Contacts of the helix formed by residues 413 - 428 (chain C) in PDB entry 1JPW
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C GLN* 4.3 18.0 - - - +
379C GLN* 4.9 3.3 + - - -
411C SER* 3.3 3.7 + - - +
412C ASP* 1.3 86.6 - - - +
414C ILE* 1.3 73.5 + - - +
415C ASN* 3.1 18.0 + - - +
416C VAL* 3.0 37.7 + - + +
417C VAL* 3.0 16.5 + - - +
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Residues in contact with ILE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412C ASP 3.5 11.3 + - - +
413C ASP* 1.3 77.9 - - - +
415C ASN* 1.3 58.4 + - - +
417C VAL* 3.1 12.1 + - + +
418C THR* 2.8 38.4 + - - +
453C ARG* 4.7 12.1 - - + +
457C ARG* 4.9 12.3 - - - +
460C ILE* 3.9 23.8 - - + -
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Residues in contact with ASN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLN* 3.6 21.0 - - - +
383C TRP* 5.9 5.3 - - + +
413C ASP* 3.1 11.2 + - - +
414C ILE* 1.3 83.8 - - - +
416C VAL* 1.3 62.3 + - - +
418C THR* 3.8 9.0 + - - -
419C CYS* 3.2 31.3 + - - -
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Residues in contact with VAL 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLN* 4.4 13.2 - - + +
378C VAL* 4.9 6.5 - - + -
379C GLN* 4.5 9.9 - - + +
382C LEU* 3.7 28.8 - - + +
408C LEU* 4.0 23.6 - - + +
411C SER* 3.7 20.9 - - - +
413C ASP* 3.0 34.5 + - + +
415C ASN* 1.3 76.9 - - - +
417C VAL* 1.3 64.0 + - - +
420C ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU 4.0 10.8 - - - +
409C LEU* 3.6 24.0 - - + +
411C SER* 3.7 17.3 - - - +
413C ASP 3.0 16.3 + - - +
414C ILE* 3.2 10.5 - - + +
416C VAL* 1.3 75.7 - - - +
418C THR* 1.3 65.4 + - - +
420C ALA* 3.5 3.2 + - - +
421C ALA* 3.0 22.9 + - - +
450C THR* 3.4 31.6 - - + -
453C ARG* 3.7 17.0 - - + +
460C ILE* 4.1 11.9 - - + -
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Residues in contact with THR 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386C ARG* 5.0 13.3 + - - +
414C ILE* 2.8 24.9 + - - +
415C ASN* 3.9 11.0 + - - -
416C VAL 3.4 0.2 - - - -
417C VAL* 1.3 74.0 - - - +
419C CYS* 1.3 63.0 + - - +
421C ALA* 3.4 3.5 + - - +
422C GLY* 3.2 18.0 + - - -
459C ASP* 3.2 44.6 - - - +
460C ILE* 3.3 25.6 - - + +
463C PRO* 4.9 1.7 - - - +
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Residues in contact with CYS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C GLN* 3.7 11.2 - - - -
382C LEU* 4.0 24.7 - - + +
383C TRP* 3.6 22.7 - - - -
386C ARG* 3.6 36.8 - - - +
415C ASN* 3.2 20.0 + - - +
416C VAL 4.0 2.7 - - - +
418C THR* 1.3 77.5 - - - +
420C ALA* 1.3 66.5 + - - +
422C GLY* 3.1 2.6 + - - -
423C ILE* 3.0 29.8 + - - +
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Residues in contact with ALA 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C LEU* 4.9 4.0 - - + +
405C LEU* 3.8 31.7 - - + +
408C LEU* 4.4 11.4 - - + +
409C LEU* 4.0 9.4 - - + -
416C VAL 3.1 17.4 + - - +
417C VAL* 3.9 3.6 - - - +
418C THR 3.4 0.2 - - - -
419C CYS* 1.3 79.8 - - - +
421C ALA* 1.3 56.5 + - - +
423C ILE* 3.6 10.9 + - - +
424C LEU* 3.1 32.9 + - - +
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C LEU* 4.1 12.3 - - + +
417C VAL 3.0 18.2 + - - +
418C THR 3.6 5.8 - - - +
419C CYS 3.1 0.2 - - - -
420C ALA* 1.3 76.6 - - - +
422C GLY* 1.3 64.8 + - - +
424C LEU* 3.3 7.5 + - - +
425C SER* 3.0 22.3 + - - -
447C LEU* 5.2 2.7 - - + -
