Contacts of the helix formed by residues 456 - 476 (chain B) in PDB entry 1JS6
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LYS* 3.1 33.0 + - - +
384B LEU* 4.0 8.7 - - - -
454B LYS 3.6 11.7 - - - +
455B VAL* 1.3 77.5 - - - +
457B SER* 1.3 67.9 + - - +
458B GLY* 3.0 5.8 - - - +
459B HIS* 3.0 31.6 + - + +
460B VAL* 3.4 12.5 + - - +
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Residues in contact with SER 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 4.4 3.3 + - - -
384B LEU* 3.6 11.5 - - - +
387B GLU* 2.6 41.1 + - - +
391B PHE* 5.5 0.5 - - - -
456B GLU* 1.3 73.6 - - - +
458B GLY* 1.3 62.5 + - - +
460B VAL* 3.3 5.3 + - - +
461B ARG* 3.0 24.3 + - - +
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Residues in contact with GLY 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B GLU* 3.0 6.2 - - - +
457B SER* 1.3 79.1 - - - +
459B HIS* 1.3 61.7 + - - +
461B ARG* 3.3 5.9 + - - +
462B LEU* 3.0 32.9 + - - +
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Residues in contact with HIS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 2.8 39.8 + - - -
74B PRO* 3.5 27.6 - - + +
75B TYR* 3.2 37.1 + - + -
77B PHE* 4.9 2.0 - - + -
454B LYS 3.8 7.1 + - - -
455B VAL* 3.9 10.3 - - + -
456B GLU* 3.0 43.0 + - + +
458B GLY* 1.3 76.0 - - - +
460B VAL* 1.3 57.8 + - - +
462B LEU* 3.5 0.3 + - - +
463B ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.9 2.7 - - + -
384B LEU* 4.4 23.6 - - + +
387B GLU* 4.8 3.6 - - + +
388B PHE* 3.9 39.7 - - + +
391B PHE* 3.9 13.7 - - + -
448B PHE* 4.4 14.1 - - + -
450B ILE* 5.0 1.3 - - + -
455B VAL* 4.3 14.4 - - + -
456B GLU 3.8 11.4 - - - +
457B SER* 3.3 7.8 + - - +
458B GLY 3.2 0.6 - - - -
459B HIS* 1.3 74.1 - - - +
461B ARG* 1.3 61.5 + - - +
463B ALA* 3.0 7.7 + - - +
464B TRP* 2.8 28.1 + - - +
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Residues in contact with ARG 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B PHE* 3.1 50.9 - - + -
457B SER 3.0 16.8 + - - +
458B GLY* 3.3 6.7 + - - +
460B VAL* 1.3 74.4 - - - +
462B LEU* 1.3 67.9 + - + +
464B TRP* 3.1 5.4 + - - +
465B GLU* 2.6 58.3 + - - +
468B ARG* 3.2 37.9 - - - +
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.8 23.6 - - + +
458B GLY* 3.0 22.8 + - - +
459B HIS 3.9 2.9 - - - +
461B ARG* 1.3 80.1 - - + +
463B ALA* 1.3 63.1 + - - +
465B GLU* 3.7 21.6 - - - +
466B HIS* 3.0 26.3 + - - +
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Residues in contact with ALA 463 (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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75B TYR* 4.9 2.2 - - + -
77B PHE* 3.9 27.6 - - + -
388B PHE* 5.3 0.2 - - - -
433B ILE* 4.2 18.6 - - + +
448B PHE* 4.2 11.0 - - + -
459B HIS 2.9 18.6 + - - +
460B VAL* 3.0 6.3 + - - +
462B LEU* 1.3 79.3 - - - +
464B TRP* 1.3 62.4 + - - +
466B HIS* 3.4 3.5 + - - +
467B ILE* 3.0 29.8 + - - +
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Residues in contact with TRP 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PHE* 3.8 25.3 - + + -
391B PHE* 3.3 64.5 + + + +
392B VAL* 4.0 18.8 - - + -
395B ASP* 4.0 16.1 - - + +
398B PHE* 3.6 45.1 - + - -
411B PHE* 4.7 2.5 - + - -
460B VAL 2.8 16.2 + - - +
461B ARG* 3.5 16.8 - - - +
463B ALA* 1.3 71.3 - - - +
465B GLU* 1.3 57.2 + - - +
467B ILE* 2.9 17.5 + - + -
468B ARG* 2.8 59.2 + - + +
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ARG* 2.6 68.2 + - - +
462B LEU* 3.7 22.1 - - - +
464B TRP* 1.3 75.4 - - - +
466B HIS* 1.3 54.6 + - - +
468B ARG* 3.0 19.3 + - - +
469B GLY* 2.7 33.1 + - - -
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Residues in contact with HIS 466 (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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427B ILE* 4.4 11.4 - - + -
430B ALA* 3.7 19.7 - - + +
432B LYS* 3.6 49.1 - - + +
433B ILE* 4.4 15.2 - - + +
462B LEU 3.0 18.8 + - - +
463B ALA* 3.5 6.1 - - - +
465B GLU* 1.3 74.7 - - - +
467B ILE* 1.3 64.3 + - - +
469B GLY* 3.5 1.6 + - - +
