Contacts of the helix formed by residues 413 - 427 (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 ASP 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375B GLN* 4.5 14.4 + - - -
379B GLN* 5.1 3.1 - - - +
411B SER* 3.0 5.6 + - - +
412B ASP* 1.3 84.2 - - - +
414B ILE* 1.3 62.3 + - - +
415B ASN* 3.0 41.3 + - - +
416B VAL* 3.2 36.5 + - + +
417B VAL* 3.4 14.3 + - - +
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Residues in contact with ILE 414 (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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412B ASP 3.4 6.8 + - - +
413B ASP* 1.3 73.7 + - - +
415B ASN* 1.3 76.9 + - - +
416B VAL 3.2 0.2 - - - -
417B VAL* 3.3 11.2 + - + +
418B THR* 3.1 24.2 + - - +
453B ARG* 5.2 12.8 - - - +
454B ALA* 6.4 0.4 - - - -
457B ARG* 4.2 20.2 - - - +
460B ILE* 3.9 28.0 - - + -
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Residues in contact with ASN 415 (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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379B GLN* 4.1 20.3 + - - +
413B ASP* 3.0 17.7 + - - +
414B ILE* 1.3 89.3 - - - +
416B VAL* 1.3 60.0 + - - +
417B VAL 3.3 0.2 - - - -
418B THR* 3.8 6.7 + - - -
419B CYS* 3.4 28.9 + - - +
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Residues in contact with VAL 416 (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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378B VAL* 5.2 11.9 - - + -
379B GLN* 4.5 7.2 - - - +
382B LEU* 3.9 26.7 - - + +
408B LEU* 4.4 29.7 - - + +
411B SER* 4.1 11.2 - - - +
413B ASP* 3.2 37.0 + - + +
414B ILE 3.2 0.2 - - - -
415B ASN* 1.3 77.6 - - - +
417B VAL* 1.3 62.4 + - - +
419B CYS 4.1 0.2 - - - -
420B ALA* 3.3 22.3 + - - +
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Residues in contact with VAL 417 (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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408B LEU 4.9 2.7 - - - -
409B LEU* 3.6 30.6 - - + +
411B SER* 4.2 8.7 - - - +
413B ASP 3.5 15.0 - - - +
414B ILE* 3.3 14.5 + - + +
416B VAL* 1.3 76.7 - - - +
418B THR* 1.3 60.0 + - - +
420B ALA* 3.3 5.4 + - - +
421B ALA* 2.9 28.4 + - - +
450B THR* 4.1 26.5 - - + -
453B ARG* 4.1 21.1 - - - +
460B ILE* 4.3 12.3 - - + -
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Residues in contact with THR 418 (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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386B ARG* 4.4 16.6 + - - +
414B ILE* 3.1 16.5 + - - +
415B ASN* 4.0 7.3 - - - -
416B VAL 3.5 0.2 - - - -
417B VAL* 1.3 79.0 - - - +
419B CYS* 1.3 62.4 + - - +
421B ALA* 3.5 17.2 + - - +
422B GLY* 3.5 5.9 + - - -
459B ASP* 3.4 36.5 + - + +
460B ILE* 3.5 21.8 - - - +
463B PRO* 5.4 1.7 - - - +
1031D TYR* 5.5 3.6 - - + +
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Residues in contact with CYS 419 (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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379B GLN* 3.9 20.4 - - - -
382B LEU* 3.9 29.2 - - + -
383B TRP* 4.4 10.5 - - - -
386B ARG* 4.0 35.7 - - + +
415B ASN 3.4 18.6 + - - +
417B VAL 3.3 0.4 - - - -
418B THR* 1.3 76.7 - - - +
420B ALA* 1.3 65.9 + - - +
421B ALA 3.4 0.2 + - - -
422B GLY* 3.6 2.1 + - - -
423B ILE* 3.3 28.2 + - + +
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Residues in contact with ALA 420 (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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382B LEU* 5.1 3.1 - - + +
405B LEU* 4.4 28.8 - - + +
408B LEU* 4.5 14.6 - - + -
409B LEU* 4.5 9.9 - - + +
416B VAL 3.3 18.2 + - - +
417B VAL* 3.3 5.5 + - - +
419B CYS* 1.3 77.4 - - - +
421B ALA* 1.3 67.5 + - - +
423B ILE* 3.5 7.8 + - - +
424B LEU* 3.3 26.7 + - - +
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Residues in contact with ALA 421 (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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409B LEU* 4.5 11.4 - - + +
