Contacts of the helix formed by residues 456 - 476 (chain A) in PDB entry 1JS3
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 GLU 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A LYS* 2.7 36.9 + - - +
384A LEU* 3.9 7.9 - - - -
454A LYS* 3.8 17.3 - - - +
455A VAL* 1.3 80.4 - - - +
457A SER* 1.3 68.4 + - - +
458A GLY* 3.1 6.5 - - - +
459A HIS* 2.9 30.2 + - + +
460A VAL* 3.3 9.4 + - - +
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Residues in contact with SER 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LYS* 5.7 0.2 - - - +
383A GLN* 4.4 3.6 + - - -
384A LEU* 3.6 13.0 - - - +
387A GLU* 2.8 38.7 + - - +
391A PHE* 5.5 0.5 - - - -
456A GLU* 1.3 74.8 + - - +
458A GLY* 1.3 63.7 + - - +
460A VAL* 3.1 4.6 + - - +
461A ARG* 2.8 25.4 + - - +
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Residues in contact with GLY 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A GLU* 3.1 5.9 - - - +
457A SER* 1.3 79.1 - - - +
459A HIS* 1.3 56.3 + - - +
461A ARG* 3.2 7.1 + - - +
462A LEU* 2.8 39.3 + - - +
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Residues in contact with HIS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.1 39.0 + - - -
74A PRO* 3.6 23.6 - - + +
75A TYR* 3.3 34.3 + - + -
77A PHE* 4.7 1.6 - - + -
454A LYS 3.7 9.7 + - - -
455A VAL* 3.7 12.1 - - + -
456A GLU* 2.9 46.6 + - + +
458A GLY* 1.3 76.0 - - - +
460A VAL* 1.3 58.2 + - - +
462A LEU* 3.3 2.1 + - - +
463A ALA* 2.8 30.9 + - - +
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.8 1.3 - - + -
384A LEU* 4.1 24.2 - - + +
387A GLU* 4.6 5.2 - - + +
388A PHE* 3.7 44.2 - - + +
391A PHE* 4.2 7.9 - - + -
448A PHE* 4.4 13.7 - - + -
450A ILE* 5.0 2.2 - - + -
455A VAL* 4.1 15.9 - - + -
456A GLU 3.3 10.7 + - - +
457A SER* 3.1 9.1 + - - +
459A HIS* 1.3 75.3 - - - +
461A ARG* 1.3 57.7 + - - +
463A ALA* 3.2 7.1 + - - +
464A TRP* 2.9 28.4 + - - +
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Residues in contact with ARG 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 3.1 50.1 - - + -
457A SER 2.8 13.1 + - - +
458A GLY* 3.4 11.7 - - - +
460A VAL* 1.3 76.8 - - - +
462A LEU* 1.3 62.2 + - + +
464A TRP* 3.1 12.5 + - - +
465A GLU* 2.5 63.5 + - - +
468A ARG* 4.1 16.4 - - - +
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Residues in contact with LEU 462 (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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75A TYR* 3.6 27.4 - - + +
458A GLY* 2.8 24.4 + - - +
459A HIS 3.8 3.4 - - - +
461A ARG* 1.3 77.7 - - + +
463A ALA* 1.3 57.2 + - - +
465A GLU* 3.4 21.2 + - + +
466A HIS* 2.9 30.7 + - - +
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 5.1 1.3 - - + -
77A PHE* 3.6 28.7 - - + -
388A PHE* 5.1 0.2 - - - -
433A ILE* 4.2 15.5 - - + -
448A PHE* 3.9 14.1 - - + -
459A HIS 2.8 18.1 + - - +
460A VAL 3.5 5.4 - - - +
461A ARG 3.2 0.2 - - - -
462A LEU* 1.3 76.0 - - - +
464A TRP* 1.3 58.5 + - - +
466A HIS* 3.4 6.2 + - - +
467A ILE* 2.9 36.3 + - - +
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Residues in contact with TRP 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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388A PHE* 3.8 26.2 - + + -
391A PHE* 3.5 59.7 + + + +
392A VAL* 3.6 26.2 - - + -
395A ASP* 3.9 18.2 - - + -
398A PHE* 3.6 46.7 - + - -
411A PHE* 4.8 1.3 - + - -
460A VAL 2.9 13.4 + - - +
461A ARG* 3.1 18.6 + - - +
463A ALA* 1.3 74.9 - - - +
465A GLU* 1.3 56.3 + - - +
467A ILE* 3.1 10.7 + - + -
468A ARG* 2.7 57.9 + - + +
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG* 2.5 62.3 + - - +
462A LEU* 3.7 18.7 - - - +
464A TRP* 1.3 76.1 - - - +
466A HIS* 1.3 57.6 + - - +
468A ARG* 3.3 32.9 + - - +
469A GLY* 2.9 27.7 + - - -
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 4.5 5.6 - - - -
430A ALA* 3.5 26.9 - - + +
432A LYS* 3.5 43.3 - - + +
433A ILE* 4.2 24.8 - - + +
462A LEU 2.9 18.4 + - - +
