Contacts of the helix formed by residues 483 - 497 (chain A) in PDB entry 4R8A
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 PRO 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A CYS 3.3 7.2 - - - +
482A LEU* 1.3 86.2 - - + +
484A ALA* 1.3 60.6 + - - +
485A ALA* 4.3 4.7 - - + +
486A HIS* 3.1 32.0 + - + +
487A LEU* 2.9 26.6 + - - +
517A ARG* 3.3 21.1 - - - +
518A TYR* 3.5 19.3 - - + -
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A LEU* 3.3 37.0 - - + +
442A GLU* 5.5 0.8 - - - +
446A TYR* 3.8 26.3 + - + +
447A ARG* 5.6 0.7 - - - +
482A LEU 3.7 2.0 + - - -
483A PRO* 1.3 72.0 - - - +
485A ALA* 1.3 57.7 + - - +
487A LEU* 3.1 12.5 + - - +
488A ARG* 3.0 24.8 + - - +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLU* 5.9 2.9 - - - -
483A PRO* 3.2 5.3 - - + +
484A ALA* 1.3 78.6 - - - +
486A HIS* 1.3 66.0 + - + +
488A ARG* 3.6 8.2 - - - +
489A ALA* 3.5 18.4 + - - +
546A MET* 5.0 0.2 - - - +
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Residues in contact with HIS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO* 3.1 40.6 + - + +
485A ALA* 1.3 83.3 - - + +
487A LEU* 1.3 64.2 + - - +
488A ARG 3.1 0.9 + - - -
489A ALA 3.4 1.6 + - - -
490A TRP* 3.3 37.8 + - + -
517A ARG* 4.5 5.6 - - - -
518A TYR* 2.8 26.6 + + - -
544A ARG* 3.9 10.3 + - + -
545A GLU 4.1 4.2 + - - -
546A MET* 3.5 44.5 - - + +
547A PRO* 4.1 7.0 - - + -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ILE* 5.9 0.7 - - + -
393A LEU* 4.2 26.2 - - + -
441A LEU* 3.8 16.8 - - + -
446A TYR* 3.7 31.0 - - + -
478A ALA 5.8 0.4 - - - +
479A LEU* 5.6 4.7 - - + -
482A LEU* 4.2 17.0 - - + +
483A PRO 2.9 18.8 + - - +
484A ALA* 3.1 9.6 + - - +
486A HIS* 1.3 75.6 - - - +
488A ARG* 1.3 62.5 + - - +
490A TRP* 3.7 26.8 + - + +
491A PHE* 3.0 47.4 + - + -
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 5.7 0.2 - - - +
435A GLU* 4.0 20.4 + - - +
438A LEU* 2.8 43.3 + - + +
439A GLY* 4.6 1.4 - - - +
441A LEU* 3.4 10.5 - - + +
442A GLU* 2.4 47.1 + - - +
484A ALA 3.0 12.2 + - - +
485A ALA* 3.6 13.2 - - - +
486A HIS 3.1 0.4 - - - -
487A LEU* 1.3 75.1 - - - +
489A ALA* 1.3 65.4 + - - +
491A PHE* 2.8 7.6 + - - +
492A GLU* 2.8 54.7 + - + +
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Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A ALA 3.5 7.2 + - - +
486A HIS 3.4 2.1 + - - +
488A ARG* 1.3 79.5 - - - +
490A TRP* 1.3 60.4 + - - +
492A GLU* 3.7 9.1 + - - +
493A ARG 3.2 15.1 + - - -
540A PHE* 3.3 17.3 - - + -
544A ARG* 4.0 19.5 - - - +
546A MET* 3.7 28.3 - - + -
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Residues in contact with TRP 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ILE* 3.7 37.6 - - + +
482A LEU* 3.6 26.5 - - + -
486A HIS* 3.3 24.1 + - + +
487A LEU* 3.7 33.9 - - + +
488A ARG 2.9 1.0 + - - -
489A ALA* 1.3 75.8 - - - +
491A PHE* 1.3 66.4 + - + +
493A ARG* 3.1 7.2 + - - +