417B VAL* 2.9 17.9 + - + +
418B THR* 3.5 10.5 - - - +
420B ALA* 1.3 80.3 - - - +
422B GLY* 1.3 62.1 + - - +
424B LEU* 3.4 5.2 + - - +
425B SER* 3.2 20.1 + - - -
447B LEU* 6.0 3.4 - - + +
450B THR* 5.6 2.5 - - + -
460B ILE* 4.6 15.5 - - + +
463B PRO* 4.1 19.0 - - + +
464B ALA* 4.8 9.0 - - + +
467B ALA* 5.2 2.3 - - - +
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Residues in contact with GLY 422 (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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386B ARG* 5.1 3.8 - - - -
418B THR 3.5 9.1 + - - -
419B CYS 3.6 1.8 + - - -
420B ALA 3.4 0.2 - - - -
421B ALA* 1.3 79.4 - - - +
423B ILE* 1.3 62.4 + - - +
425B SER* 3.1 5.0 + - - -
426B ASN* 3.0 23.0 + - - +
463B PRO* 3.9 9.3 - - - +
1027D TYR* 3.6 33.9 - - - -
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Residues in contact with ILE 423 (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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363B MET* 5.7 3.1 - - + -
382B LEU* 4.3 13.5 - - + +
385B LEU* 3.6 38.6 - - + +
386B ARG* 3.9 23.3 - - + +
389B SER* 4.8 9.0 - - - -
401B LEU* 5.6 2.0 - - + -
405B LEU* 3.6 35.7 - - + -
419B CYS 3.3 19.3 + - - +
420B ALA* 3.9 5.2 - - - +
421B ALA 3.3 0.6 - - - -
422B GLY* 1.3 75.9 - - - +
424B LEU* 1.3 63.9 + - - +
426B ASN* 3.2 2.8 + - - +
427B LEU* 3.1 36.6 + - + +
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Residues in contact with LEU 424 (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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402B LEU* 3.6 28.4 - - + +
405B LEU* 4.1 29.6 - - + +
406B VAL* 4.5 11.0 - - + -
409B LEU* 4.0 31.4 - - + -
420B ALA 3.3 16.3 + - - +
421B ALA* 3.8 4.7 - - - +
423B ILE* 1.3 79.1 - - - +
425B SER* 1.3 59.4 + - - +
427B LEU* 3.9 3.4 + - - +
428B THR* 2.7 33.6 + - - +
438B VAL* 4.5 15.5 - - + -
447B LEU* 4.6 13.7 - - + -
467B ALA* 4.8 8.3 - - + +
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Residues in contact with SER 425 (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 3.2 12.7 + - - -
422B GLY* 3.1 14.8 - - - -
423B ILE 3.1 0.4 - - - -
424B LEU* 1.3 79.0 - - - +
426B ASN* 1.3 64.7 + - - +
428B THR 3.7 1.6 + - - -
429B CYS* 3.7 0.2 - - - -
463B PRO* 3.6 25.1 + - - +
466B CYS* 3.7 15.8 - - - +
467B ALA* 4.1 12.0 - - - +
470B HIS* 3.1 33.6 + - - -
1025D ILE* 5.5 4.2 - - - +
1027D TYR* 4.7 4.8 + - - -
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Residues in contact with ASN 426 (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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389B SER* 3.0 40.1 + - - +
390B ASP* 3.8 10.9 - - - +
393B THR* 3.2 18.1 - - + +
422B GLY 3.0 13.8 + - - +
423B ILE 3.2 2.9 + - - +
425B SER* 1.3 77.0 + - - +
427B LEU* 1.3 59.2 + - - +
428B THR 2.9 10.3 + - - -
429B CYS* 3.1 16.9 + - - -
470B HIS* 5.9 0.2 - - - -
1024D PRO* 3.7 8.8 - - - +
1025D ILE* 3.3 44.9 + - - +
1027D TYR* 3.7 9.1 + - - -
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Residues in contact with LEU 427 (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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363B MET* 4.3 7.6 - - + -
389B SER* 4.7 8.1 - - - +
392B ALA* 3.9 33.4 - - + +
393B THR* 4.4 7.8 - - - +
398B MET* 4.1 27.4 - - + -
401B LEU* 4.4 7.6 - - + -
402B LEU* 4.1 28.9 - - + -
405B LEU* 4.4 5.6 - - + -
423B ILE* 3.1 36.0 + - + +
424B LEU 4.6 2.0 - - - +
426B ASN* 1.3 75.4 - - + +
428B THR* 1.3 58.9 + - - +
429B CYS 3.4 1.4 + - - +
431B ASN* 4.4 4.3 - - - +
434B ASN* 3.6 30.7 + - - +
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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
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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