Contacts of the helix formed by residues 457 - 472 (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 ARG 457 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414C ILE* 4.9 10.3 - - - +
453C ARG 4.1 7.7 + - - -
454C ALA* 2.8 37.1 + - - +
455C GLY* 3.2 3.8 - - - -
456C ASP* 1.3 89.0 + - - +
458C GLU* 1.3 57.0 + - - +
459C ASP* 3.0 14.4 + - + +
460C ILE* 3.2 34.1 + - + +
461C THR* 3.2 17.5 + - - +
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Residues in contact with GLU 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C ASP* 2.9 18.7 + - - +
457C ARG* 1.3 67.6 - - - +
459C ASP* 1.3 59.8 + - - +
460C ILE 3.1 6.1 - - - -
461C THR* 3.1 10.1 - - - +
462C GLU* 3.2 33.7 + - - +
463C PRO* 4.0 0.3 - - - +
497C LEU* 6.0 0.2 - - + -
501C PRO* 3.7 5.5 - - - +
502C SER* 3.6 8.4 + - - +
503C HIS* 3.1 56.7 + - - +
506C LEU* 3.6 32.0 + - + +
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Residues in contact with ASP 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 5.1 5.0 + - - -
418C THR* 3.2 27.0 - - + +
457C ARG* 3.0 5.6 - - + -
458C GLU* 1.3 78.0 - - - +
460C ILE* 1.3 64.2 + - + +
463C PRO* 3.6 14.5 - - - +
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Residues in contact with ILE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ILE* 3.9 24.2 - - + +
417C VAL* 4.1 24.7 - - + -
418C THR* 3.3 33.9 - - + +
421C ALA* 4.4 5.6 - - + -
450C THR* 4.2 13.5 - - + -
451C VAL* 6.3 0.2 - - - -
453C ARG* 6.5 0.2 - - + -
454C ALA* 4.1 22.0 - - + -
457C ARG* 3.2 21.2 + - + +
458C GLU 3.1 0.2 - - - -
459C ASP* 1.3 86.5 - - + +
461C THR* 1.3 61.6 + - - +
462C GLU 3.3 1.8 - - - -
463C PRO* 3.3 6.2 - - - +
464C ALA* 3.1 30.1 + - + +
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Residues in contact with THR 461 (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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451C VAL* 4.2 15.3 - - + +
454C ALA* 3.5 21.1 - - + -
455C GLY 3.8 16.4 - - - +
457C ARG 3.3 13.0 - - - +
458C GLU* 3.1 17.8 - - - +
460C ILE* 1.3 75.9 - - - +
462C GLU* 1.3 59.9 + - - +
464C ALA* 4.4 4.0 - - - -
465C ILE* 2.7 43.2 + - - +
497C LEU* 4.5 13.0 - - + +
506C LEU* 3.7 18.9 - - - +
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Residues in contact with GLU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C GLU* 3.2 19.8 + - - +
461C THR* 1.3 78.1 + - - +
463C PRO* 1.3 75.8 - - + +
465C ILE* 3.2 2.3 + - - +
466C CYS* 2.9 36.7 + - - -
505C PRO* 3.4 43.3 - - - +
506C LEU* 3.6 21.0 + - + +
509C ALA* 4.8 1.1 - - + +
19F ILE* 5.0 14.6 - - + +
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Residues in contact with PRO 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C THR 4.9 2.0 - - - +
421C ALA* 4.1 3.8 - - + +
422C GLY* 3.7 33.4 - - - +
425C SER* 3.5 6.2 + - - +
458C GLU 4.0 0.7 - - - +
459C ASP 3.6 22.0 - - - +
460C ILE* 3.3 11.0 - - - +
462C GLU* 1.3 95.6 - - + +
464C ALA* 1.3 57.5 + - - +
466C CYS* 3.1 3.9 + - + +
467C ALA* 2.8 29.6 + - - +
19F ILE* 3.9 24.0 - - + -
21F PHE* 5.0 4.3 - - + -
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Residues in contact with ALA 464 (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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421C ALA* 4.4 11.1 - - + +
447C LEU* 4.2 19.5 - - + +
450C THR* 4.7 10.1 - - - -
451C VAL* 4.4 18.4 - - + +
460C ILE 3.1 22.5 + - - +
461C THR* 4.1 2.2 - - - +
463C PRO* 1.3 77.8 - - - +
465C ILE* 1.3 59.8 + - - +
467C ALA* 3.4 9.0 + - - +
468C LEU* 3.2 24.9 + - - +
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Residues in contact with ILE 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C VAL* 4.6 12.6 - - + -
461C THR* 2.7 31.5 + - - +
462C GLU 3.8 2.5 - - - +
464C ALA* 1.3 73.5 - - - +
466C CYS* 1.3 67.4 + - - +
468C LEU* 3.2 9.6 + - + +
469C ARG* 2.9 19.9 + - - +
494C VAL* 5.1 4.9 - - + -
497C LEU* 3.2 34.8 - - + -
