Contacts of the helix formed by residues 489 - 504 (chain A) in PDB entry 4B18
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 ASN 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A SER* 3.9 15.5 + - - +
441A GLN* 4.8 6.7 + - - +
487A HIS* 2.9 17.2 + - + +
488A GLU* 1.3 80.9 + - - +
490A GLN* 1.3 61.3 + - - +
491A GLU* 3.2 23.6 + - - +
492A ILE* 3.3 29.3 + - + +
493A TYR* 3.0 30.4 + - - +
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Residues in contact with GLN 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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488A GLU 3.5 4.6 + - - +
489A ASN* 1.3 74.9 + - - +
491A GLU* 1.3 67.5 + - + +
493A TYR* 3.3 34.1 + - - -
494A GLN* 3.0 43.8 + - + +
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Residues in contact with GLU 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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441A GLN* 3.8 30.9 + - - +
489A ASN* 3.2 12.3 + - - +
490A GLN* 1.3 80.3 - - + +
492A ILE* 1.3 61.0 + - - +
494A GLN* 3.6 6.3 - - - +
495A LYS* 2.8 35.4 + - + +
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A SER* 3.5 33.9 - - - +
440A VAL* 3.7 18.2 - - + -
441A GLN* 3.7 17.9 - - + +
444A LEU* 4.2 10.4 - - + +
484A LEU* 3.5 36.1 - - + +
487A HIS* 4.0 12.8 - - + +
489A ASN* 3.3 32.3 - - + +
491A GLU* 1.3 77.8 - - - +
493A TYR* 1.3 64.0 + - - +
495A LYS* 3.6 1.8 - - - +
496A ALA* 3.0 22.9 + - - +
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Residues in contact with TYR 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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484A LEU 3.6 13.4 + - - +
485A GLN* 3.5 31.7 - - + +
487A HIS 4.1 8.5 - - - +
488A GLU 6.0 0.2 - - - -
489A ASN 3.0 14.3 + - - +
490A GLN* 3.3 44.1 + - - -
492A ILE* 1.3 74.6 - - - +
494A GLN* 1.3 67.9 + - + +
496A ALA* 3.5 2.3 + - - +
497A PHE* 2.8 47.7 + + + +
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Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLN* 3.0 36.6 + - + +
491A GLU* 3.6 7.6 - - - +
493A TYR* 1.3 93.7 + - + +
495A LYS* 1.3 60.5 + - - +
497A PHE* 2.9 12.0 + - - -
498A ASP* 2.7 68.7 + - - +
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Residues in contact with LYS 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 6.5 0.9 - - + -
444A LEU* 4.3 28.7 - - + +
445A ASN* 5.0 11.7 + - - +
448A GLU* 2.8 36.8 + - - +
491A GLU* 2.8 21.5 + - + +
492A ILE* 3.6 3.8 - - - +
494A GLN* 1.3 70.1 - - - +
496A ALA* 1.3 67.1 + - - +
497A PHE 3.1 0.2 + - - -
498A ASP* 3.1 14.1 + - - +
499A LEU* 2.9 39.2 + - + +
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Residues in contact with ALA 496 (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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444A LEU* 4.9 6.6 - - + +
481A ILE* 3.3 38.7 - - + +
484A LEU* 4.0 14.1 - - + -
485A GLN* 4.1 7.2 - - + -
492A ILE 3.0 17.0 + - - +
493A TYR 3.7 4.0 - - - +
495A LYS* 1.3 75.4 - - - +
497A PHE* 1.3 62.5 + - - +
499A LEU* 3.9 2.3 - - - +
500A ILE* 3.1 29.9 + - - +
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Residues in contact with PHE 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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485A GLN* 3.6 27.3 - - + +
493A TYR* 2.8 34.3 + + + +
494A GLN* 2.9 13.7 + - - +
496A ALA* 1.3 78.0 - - - +
498A ASP* 1.3 70.6 + - - +
500A ILE* 3.4 5.6 + - + +
501A GLU* 3.1 52.0 + - + +
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Residues in contact with ASP 498 (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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494A GLN* 2.7 48.2 + - - +
495A LYS* 3.8 12.9 + - - +
497A PHE* 1.3 77.2 - - - +
499A LEU* 1.3 57.8 + - + +
501A GLU* 3.4 9.8 + - - +
502A HIS* 2.7 38.6 + - + +
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Residues in contact with LEU 499 (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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444A LEU* 4.3 37.5 - - + +
447A LEU* 5.2 1.3 - - + -
448A GLU* 3.6 44.9 - - + +
451A LEU* 4.8 11.2 - - + -
481A ILE* 5.0 11.0 - - + -
495A LYS* 2.9 26.3 + - + +
496A ALA* 4.0 3.6 - - - +
498A ASP* 1.3 77.8 - - + +
500A ILE* 1.3 59.8 + - - +
501A GLU 3.1 1.1 - - - -
502A HIS* 5.3 1.6 - - + +
503A TYR* 2.8 53.3 + - + +
504A PHE* 3.7 7.2 - - + -
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Residues in contact with ILE 500 (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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478A LEU* 5.2 5.6 - - + -
481A ILE* 4.1 12.5 - - + +
482A GLU* 4.0 22.9 - - + -
485A GLN* 3.4 39.5 - - - +
496A ALA 3.1 21.4 + - - +
497A PHE* 3.6 9.9 - - + +
499A LEU* 1.3 74.0 - - - +
501A GLU* 1.3 61.5 + - + +
504A PHE* 2.8 58.0 + - + +
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Residues in contact with GLU 501 (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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497A PHE* 3.1 41.2 + - + +
498A ASP* 3.7 8.0 - - - +
500A ILE* 1.3 86.8 - - + +
502A HIS* 1.3 59.9 + - - +
504A PHE 4.7 3.0 + - - +
505A GLY 5.6 3.3 - - - -
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Residues in contact with HIS 502 (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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448A GLU* 5.9 1.0 + - - -
452A ARG* 5.6 2.5 - - + -
455A GLU* 3.1 31.2 + - - +
498A ASP* 2.7 22.9 + - + +
499A LEU* 5.3 1.0 - - + +
501A GLU* 1.3 75.3 - - - +
503A TYR* 1.3 91.4 + + + +
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Residues in contact with TYR 503 (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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448A GLU* 4.3 5.4 + - + +
451A LEU* 3.4 42.4 - - + -
452A ARG* 2.7 32.7 - - - +
455A GLU* 3.9 18.9 + - + -
466A ASN* 3.7 17.9 - - - -
469A CYS* 3.2 25.2 - - - +
499A LEU* 2.8 43.9 + - + +
502A HIS* 1.3 107.3 - + + +
504A PHE* 1.3 75.4 + - + +
505A GLY 3.8 3.1 + - - -
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Residues in contact with PHE 504 (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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451A LEU* 4.2 12.8 - - + -
469A CYS* 3.6 39.3 - - + -
472A ILE* 4.0 28.9 - - + -
473A GLU* 5.1 4.3 - - + -
478A LEU* 3.6 35.9 - - + -
481A ILE* 5.1 9.9 - - + -
499A LEU* 3.7 15.5 - - + -
500A ILE* 2.8 35.7 + - + +
501A GLU* 5.1 1.4 - - - +
502A HIS 3.9 0.4 - - - -
503A TYR* 1.3 92.7 - - + +
505A GLY* 1.3 65.3 + - - +
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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