494A LEU* 3.1 30.7 + - + +
505A LEU* 5.6 0.2 - - - +
518A TYR* 3.4 27.4 - + - -
520A MET* 3.7 20.9 - - + -
537A TRP* 3.9 21.4 - - - +
540A PHE* 4.1 10.5 - + - -
541A CYS* 3.6 11.6 - - - -
546A MET* 3.3 25.5 - - - -
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Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ILE* 3.9 17.7 - - + -
393A LEU* 3.8 13.9 - - + -
394A PHE* 3.5 58.9 - + + -
397A LEU* 3.9 21.5 - - + -
438A LEU* 3.7 31.0 - - + -
441A LEU* 4.2 5.2 - - + -
487A LEU* 3.0 44.6 - - + +
488A ARG* 2.8 4.7 + - - +
490A TRP* 1.3 77.8 - - + +
492A GLU* 1.3 62.3 + - - +
494A LEU* 3.4 6.9 + - + +
495A LEU* 3.3 26.0 + - - +
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 3.2 33.8 + - - +
438A LEU* 4.0 9.8 - - + +
488A ARG* 2.8 62.7 + - + +
489A ALA* 3.9 7.0 - - - +
491A PHE* 1.3 77.3 - - - +
493A ARG* 1.3 60.9 + - - +
495A LEU* 3.1 13.6 + - - +
496A GLU* 3.2 20.1 + - - +
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Residues in contact with ARG 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ASP* 4.8 11.5 + - - +
489A ALA 3.2 15.2 + - - +
490A TRP* 3.1 7.3 + - - +
492A GLU* 1.3 78.7 - - - +
494A LEU* 1.3 62.0 + - - +
496A GLU* 3.3 22.1 + - + +
501A ASN* 2.9 51.3 + - - +
533A ASN 4.8 0.2 + - - -
536A ARG* 3.6 42.0 + - - +
537A TRP* 3.5 43.6 - - + -
540A PHE* 3.6 41.1 - - + +
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE* 5.1 9.4 - - + +
391A ASN* 3.7 28.0 - - - +
394A PHE* 3.8 40.4 - - + -
464A PHE* 5.1 3.4 - - + -
490A TRP 3.1 24.7 + - - +
491A PHE* 3.6 10.3 - - - +
492A GLU 3.2 0.2 - - - -
493A ARG* 1.3 76.2 - - - +
495A LEU* 1.3 57.8 + - - +
497A ASP 3.1 0.7 - - - -
498A ILE* 3.0 41.0 + - + +
501A ASN* 3.7 14.8 - - - +
502A ARG* 5.3 1.1 - - + -
505A LEU* 5.7 2.2 - - + -
537A TRP* 3.5 31.2 - - + -
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A PHE* 3.6 26.0 - - + -
426A PHE* 4.7 4.9 - - + -
427A ARG* 3.4 63.4 - - + +
434A PHE* 3.6 36.6 - - + -
438A LEU* 4.8 7.2 - - + -
491A PHE 3.3 11.8 + - - +
492A GLU* 3.1 5.8 + - - +
494A LEU* 1.3 72.7 - - - +
496A GLU* 1.3 66.1 + - - +
497A ASP* 3.2 2.0 - - - -
498A ILE* 4.0 22.4 + - + +
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Residues in contact with GLU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 5.8 2.3 + - - -
492A GLU* 3.2 20.5 + - - +
493A ARG* 3.4 21.9 - - + +
494A LEU 3.2 0.2 - - - -
495A LEU* 1.3 78.6 - - - +
497A ASP* 1.3 63.2 + - + +
501A ASN* 4.3 4.0 - - - +
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Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A ARG 3.7 1.4 + - - -
494A LEU 3.1 2.6 + - - -
495A LEU 3.2 1.0 - - - -
496A GLU* 1.3 84.5 - - + +
498A ILE* 1.3 58.8 + - - +
499A PRO* 3.2 19.1 - - - +
500A GLY* 3.1 22.8 + - - -
501A ASN* 2.8 39.4 + - - +
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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