Contacts of the helix formed by residues 456 - 474 (chain C) 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 GLU 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453C ALA 5.1 0.6 + - - -
454C GLY* 4.4 3.1 - - - -
455C ASP* 1.3 82.2 + - - +
457C LYS* 1.3 63.3 + - + +
458C ILE 2.8 0.2 - - - -
459C GLN* 2.5 32.1 + - - +
460C SER* 2.8 20.5 + - - +
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Residues in contact with LYS 457 (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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455C ASP* 2.3 30.0 + - - +
456C GLU* 1.3 78.0 - - + +
458C ILE* 1.3 62.4 + - + +
460C SER* 3.6 7.0 + - - -
461C ALA* 3.2 22.0 + - - +
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Residues in contact with ILE 458 (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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431C LEU* 4.5 12.7 - - + +
435C ILE* 3.3 37.0 - - + -
451C LYS* 3.7 11.4 - - + +
452C LEU* 3.5 35.2 - - + +
455C ASP* 2.9 44.0 + - + +
456C GLU 2.6 4.2 + - - -
457C LYS* 1.3 73.0 - - + +
459C GLN* 1.3 61.8 + - - +
460C SER 3.1 4.5 - - - -
461C ALA* 3.2 6.3 + - - +
462C VAL* 3.1 22.5 + - + +
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Residues in contact with GLN 459 (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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379C ALA* 6.2 2.2 - - - +
452C LEU 5.0 2.3 + - - +
453C ALA* 3.9 31.8 + - - +
455C ASP 4.6 0.2 - - - -
456C GLU* 2.5 18.7 + - - +
458C ILE* 1.3 76.9 - - - +
460C SER* 1.3 55.9 - - - +
462C VAL* 2.9 30.3 - - + +
463C ALA* 3.0 16.3 - - + +
466C ARG* 4.8 12.1 - - - +
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Residues in contact with SER 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C GLU* 2.8 21.7 + - - +
457C LYS* 3.7 7.8 + - - -
459C GLN* 1.3 77.0 - - - +
461C ALA* 1.3 56.5 + - - +
463C ALA* 3.9 6.3 - - - +
464C THR* 2.7 32.6 + - - -
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 4.2 19.7 - - + -
457C LYS 3.2 13.2 + - - +
458C ILE* 3.5 11.4 - - - +
460C SER* 1.3 76.6 - - - +
462C VAL* 1.3 66.7 + - - +
464C THR* 3.0 16.3 + - - -
465C LEU* 3.1 13.9 + - - +
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Residues in contact with VAL 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C VAL* 6.1 0.7 - - + -
379C ALA* 3.3 40.8 - - + +
380C CYS* 3.3 20.6 - - - -
431C LEU* 4.1 14.9 - - + +
452C LEU* 6.0 5.4 - - + +
458C ILE* 3.1 7.5 + - + +
459C GLN* 2.9 42.6 - - + +
461C ALA* 1.3 79.0 - - - +
463C ALA* 1.3 65.9 + - - +
464C THR 3.0 0.5 + - - -
465C LEU* 3.0 1.8 + - - +
466C ARG* 2.6 42.2 + - - +
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Residues in contact with ALA 463 (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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459C GLN* 3.0 18.3 + - + +
460C SER* 3.9 8.3 - - - +
461C ALA 3.2 0.2 - - - -
462C VAL* 1.3 82.3 - - - +
464C THR* 1.3 61.1 + - - +
466C ARG* 3.8 29.4 + - - +
467C GLU* 3.2 21.8 + - - +
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Residues in contact with THR 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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427C ARG* 6.2 1.6 - - - +
460C SER 2.7 20.3 + - - -
461C ALA* 3.0 10.0 + - - -
463C ALA* 1.3 77.0 - - - +
465C LEU* 1.3 67.3 + - - +
467C GLU* 3.1 16.3 + - - +
468C GLU* 3.1 23.9 + - + +
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C CYS* 4.1 23.3 - - + -
382C ILE* 5.6 1.3 - - + -
424C PHE* 3.8 25.8 - - + +
427C ARG* 3.7 53.8 - - + +
428C GLY* 4.0 16.2 - - - +
431C LEU* 4.9 7.6 - - + -
461C ALA 3.1 8.6 + - - +
462C VAL* 3.0 5.7 + - - +
464C THR* 1.3 76.6 - - - +
466C ARG* 1.3 67.9 + - - +
467C GLU 3.1 0.2 + - - -
468C GLU* 3.2 4.3 + - - +
469C VAL* 2.9 33.8 + - + +
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Residues in contact with ARG 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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379C ALA* 3.4 26.1 + - - +