463A ALA* 3.5 6.5 - - - +
465A GLU* 1.3 77.3 - - - +
467A ILE* 1.3 64.9 + - - +
469A GLY* 3.4 1.0 + - - -
470A LEU* 3.2 51.6 + - + +
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Residues in contact with ILE 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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388A PHE* 4.2 19.5 - - + -
398A PHE* 4.3 13.2 - - + -
411A PHE* 4.0 37.7 - - + -
423A LEU* 4.2 5.2 - - + +
427A ILE* 4.3 18.4 - - + -
433A ILE* 3.8 25.1 - - + -
435A LEU* 4.2 9.2 - - + -
448A PHE* 4.5 2.0 - - + -
463A ALA 2.9 22.1 + - - +
464A TRP* 3.6 9.2 - - + +
466A HIS* 1.3 76.5 - - - +
468A ARG* 1.3 67.4 + - - +
470A LEU* 3.4 8.1 + - - +
471A ALA* 3.0 20.8 + - - +
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Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASP* 3.7 17.3 - - - +
397A ARG* 3.3 24.4 + - - +
398A PHE* 4.3 6.1 - - + -
461A ARG* 4.1 17.6 - - - +
464A TRP* 2.7 50.0 + - + +
465A GLU* 3.5 31.7 + - - +
467A ILE* 1.3 72.4 - - - +
469A GLY* 1.3 62.9 + - - +
471A ALA* 3.2 8.1 + - - +
472A ALA* 3.0 22.2 + - + +
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Residues in contact with GLY 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 GLU 2.9 15.9 + - - -
466A HIS* 3.9 1.3 - - - -
467A ILE 3.2 0.2 - - - -
468A ARG* 1.3 77.9 - - - +
470A LEU* 1.3 61.8 + - - +
472A ALA* 3.0 17.8 + - - +
473A GLU* 3.1 21.8 + - - +
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Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.1 11.4 - - + +
426A ARG* 3.8 22.2 + - + +
427A ILE* 3.7 35.0 - - + +
430A ALA* 4.4 4.5 - - + -
466A HIS* 3.2 49.7 + - + +
467A ILE 3.8 2.9 - - - +
469A GLY* 1.3 75.7 - - - +
471A ALA* 1.3 63.9 + - - +
473A GLU* 3.4 23.4 + - - +
474A LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 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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397A ARG* 5.5 1.1 - - - +
398A PHE* 3.4 35.2 - - + -
413A LEU* 3.9 18.1 - - + +
423A LEU* 3.9 10.5 - - + +
467A ILE 3.0 9.8 + - - +
468A ARG 3.4 7.2 - - - +
469A GLY 3.1 0.2 - - - -
470A LEU* 1.3 77.2 - - - +
472A ALA* 1.3 58.1 + - - +
474A LEU* 3.4 4.4 + - - +
475A LEU* 2.9 37.9 + - + +
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Residues in contact with ALA 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ARG* 3.9 21.2 - - - +
468A ARG 3.0 11.7 + - - +
469A GLY* 3.0 12.3 + - - +
471A ALA* 1.3 73.2 - - - +
473A GLU* 1.3 67.5 + - + +
475A LEU* 3.1 15.3 + - - +
476A ALA* 3.1 13.2 + - - +
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Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 5.9 7.8 + - - +
469A GLY 3.1 16.0 + - - +
470A LEU* 3.7 25.9 - - + +
472A ALA* 1.3 77.2 - - + +
474A LEU* 1.3 64.0 + - - +
476A ALA* 3.1 25.1 + - - +
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Residues in contact with LEU 474 (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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413A LEU* 4.6 2.7 - - + -
419A LEU* 3.5 33.9 - - + +
422A ALA* 3.9 13.7 - - + -
423A LEU* 3.4 42.4 - - + +
426A ARG* 3.7 36.1 - - + +
470A LEU 3.0 14.5 + - - +
471A ALA 3.6 4.5 - - - +
473A GLU* 1.3 80.7 - - - +
475A LEU* 1.3 61.7 + - - +
476A ALA 3.1 9.2 - - - +
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ARG* 3.5 42.2 - - + +
413A LEU* 4.5 13.7 - - + -
414A LYS 5.5 2.9 - - - +
419A LEU* 4.2 27.4 - - + -
471A ALA 2.9 29.0 + - - +
472A ALA* 3.1 5.4 + - - +
474A LEU* 1.3 75.8 - - - +
476A ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ALA 3.1 10.0 + - - +
473A GLU* 3.1 18.6 + - - +
474A LEU 3.1 13.0 - - - +
475A LEU* 1.3 79.6 - - - +
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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
------------------------------------------------------------
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