450C THR* 5.2 1.1 - - + -
460C ILE* 4.4 15.5 - - + -
463C PRO* 4.1 10.5 - - + +
464C ALA* 4.4 18.8 - - + -
467C ALA* 4.8 1.6 - - - +
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Residues in contact with GLY 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386C ARG* 4.7 3.6 - - - -
418C THR 3.2 7.7 + - - -
419C CYS 3.1 6.7 + - - -
421C ALA* 1.3 78.8 - - - +
423C ILE* 1.3 61.9 + - - +
425C SER* 3.1 16.3 - - - -
426C ASN* 3.1 15.4 + - - -
463C PRO* 3.7 19.6 - - - +
21F PHE* 4.2 20.3 - - - -
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C MET* 5.0 2.2 - - + -
382C LEU* 3.6 37.7 - - + +
385C LEU* 3.7 26.7 - - + +
386C ARG* 3.8 19.5 - - + -
389C SER* 4.4 8.5 - - - -
401C LEU* 5.1 0.9 - - + -
405C LEU* 3.4 28.7 - - + -
419C CYS 3.0 22.4 + - - +
420C ALA 3.8 4.5 - - - +
422C GLY* 1.3 72.9 - - - +
424C LEU* 1.3 59.7 + - - +
425C SER 3.1 0.2 + - - -
426C ASN* 3.3 1.4 + - - +
427C LEU* 2.8 43.0 + - + +
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Residues in contact with LEU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C LEU* 4.0 29.6 - - + +
405C LEU* 3.9 28.5 - - + +
406C VAL* 4.3 7.4 - - + +
409C LEU* 3.8 35.0 - - + -
420C ALA 3.1 22.1 + - - +
421C ALA* 3.7 4.7 - - - +
423C ILE* 1.3 77.0 - - - +
425C SER* 1.3 52.0 + - - +
427C LEU* 3.9 3.8 - - - -
428C THR* 2.5 42.2 + - + +
438C VAL* 4.1 18.4 - - + -
447C LEU* 4.4 11.2 - - + -
467C ALA* 4.4 9.6 - - + +
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Residues in contact with SER 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ALA 3.0 13.7 + - - -
422C GLY* 3.1 14.6 - - - -
423C ILE 3.0 0.2 - - - -
424C LEU* 1.3 77.3 - - - +
426C ASN* 1.3 61.4 + - - +
428C THR* 2.7 19.3 + - - -
463C PRO* 3.5 23.1 + - - -
466C CYS* 3.6 16.3 - - - +
467C ALA* 3.9 8.5 - - - +
470C HIS* 2.9 21.1 + - - -
19F ILE* 3.8 14.3 - - - +
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Residues in contact with ASN 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C SER* 2.8 42.4 + - - +
390C ASP* 4.1 4.1 - - - +
393C THR* 3.5 11.2 - - - +
422C GLY 3.1 6.7 + - - +
425C SER* 1.3 75.5 + - - +
427C LEU* 1.3 58.4 + - - +
428C THR 2.9 4.9 - - - -
429C CYS* 2.9 30.5 + - - +
18F LEU* 3.6 16.1 - - + +
19F ILE* 3.0 35.8 + - - +
21F PHE* 3.2 29.4 - - - -
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Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C MET* 3.6 20.4 - - + -
389C SER* 4.3 9.2 - - - +
392C ALA* 4.0 23.8 - - + +
393C THR* 5.1 5.6 - - - +
398C MET* 4.4 7.2 - - - -
401C LEU* 3.8 27.8 - - + -
402C LEU* 3.6 27.1 - - + -
405C LEU* 4.1 2.2 - - + -
423C ILE* 2.8 32.8 + - + +
424C LEU 4.2 2.0 - - - +
426C ASN* 1.3 75.2 - - - +
428C THR* 1.3 58.8 + - - +
429C CYS 3.4 1.0 + - - -
431C ASN* 4.3 4.0 - - - +
434C ASN* 2.5 40.1 + - - +
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Residues in contact with THR 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C LEU* 2.5 27.8 + - + +
425C SER* 2.7 15.2 + - - -
426C ASN 2.9 0.2 + - - -
427C LEU* 1.3 81.8 - - + +
429C CYS* 1.3 58.9 + - - +
431C ASN 4.4 2.7 - - - -
434C ASN* 4.4 5.8 - - + +
435C LYS* 3.1 37.4 - - - -
438C VAL* 3.7 30.1 - - + -
467C ALA* 4.2 5.3 - - + +
470C HIS* 3.3 21.6 + - - +
471C LEU* 3.9 15.3 - - + -
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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