Contacts of the helix formed by residues 461 - 473 (chain B) in PDB entry 1JEH
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 SER 461 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A GLY 4.3 2.4 + - - -
432A GLU* 3.0 17.1 + - - -
435A ALA* 3.7 20.7 - - - +
433B MET* 4.1 11.7 - - - -
436B GLU* 4.2 4.0 - - - -
455B HIS* 3.2 32.6 - - - +
456B ALA 4.6 1.7 + - - -
459B THR* 2.7 24.4 + - - +
460B LEU* 1.3 76.9 - - - +
462B GLU* 1.3 59.9 + - - +
463B ALA 3.2 0.2 - - - -
464B PHE* 3.1 20.2 + - - +
465B LYS 3.3 1.2 + - - -
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Residues in contact with GLU 462 (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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334A HIS* 4.8 0.7 - - - +
337A GLU* 4.2 10.9 - - - +
396B ASN* 3.8 5.2 - - - +
397B SER* 4.2 7.7 + - - -
455B HIS* 3.9 16.4 - - + +
456B ALA 3.2 25.8 - - - +
457B HIS* 3.1 35.7 + - - +
458B PRO* 3.7 1.2 - - - +
459B THR* 3.2 25.6 + - - +
460B LEU 3.1 0.2 - - - -
461B SER* 1.3 77.6 + - - +
463B ALA* 1.3 55.6 + - - +
465B LYS* 3.3 13.4 + - + +
466B GLU* 2.9 38.0 + - + +
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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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391B PHE* 3.5 27.4 - - + +
393B PHE* 3.6 24.2 - - + -
396B ASN* 3.1 16.9 - - - +
409B VAL* 3.6 12.5 - - + +
460B LEU 2.9 14.3 + - - +
462B GLU* 1.3 72.8 - - - +
464B PHE* 1.3 61.1 + - - +
466B GLU 4.0 0.4 - - - -
467B ALA* 3.1 28.2 + - - +
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Residues in contact with PHE 464 (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 VAL* 3.7 20.6 - - + +
411B ILE* 3.8 18.2 - - + -
420B ILE* 5.5 1.6 - - + -
423B ALA* 4.5 3.1 - - + -
425B ILE* 4.1 17.7 - - + -
433B MET* 3.9 17.7 - - + -
436B GLU* 3.5 32.5 - - + +
437B ALA* 3.5 42.4 - - + -
440B ALA* 5.3 2.0 - - + -
450B VAL* 3.5 18.8 - - + -
460B LEU 4.0 1.2 + - - -
461B SER 3.1 13.1 + - - +
463B ALA* 1.3 79.2 - - - +
465B LYS* 1.3 60.1 + - - +
467B ALA* 3.3 4.2 + - - +
468B ASN* 2.8 51.2 + - - +
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Residues in contact with LYS 465 (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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337A GLU* 6.2 0.4 - - - -
338A GLU* 3.2 23.0 + - - -
341A ILE* 5.6 2.5 - - - -
450B VAL* 4.0 8.3 - - - +
451B ALA* 2.8 35.4 + - - +
453B VAL 2.9 18.9 + - - +
455B HIS* 3.5 47.5 - - + +
461B SER 3.3 1.2 + - - +
462B GLU* 3.3 14.8 + - + +
464B PHE* 1.3 79.5 - - - +
466B GLU* 1.3 64.5 + - - +
468B ASN* 3.3 8.4 + - - +
469B MET* 2.9 42.9 + - + +
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Residues in contact with GLU 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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337A GLU* 5.6 0.7 - - - +
391B PHE* 3.5 34.2 - - + +
462B GLU* 2.9 24.8 + - + +
465B LYS* 1.3 83.1 - - + +
467B ALA* 1.3 58.3 + - - +
469B MET* 3.6 26.3 - - - +
470B ALA* 3.0 26.3 + - - +
475B ALA* 3.6 6.2 - - - +
476B ILE* 3.2 16.0 + - - +
477B HIS* 2.9 49.3 + - - +
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Residues in contact with ALA 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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389B GLY* 3.5 14.9 - - - +