470B LEU* 3.1 54.3 + - + +
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Residues in contact with ILE 467 (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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388B PHE* 4.3 20.6 - - + -
398B PHE* 4.5 2.0 - - + -
411B PHE* 4.1 25.1 - - + -
423B LEU* 4.0 9.2 - - + +
427B ILE* 4.0 19.5 - - + -
433B ILE* 3.7 26.0 - - + -
435B LEU* 4.1 16.8 - - + -
448B PHE* 4.6 2.9 - - + -
463B ALA 3.0 16.4 + - - +
464B TRP* 2.9 17.5 + - + +
466B HIS* 1.3 76.0 - - - +
468B ARG* 1.3 61.1 + - - +
470B LEU* 3.4 7.2 + - - +
471B ALA* 2.9 26.7 + - - +
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Residues in contact with ARG 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASP* 3.3 27.1 - - - +
397B ARG* 3.6 14.0 + - - +
398B PHE* 4.3 12.6 - - + -
461B ARG* 3.2 34.2 - - - +
464B TRP* 2.8 48.1 + - + +
465B GLU* 3.4 21.2 + - - +
467B ILE* 1.3 70.2 - - - +
469B GLY* 1.3 61.8 + - - +
471B ALA* 3.3 1.6 + - - +
472B ALA* 2.9 31.1 + - - +
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Residues in contact with GLY 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B GLU 2.7 14.7 + - - -
466B HIS* 3.9 2.5 - - - -
468B ARG* 1.3 77.5 - - - +
470B LEU* 1.3 61.0 + - - +
472B ALA* 3.1 8.8 + - - +
473B GLU* 2.9 31.0 + - - +
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Residues in contact with LEU 470 (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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423B LEU* 4.0 11.2 - - + -
426B ARG* 3.7 24.0 - - + +
427B ILE* 3.6 31.9 - - + +
430B ALA* 4.4 4.5 - - + -
466B HIS* 3.1 50.1 + - + +
467B ILE 3.8 3.8 - - - +
469B GLY* 1.3 74.4 - - - +
471B ALA* 1.3 63.4 + - - +
473B GLU* 3.5 22.2 + - - +
474B LEU* 3.0 25.5 + - - +
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Residues in contact with ALA 471 (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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397B ARG* 5.8 1.1 - - - +
398B PHE* 3.5 29.4 - - + -
413B LEU* 3.9 20.4 - - + +
423B LEU* 3.6 11.9 - - + +
467B ILE 2.9 18.7 + - - +
468B ARG 3.6 3.1 - - - +
469B GLY 3.2 0.2 - - - -
470B LEU* 1.3 75.4 - - - +
472B ALA* 1.3 58.3 + - - +
474B LEU* 3.3 5.8 + - - +
475B LEU* 2.8 36.0 + - + +
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Residues in contact with ALA 472 (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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397B ARG* 3.8 24.4 - - - +
468B ARG* 2.9 14.5 + - + +
469B GLY* 3.3 11.4 - - - +
471B ALA* 1.3 72.9 - - - +
473B GLU* 1.3 68.1 + - + +
475B LEU* 2.8 22.1 + - - +
476B ALA* 3.3 5.7 + - - +
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Residues in contact with GLU 473 (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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426B ARG* 4.1 16.9 + - - +
469B GLY 2.9 17.6 + - - +
470B LEU* 3.6 26.3 - - - +
472B ALA* 1.3 73.1 - - + +
474B LEU* 1.3 59.3 + - - +
476B ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 474 (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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413B LEU* 4.3 8.7 - - + -
419B LEU* 3.4 43.0 - - + +
422B ALA* 3.9 16.8 - - + -
423B LEU* 3.7 26.5 - - + +
426B ARG* 3.6 39.8 + - - +
470B LEU 3.0 14.2 + - - +
471B ALA 3.4 2.5 - - - +
473B GLU* 1.3 80.5 - - - +
475B LEU* 1.3 61.8 + - - +
476B ALA 3.1 5.8 + - - -
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Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ARG* 3.6 40.6 - - + +
413B LEU* 4.4 14.6 - - + -
414B LYS 5.5 2.5 - - - +
419B LEU* 4.3 27.6 - - + -
471B ALA 2.8 17.9 + - - +
472B ALA* 2.8 16.4 + - - +
474B LEU* 1.3 71.8 - - - +
476B ALA* 1.3 57.2 + - - +
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ALA 3.3 5.0 + - - +
473B GLU* 2.8 17.8 + - - +
474B LEU 3.1 5.1 - - - -
475B LEU* 1.3 82.2 - - - +
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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