Contacts of the helix formed by residues 458 - 474 (chain B) in PDB entry 1EJI
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 ILE 458 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B LEU* 3.9 20.4 - - + -
435B ILE* 3.2 44.4 - - + -
451B LYS* 3.3 15.9 - - + +
452B LEU* 4.4 21.8 - - + +
456B GLU* 3.0 31.4 - - + +
457B LYS* 1.3 81.3 - - - +
459B GLN* 1.3 62.7 + - + +
460B SER 2.9 5.2 - - - -
461B ALA* 3.0 21.5 + - + +
462B VAL* 3.1 12.6 + - + +
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Residues in contact with GLN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA* 6.1 2.0 - - - +
452B LEU* 3.8 19.3 + - - +
453B ALA* 3.9 11.0 - - - +
454B GLY* 2.8 34.4 - - - +
456B GLU 3.9 10.0 + - - +
457B LYS 3.2 1.2 - - - -
458B ILE* 1.3 83.8 - - - +
460B SER* 1.3 58.4 + - - +
462B VAL* 3.0 27.2 - - + +
463B ALA* 3.0 15.2 - - + +
466B ARG* 4.8 11.8 - - - +
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Residues in contact with SER 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B GLU 4.3 2.6 + - - -
457B LYS* 2.9 28.9 + - - +
458B ILE 2.9 0.4 - - - -
459B GLN* 1.3 79.5 - - - +
461B ALA* 1.3 54.3 + - - +
463B ALA* 3.9 6.5 - - - +
464B THR* 2.7 32.7 + - - -
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B LEU* 4.2 19.1 - - + -
457B LYS 3.5 2.7 + - - +
458B ILE* 3.0 17.8 + - + +
460B SER* 1.3 77.5 - - - +
462B VAL* 1.3 65.6 + - - +
464B THR* 3.0 16.6 + - - -
465B LEU* 3.1 13.9 + - - +
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 6.0 1.3 - - + -
379B ALA* 3.2 41.3 - - + +
380B CYS* 3.3 21.5 - - - -
431B LEU* 4.1 14.5 - - + +
452B LEU* 5.5 10.3 - - + +
458B ILE* 3.1 4.4 + - + +
459B GLN* 3.0 42.0 - - + +
461B ALA* 1.3 79.5 - - - +
463B ALA* 1.3 64.4 + - - +
464B THR 3.0 0.5 + - - -
465B LEU* 3.0 2.1 + - - +
466B ARG* 2.6 41.1 + - - +
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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
----------------------------------------------------------
459B GLN* 3.0 19.4 + - + +
460B SER* 3.9 8.1 - - - +
461B ALA 3.3 0.2 - - - -
462B VAL* 1.3 82.2 - - - +
464B THR* 1.3 61.7 + - - +
466B ARG* 3.8 29.2 + - - +
467B GLU* 3.3 20.8 + - - +
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Residues in contact with THR 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 6.2 2.0 - - - +
460B SER 2.7 20.5 + - - -
461B ALA* 3.0 9.7 + - - -
463B ALA* 1.3 75.9 - - - +
465B LEU* 1.3 67.5 + - - +
467B GLU* 3.1 15.8 + - - +
468B GLU* 3.1 23.7 + - + +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B CYS* 4.2 19.5 - - + -
382B ILE* 5.6 1.8 - - + -
424B PHE* 3.8 26.2 - - + +
427B ARG* 3.7 54.5 - - + +
428B GLY* 4.0 18.6 - - - +
431B LEU* 5.0 7.6 - - + -
461B ALA 3.1 7.7 + - - +
462B VAL* 3.0 6.8 + - - +
464B THR* 1.3 76.9 - - - +
466B ARG* 1.3 68.2 + - - +
468B GLU* 3.2 4.1 + - - +
469B VAL* 2.9 33.2 + - + +
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Residues in contact with ARG 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA* 3.4 19.8 + - - +
380B CYS* 3.9 19.0 - - - +
381B SER* 3.5 13.9 - - - +
459B GLN* 4.8 12.9 - - - +
462B VAL* 2.6 29.0 + - - +
463B ALA* 3.8 36.8 + - - +
465B LEU* 1.3 72.3 - - - +
467B GLU* 1.3 58.7 - - - +
469B VAL* 3.3 2.1 + - - +
470B GLU* 2.8 61.0 + - - +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ALA 3.3 11.2 + - - +
