Contacts of the helix formed by residues 458 - 474 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431D LEU* 6.1 0.2 - - - +
456D GLU* 2.4 48.4 + - + +
457D LYS* 1.3 76.3 - - - +
459D GLN* 1.3 49.4 + - - +
460D SER* 2.3 13.2 + - - +
461D ALA* 2.4 50.7 + - + +
462D VAL* 3.5 1.6 + - - +
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Residues in contact with GLN 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ALA* 6.2 1.6 - - - +
453D ALA* 4.1 39.3 + - - +
455D ASP 5.8 0.2 - - - +
456D GLU* 3.4 7.4 + - - +
457D LYS* 3.3 15.2 + - - -
458D ILE* 1.3 76.0 - - - +
460D SER* 1.3 56.9 + - - +
462D VAL* 2.9 36.3 - - + +
463D ALA* 3.0 15.7 - - + +
466D ARG* 4.7 12.0 - - - +
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Residues in contact with SER 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D LYS* 2.7 27.2 + - - +
458D ILE* 2.3 24.8 - - - -
459D GLN 1.3 68.0 - - - +
461D ALA* 1.3 54.0 + - - -
463D ALA* 3.9 6.3 - - - +
464D THR* 2.7 32.7 + - - -
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Residues in contact with ALA 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D LEU* 4.3 21.1 - - + -
458D ILE* 2.4 35.5 + - + +
460D SER* 1.3 71.4 - - - +
462D VAL* 1.3 66.5 + - - +
464D THR* 3.1 15.8 + - - -
465D LEU* 3.1 13.7 + - - +
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Residues in contact with VAL 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D VAL* 4.9 0.9 - - + +
379D ALA* 3.3 41.1 - - + +
380D CYS* 3.3 24.0 - - - -
431D LEU* 4.1 12.4 - - + +
453D ALA* 6.4 1.3 - - + -
458D ILE 3.5 1.0 + - - +
459D GLN* 2.9 42.0 - - + +
461D ALA* 1.3 79.4 - - - +
463D ALA* 1.3 64.8 + - - +
464D THR 3.0 0.7 + - - -
465D LEU* 3.0 2.0 + - - +
466D ARG* 2.6 40.7 + - - +
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Residues in contact with ALA 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D GLN* 3.0 18.5 + - + +
460D SER* 3.9 8.7 - - - +
461D ALA 3.3 0.2 - - - -
462D VAL* 1.3 81.9 - - - +
464D THR* 1.3 61.1 + - - +
466D ARG* 3.7 28.5 + - - +
467D GLU* 3.2 21.7 + - - +
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Residues in contact with THR 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D ARG* 6.2 1.8 - - - +
460D SER 2.7 19.9 + - - -
461D ALA* 3.1 9.1 + - - -
462D VAL 3.1 0.6 - - - -
463D ALA* 1.3 76.5 - - - +
465D LEU* 1.3 66.1 + - - +
467D GLU* 3.1 16.6 + - - +
468D GLU* 3.1 23.0 + - + +
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Residues in contact with LEU 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D CYS* 3.9 22.9 - - + -
382D ILE* 5.6 1.3 - - + -
424D PHE* 3.8 26.9 - - + +
427D ARG* 3.7 52.9 - - + +
428D GLY* 4.0 17.0 - - - +
431D LEU* 4.9 7.2 - - + -
461D ALA 3.1 8.3 + - - +
462D VAL* 3.0 6.4 + - - +
464D THR* 1.3 76.4 - - - +
466D ARG* 1.3 66.9 + - - +
467D GLU 3.2 0.2 + - - -
468D GLU* 3.2 4.1 + - - +
469D VAL* 2.9 34.3 + - + +
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Residues in contact with ARG 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D ALA 3.4 19.7 + - - +
380D CYS* 3.9 19.9 - - - +
381D SER* 3.6 13.9 - - - +
459D GLN* 4.7 12.5 - - - +
462D VAL* 2.6 27.7 + - - +
463D ALA* 3.7 37.0 + - - +