506C LEU* 4.4 5.2 - - + -
509C ALA* 3.8 27.6 - - + +
510C THR* 4.0 14.6 - - + +
513C LEU* 3.7 26.8 - - + +
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Residues in contact with CYS 466 (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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425C SER* 3.6 13.2 - - - +
462C GLU* 2.9 28.6 + - - -
463C PRO 3.1 7.6 + - - +
465C ILE* 1.3 76.2 - - - +
467C ALA* 1.3 57.5 + - - +
469C ARG* 3.0 12.4 + - - +
470C HIS* 2.8 45.9 + - + +
505C PRO 5.7 0.2 - - - -
509C ALA* 3.8 22.2 - - - -
17F GLU* 5.9 4.3 - - - +
19F ILE* 4.5 14.6 - - + -
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Residues in contact with ALA 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ALA 4.8 1.8 - - - +
424C LEU* 4.4 5.6 - - + -
425C SER* 3.9 19.9 + - - +
428C THR* 4.2 4.7 + - + +
447C LEU* 4.0 20.0 - - + -
463C PRO 2.8 16.6 + - - +
464C ALA* 3.5 10.8 - - - +
466C CYS* 1.3 77.6 - - - +
468C LEU* 1.3 61.1 + - - +
470C HIS* 3.6 12.1 + - - +
471C LEU* 3.1 29.4 + - + +
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Residues in contact with LEU 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ILE* 3.9 46.4 - - + +
447C LEU* 4.1 20.0 - - + +
448C VAL* 4.2 20.2 - - + +
451C VAL* 4.8 8.3 - - + -
464C ALA 3.2 12.8 + - - +
465C ILE* 3.2 11.2 + - + +
467C ALA* 1.3 76.0 - - - +
469C ARG* 1.3 64.3 + - - +
471C LEU* 3.1 5.9 + - - +
472C THR* 2.8 30.6 + - - +
485C VAL* 4.5 11.2 - - + -
494C VAL* 5.3 4.7 - - + -
513C LEU* 4.0 26.0 - - + -
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Residues in contact with ARG 469 (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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465C ILE 2.9 13.0 + - - +
466C CYS* 3.2 15.6 - - - +
468C LEU* 1.3 77.0 - - - +
470C HIS* 1.3 69.0 + - + +
472C THR* 3.1 12.8 + - - -
473C SER* 3.8 6.6 + - - +
508C LYS* 3.9 20.8 + - - +
509C ALA* 3.8 28.5 - - - +
512C GLY* 3.2 32.6 + - - -
513C LEU* 4.1 10.5 - - + +
515C ARG* 5.9 4.4 - - - +
516C ASN* 3.1 32.0 + - - +
16F ASP* 5.6 1.8 - - - +
17F GLU* 6.0 3.2 - - - +
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Residues in contact with HIS 470 (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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425C SER* 2.9 40.2 + - - -
428C THR* 3.3 27.0 + - - +
429C CYS* 3.2 19.6 - - - -
435C LYS* 3.1 28.7 + - - +
466C CYS* 2.8 30.6 + - + +
467C ALA 3.7 5.2 - - - +
468C LEU 3.2 0.2 - - - -
469C ARG* 1.3 86.1 - - + +
471C LEU* 1.3 60.7 + - - +
473C SER* 3.4 6.3 + - - +
16F ASP* 3.6 31.8 - - + +
17F GLU* 3.8 11.5 + - - +
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Residues in contact with LEU 471 (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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428C THR* 3.9 13.5 - - + -
435C LYS* 3.5 41.1 - - + +
438C VAL* 3.7 30.1 - - + -
439C CYS* 4.1 11.7 - - - -
444C ILE* 3.5 31.2 - - + +
447C LEU* 4.3 11.9 - - + -
467C ALA 3.1 18.3 + - - +
468C LEU* 3.1 8.1 + - - +
470C HIS* 1.3 77.3 - - - +
472C THR* 1.3 58.3 + - - +
473C SER 3.2 0.4 - - - -
475C HIS* 2.7 32.3 + - - -
478C ALA* 4.1 0.2 - - - -
481C ALA* 3.7 4.1 - - - +
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Residues in contact with THR 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ILE* 5.2 0.4 - - + -
468C LEU 2.8 18.1 + - - +
469C ARG* 3.1 11.5 + - - -
470C HIS 3.3 0.4 - - - -
471C LEU* 1.3 76.0 - - + +
473C SER* 1.3 60.8 + - - +
478C ALA* 3.8 8.6 - - - +
481C ALA* 3.7 12.8 - - + -
482C GLN* 3.2 56.6 + - - +
485C VAL* 3.9 16.4 - - + -
513C LEU* 4.0 5.1 - - + +
516C ASN* 3.5 21.1 + - - +
517C LEU* 4.0 6.3 - - + -
519C LEU* 5.0 0.3 - - - +
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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
------------------------------------------------------------
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