464B THR* 3.1 19.1 + - - +
465B LEU 3.1 0.4 - - - -
466B ARG* 1.3 76.5 - - - +
468B GLU* 1.3 64.5 + - - +
469B VAL 2.9 2.1 + - - -
470B GLU* 3.0 7.4 + - - +
471B ASN* 2.7 49.7 + - - +
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Residues in contact with GLU 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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424B PHE* 3.5 20.3 - - + -
427B ARG* 2.6 34.2 + - - +
464B THR* 3.1 11.6 + - + +
465B LEU 3.2 6.3 + - - +
467B GLU* 1.3 80.9 + - - +
469B VAL* 1.3 59.6 + - - +
471B ASN* 3.7 9.8 - - - +
472B PHE* 3.2 22.0 + - - +
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.0 23.1 - - + +
380B CYS 3.5 22.9 - - - +
381B SER* 3.9 17.3 - - - +
382B ILE* 4.2 9.9 - - + -
424B PHE* 3.7 33.2 - - + -
465B LEU* 2.9 25.6 + - + +
466B ARG 3.4 7.6 - - - +
468B GLU* 1.3 75.4 - - - +
470B GLU* 1.3 62.2 + - - +
472B PHE* 3.0 4.7 + - - +
473B ALA* 2.8 28.3 + - + +
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Residues in contact with GLU 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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46B VAL* 3.2 38.6 - - + +
381B SER* 3.3 21.6 + - - +
466B ARG* 2.8 51.5 + - - +
467B GLU* 3.8 5.6 - - - +
469B VAL* 1.3 73.5 - - - +
471B ASN* 1.3 58.0 + - - +
473B ALA* 3.8 6.6 - - - +
474B SER* 2.8 31.7 + - - -
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Residues in contact with ASN 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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467B GLU* 2.7 51.7 + - - +
468B GLU* 3.7 8.6 - - - +
470B GLU* 1.3 74.5 - - - +
472B PHE* 1.3 58.9 + - - +
474B SER* 3.0 15.6 + - - -
475B ASN* 2.5 30.3 + - - +
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Residues in contact with PHE 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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48B LEU* 4.1 17.3 - - + -
413B LEU* 3.8 24.9 - - + -
417B ASP* 3.8 17.9 - - + -
420B LYS* 4.0 25.8 - - + -
421B VAL* 3.9 21.1 - - + -
424B PHE* 3.5 27.8 - + + -
468B GLU 3.2 12.3 + - - +
469B VAL 3.0 6.7 + - - +
471B ASN* 1.3 80.4 - - - +
473B ALA* 1.3 63.2 + - - +
475B ASN* 3.3 16.0 + - - +
476B PHE* 3.2 41.0 - + - -
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Residues in contact with ALA 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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45B ARG 3.9 5.4 - - - +
46B VAL 3.8 1.6 - - - -
47B GLY* 3.4 40.8 - - - +
48B LEU* 4.4 9.4 - - + +
411B ARG* 3.7 8.6 + - - +
469B VAL 2.8 16.8 + - - +
470B GLU* 3.8 3.8 - - - +
472B PHE* 1.3 77.1 - - - +
474B SER* 1.3 53.3 + - - +
475B ASN 2.6 18.0 + - - -
476B PHE* 2.9 22.9 + - - -
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Residues in contact with SER 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 3.5 40.2 + - - +
46B VAL* 3.6 8.7 - - - +
411B ARG* 4.8 1.1 - - - +
470B GLU 2.8 20.3 + - - -
471B ASN* 3.0 14.2 + - - -
473B ALA* 1.3 73.9 - - - +
475B ASN* 1.3 59.8 + - - +
476B PHE 3.2 8.7 + - - +
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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
------------------------------------------------------------
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