380C CYS* 3.9 13.1 - - - +
381C SER* 3.5 15.0 - - - +
459C GLN* 4.8 12.7 - - - +
462C VAL* 2.6 28.5 + - - +
463C ALA* 3.8 36.8 + - - +
465C LEU* 1.3 71.5 - - - +
467C GLU* 1.3 57.6 + - - +
469C VAL* 3.3 1.9 + - - +
470C GLU* 2.8 59.6 + - - +
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Residues in contact with GLU 467 (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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463C ALA 3.2 11.2 + - - +
464C THR* 3.1 19.0 + - - +
465C LEU 3.1 0.2 - - - -
466C ARG* 1.3 76.9 - - - +
468C GLU* 1.3 64.1 + - - +
469C VAL 2.9 2.0 + - - -
470C GLU* 3.0 6.8 + - - +
471C ASN* 2.7 50.1 + - - +
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Residues in contact with GLU 468 (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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424C PHE* 3.5 20.2 - - + -
427C ARG* 2.5 34.9 + - - +
464C THR* 3.1 11.4 + - + +
465C LEU 3.8 6.5 - - - +
467C GLU* 1.3 81.9 + - - +
469C VAL* 1.3 59.9 - - - +
471C ASN* 3.7 9.6 - - - +
472C PHE* 3.2 22.5 + - - +
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Residues in contact with VAL 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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48C LEU* 3.9 23.6 - - + +
380C CYS 3.5 22.0 - - - +
381C SER* 3.9 17.9 - - - +
382C ILE* 4.2 8.1 - - + -
424C PHE* 3.7 31.4 - - + -
465C LEU* 2.9 31.4 + - + +
466C ARG 3.3 7.4 - - - +
468C GLU* 1.3 75.0 - - - +
470C GLU* 1.3 63.4 + - - +
472C PHE* 3.0 5.8 + - - +
473C ALA* 2.8 27.9 + - + +
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Residues in contact with GLU 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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46C VAL* 3.1 39.3 - - + +
381C SER* 3.3 21.9 + - - +
466C ARG* 2.8 51.1 + - - +
467C GLU* 3.7 5.7 - - - +
469C VAL* 1.3 72.1 - - - +
471C ASN* 1.3 52.8 + - - +
473C ALA* 3.7 7.1 - - - +
474C SER* 2.8 38.7 + - - -
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Residues in contact with ASN 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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467C GLU* 2.7 52.2 + - - +
468C GLU* 3.7 8.2 - - - +
470C GLU* 1.3 74.8 - - - +
472C PHE* 1.3 58.0 + - - +
474C SER* 3.1 11.3 + - - -
475C ASN* 2.4 34.2 + - - +
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Residues in contact with PHE 472 (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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48C LEU* 4.0 17.7 - - + -
413C LEU* 3.8 25.4 - - + -
417C ASP* 3.8 17.5 - - + -
420C LYS* 4.1 24.9 - - + -
421C VAL* 3.9 21.3 - - + -
424C PHE* 3.5 27.6 - + + -
468C GLU 3.2 12.7 + - - +
469C VAL 3.0 7.3 + - - +
471C ASN* 1.3 80.6 - - - +
473C ALA* 1.3 62.9 + - - +
475C ASN* 3.3 16.3 + - - +
476C PHE* 3.2 41.2 - + - -
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Residues in contact with ALA 473 (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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45C ARG 3.9 5.4 - - - +
46C VAL 3.8 0.9 - - - -
47C GLY* 3.4 41.5 - - - +
48C LEU* 4.5 8.1 - - + +
411C ARG* 3.8 6.5 + - - +
469C VAL 2.8 16.4 + - - +
470C GLU 3.7 4.5 - - - +
472C PHE* 1.3 76.6 - - - +
474C SER* 1.3 52.6 + - - +
475C ASN 2.6 17.8 + - - -
476C PHE* 2.8 27.7 + - - +
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Residues in contact with SER 474 (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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45C ARG* 3.5 41.7 + - - +
46C VAL* 3.6 7.6 - - - -
411C ARG* 4.9 1.1 - - - +
470C GLU 2.8 21.4 + - - -
471C ASN* 3.1 13.9 + - - -
473C ALA* 1.3 73.5 - - - +
475C ASN* 1.3 60.4 + - - +
476C PHE 3.2 7.9 + - - +
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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