465D LEU* 1.3 71.5 - - - +
467D GLU* 1.3 58.7 + - - +
469D VAL* 3.3 1.7 + - - +
470D GLU* 2.8 59.4 + - - +
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Residues in contact with GLU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D ALA 3.2 11.6 + - - +
464D THR* 3.1 18.4 + - - +
465D LEU 3.1 0.6 - - - -
466D ARG* 1.3 75.7 - - - +
468D GLU* 1.3 64.2 + - - +
469D VAL 2.9 2.4 + - - -
470D GLU* 3.0 7.0 + - - +
471D ASN* 2.6 50.5 + - - +
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Residues in contact with GLU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D PHE* 3.4 21.4 - - + -
427D ARG* 2.6 34.7 + - - +
464D THR* 3.1 11.3 + - + +
465D LEU* 3.8 6.7 - - - +
467D GLU* 1.3 81.6 + - - +
469D VAL* 1.3 59.5 - - - +
471D ASN* 3.7 9.5 - - - +
472D PHE* 3.2 22.2 + - - +
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Residues in contact with VAL 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 3.8 27.1 - - + +
380D CYS 3.6 22.9 - - - +
381D SER* 3.9 14.6 - - - +
382D ILE* 4.1 8.5 - - + -
424D PHE* 3.8 31.0 - - + -
465D LEU* 2.9 31.1 + - + +
466D ARG 3.4 7.0 - - - +
468D GLU* 1.3 75.2 - - - +
470D GLU* 1.3 61.7 + - - +
472D PHE* 3.0 5.3 + - - +
473D ALA* 2.8 27.9 + - + +
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Residues in contact with GLU 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 3.2 39.4 - - + +
381D SER* 3.3 21.8 + - - +
466D ARG* 2.8 57.7 + - - +
467D GLU* 3.7 5.7 - - - +
469D VAL* 1.3 73.2 - - - +
471D ASN* 1.3 52.9 + - - +
473D ALA* 3.6 6.4 - - - +
474D SER* 2.7 39.2 + - - -
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Residues in contact with ASN 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D GLU* 2.6 52.2 + - - +
468D GLU* 3.7 8.4 - - - +
470D GLU* 1.3 74.8 - - - +
472D PHE* 1.3 57.9 + - - +
474D SER* 3.1 11.5 + - - -
475D ASN* 2.4 34.6 + - - +
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Residues in contact with PHE 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.0 17.3 - - + -
413D LEU* 3.7 25.6 - - + -
417D ASP* 3.8 19.1 - - + -
420D LYS* 4.1 24.5 - - + -
421D VAL* 3.9 21.8 - - + -
424D PHE* 3.5 27.6 - + + -
468D GLU 3.2 12.8 + - - +
469D VAL 3.0 6.9 + - - +
471D ASN* 1.3 80.2 - - - +
473D ALA* 1.3 63.3 + - - +
475D ASN* 3.3 16.8 + - - +
476D PHE* 3.1 39.9 - + - -
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Residues in contact with ALA 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ARG 3.9 4.7 - - - +
46D VAL 3.8 0.9 - - - -
47D GLY* 3.4 41.3 - - - +
48D LEU* 4.6 9.2 - - + -
411D ARG* 4.0 6.0 + - - +
469D VAL 2.8 15.7 + - - +
470D GLU 3.6 4.5 - - - +
472D PHE* 1.3 76.4 - - - +
474D SER* 1.3 52.4 + - - +
475D ASN 2.5 17.7 + - - -
476D PHE* 2.8 28.6 + - - +
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Residues in contact with SER 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ARG* 3.5 38.3 + - - +
46D VAL* 3.6 8.7 - - - +
411D ARG* 4.9 1.3 - - - +
470D GLU 2.7 20.9 + - - -
471D ASN* 3.1 14.6 + - - -
473D ALA* 1.3 73.7 - - - +
475D ASN* 1.3 60.1 + - - +
476D PHE 3.2 7.8 + - - +
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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