4.4 12.3 - - + -
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Residues in contact with THR 418 (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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386A ARG* 4.3 17.7 + - - +
414A ILE* 3.0 19.6 + - - +
415A ASN* 4.2 6.3 - - - -
417A VAL* 1.3 79.8 - - - +
419A CYS* 1.3 61.7 + - - +
421A ALA* 3.3 20.4 + - - +
422A GLY* 3.5 5.7 + - - -
459A ASP* 3.5 36.6 + - + +
460A ILE* 3.3 23.1 - - - +
463A PRO* 5.4 1.6 - - + +
1031C TYR* 5.8 2.0 - - - +
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Residues in contact with CYS 419 (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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379A GLN* 4.0 18.4 - - - -
382A LEU* 3.9 36.8 - - + +
383A TRP* 4.4 8.5 - - - -
386A ARG* 4.1 34.9 - - - +
415A ASN 3.3 17.7 + - - +
418A THR* 1.3 79.6 - - - +
420A ALA* 1.3 63.1 + - - +
421A ALA 3.5 0.3 + - - -
422A GLY* 3.8 1.4 + - - -
423A ILE* 3.2 28.4 + - - +
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Residues in contact with ALA 420 (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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382A LEU* 5.2 5.4 - - + +
405A LEU* 4.4 23.6 - - + +
408A LEU* 4.3 17.3 - - + +
409A LEU* 4.6 7.9 - - + -
416A VAL 3.2 19.7 + - - +
417A VAL* 3.3 4.9 + - - +
418A THR 3.3 0.4 - - - -
419A CYS* 1.3 77.3 - - - +
421A ALA* 1.3 67.3 + - - +
423A ILE* 3.7 8.5 + - - +
424A LEU* 3.3 26.3 + - - +
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Residues in contact with ALA 421 (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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409A LEU* 4.7 11.0 - - + +
417A VAL* 2.9 13.5 + - + +
418A THR* 3.4 13.7 - - - +
419A CYS 3.2 0.2 - - - -
420A ALA* 1.3 80.0 - - - +
422A GLY* 1.3 64.1 + - - +
424A LEU* 3.3 4.5 + - - +
425A SER* 3.1 20.6 + - - -
447A LEU* 6.0 3.7 - - + +
450A THR* 5.6 2.0 - - + -
460A ILE* 4.5 15.5 - - + +
463A PRO* 4.1 18.8 - - + +
464A ALA* 4.7 8.4 - - + +
467A ALA* 5.1 1.7 - - - +
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Residues in contact with GLY 422 (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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386A ARG* 5.1 4.5 - - - -
389A SER* 5.7 0.2 - - - -
418A THR 3.5 8.0 + - - -
419A CYS 3.8 2.2 + - - -
421A ALA* 1.3 79.3 - - - +
423A ILE* 1.3 62.3 + - - +
425A SER* 3.1 5.4 + - - -
426A ASN* 3.0 22.9 + - - +
463A PRO* 3.9 8.8 - - - +
1027C TYR* 3.7 34.0 - - - -
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Residues in contact with ILE 423 (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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363A MET* 5.6 3.1 - - + -
382A LEU* 4.2 13.2 - - + +
385A LEU* 3.4 40.8 - - + +
386A ARG* 3.8 21.0 - - - +
389A SER* 4.6 8.5 - - - -
401A LEU* 5.8 1.6 - - + -
405A LEU* 3.7 36.1 - - + -
419A CYS 3.2 22.7 + - - +
420A ALA* 4.0 4.3 - - - +
421A ALA 3.3 0.8 - - - -
422A GLY* 1.3 74.1 - - - +
424A LEU* 1.3 63.4 + - - +
426A ASN* 3.2 2.1 + - - +
427A LEU* 3.0 36.4 + - + +
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Residues in contact with LEU 424 (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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402A LEU* 3.6 28.0 - - + -
405A LEU* 4.1 28.3 - - + +
406A VAL* 4.4 12.3 - - + -
409A LEU* 4.0 30.5 - - + -
420A ALA 3.3 13.1 + - - +
421A ALA* 3.3 8.6 + - - +
423A ILE* 1.3 79.1 - - - +
425A SER* 1.3 58.8 + - - +
427A LEU* 4.7 2.6 - - - +
428A THR* 2.6 33.2 + - - +
438A VAL* 4.5 16.2 - - + -
447A LEU* 4.6 11.9 - - + -
467A ALA* 4.7 8.3 - - + +
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Residues in contact with SER 425 (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 3.1 10.2 + - - -
422A GLY* 3.1 17.2 + - - -
424A LEU* 1.3 80.0 - - - +
426A ASN* 1.3 62.2 + - - +
428A THR 3.6 2.3 + - - -
463A PRO* 3.5 27.8 + - - +
466A CYS* 3.8 15.4 - - - +
467A ALA* 4.0 11.6 - - - +
470A HIS* 3.1 32.1 + - - -
1027C TYR* 4.6 5.2 + - - -
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Residues in contact with ASN 426 (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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389A SER* 2.9 41.6 + - - +
390A ASP* 3.4 15.6 - - - +
393A THR* 3.1 21.9 - - - +
422A GLY 3.0 12.3 + - - +
423A ILE 3.2 0.9 + - - +
425A SER* 1.3 77.1 + - - +
427A LEU* 1.3 61.6 + - - +
428A THR 3.0 6.8 + - - -
429A CYS* 3.2 13.6 + - - +
470A HIS* 5.9 0.2 - - - -
1024C PRO* 3.6 8.8 - - - +
1025C ILE* 3.2 41.9 + - - +
1027C TYR* 3.7 10.5 + - - -
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Residues in contact with LEU 427 (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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363A MET* 4.2 9.9 - - + -
389A SER* 4.4 8.5 - - - +
392A ALA* 3.8 36.8 - - + +
393A THR* 4.4 6.4 - - - +
398A MET* 4.2 21.5 - - + -
401A LEU* 4.6 6.3 - - + -
402A LEU* 4.1 29.2 - - + -
405A LEU* 4.3 6.3 - - + -
423A ILE* 3.0 35.3 + - + +
424A LEU 4.7 1.3 - - - +
426A ASN* 1.3 77.2 - - + +
428A THR* 1.3 58.9 + - - +
429A CYS 3.3 3.9 + - - +
431A ASN* 4.4 3.3 - - - +
434A ASN* 3.5 32.1 + - - +
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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