391B PHE* 3.7 13.4 - - + +
409B VAL* 3.6 23.6 - - + +
411B ILE* 3.5 23.6 - - + +
463B ALA 3.1 19.5 + - - +
464B PHE 3.3 1.5 + - - +
466B GLU* 1.3 74.5 - - - +
468B ASN* 1.3 59.8 + - - +
470B ALA* 3.5 3.0 + - - +
471B ALA* 3.1 21.0 + - - +
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Residues in contact with ASN 468 (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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411B ILE* 3.5 22.1 - - - +
420B ILE* 3.4 30.9 - - - +
447B ALA* 3.2 41.6 - - - +
450B VAL* 3.3 26.8 - - + +
451B ALA 4.2 0.7 - - - +
464B PHE* 2.8 34.6 + - - +
465B LYS 3.5 7.9 - - - +
467B ALA* 1.3 73.9 - - - +
469B MET* 1.3 64.5 + - - +
471B ALA* 3.2 12.2 + - - -
472B TYR* 3.3 4.3 - - - -
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Residues in contact with MET 469 (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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23A LYS* 5.5 4.3 - - - +
341A ILE* 4.7 13.0 - - + -
451B ALA* 3.2 35.4 - - + +
465B LYS* 2.9 34.9 + - + +
466B GLU* 3.6 26.5 - - - +
468B ASN* 1.3 76.9 - - - +
470B ALA* 1.3 56.5 + - - +
471B ALA 3.4 0.2 + - - -
472B TYR* 3.4 19.1 - - + +
473B ASP* 3.0 26.2 + - - +
474B LYS 3.2 21.5 + - - +
475B ALA* 4.6 0.4 - - - -
476B ILE* 3.5 29.2 - - + -
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Residues in contact with ALA 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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388B ILE 4.2 5.7 - - - +
389B GLY* 4.0 2.6 - - - -
390B LYS 4.1 22.2 - - - +
466B GLU 3.0 17.9 + - - +
467B ALA 3.8 5.6 - - - +
468B ASN 3.3 0.2 - - - -
469B MET* 1.3 74.1 - - - +
471B ALA* 1.3 64.7 + - - +
472B TYR 3.5 0.2 - - - -
473B ASP 3.7 11.2 - - - +
474B LYS* 4.2 4.3 - - + +
475B ALA* 3.9 23.5 - - + +
478B CYS* 5.2 2.0 - - - -
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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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387B LYS* 3.9 17.2 - - - +
388B ILE 4.1 2.4 - - - +
389B GLY* 3.5 21.3 - - - +
411B ILE* 4.2 10.8 - - + +
413B ILE* 3.7 22.0 - - + +
447B ALA* 3.9 12.1 - - + -
467B ALA 3.1 12.9 + - - +
468B ASN 3.2 12.1 + - - +
470B ALA* 1.3 80.7 - - - +
472B TYR* 1.3 59.4 + - - +
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Residues in contact with TYR 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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387B LYS* 4.5 5.9 + - - +
413B ILE* 4.1 3.1 - - + -
418B GLU* 3.6 36.5 - - + +
447B ALA* 3.9 16.6 - - + -
448B GLU* 3.3 46.8 - - + +
451B ALA* 3.8 10.3 - - + +
452B ARG* 2.8 27.3 + - - -
468B ASN 3.3 19.7 - - - -
469B MET* 3.4 29.5 - - + +
471B ALA* 1.3 79.4 - - - +
473B ASP* 1.3 77.2 + - + +
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Residues in contact with ASP 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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23A LYS* 3.5 24.1 + - - -
26A GLN* 5.0 0.3 - - - +
27A LEU* 5.8 2.0 - - - +
469B MET* 3.0 10.0 + - - +
470B ALA 3.7 10.4 - - - +
472B TYR* 1.3 103.9 + - + +
474B LYS* 1.3 84.7 + - - +
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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