Contacts of the helix formed by residues 492 - 501 (chain A) in PDB entry 2DFS
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 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A GLU* 2.9 50.4 + - - +
462A GLN* 4.7 2.4 - - - +
463A GLN* 3.3 31.2 - - - +
466A ASN* 3.7 16.2 + - - +
489A PHE* 6.0 1.4 - - - -
490A TYR 3.8 0.6 + - - +
491A ASP* 1.4 74.5 + - - +
493A GLN* 1.4 64.0 + - - +
494A PRO* 3.5 5.2 - - - -
495A CYS* 3.2 18.1 + - + +
496A ILE* 3.3 20.1 + - - +
553A PHE* 4.7 12.1 - - + -
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Residues in contact with GLN 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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460A LYS* 5.5 1.0 + - - -
463A GLN* 2.8 32.5 + - - +
491A ASP* 3.0 24.1 + - - +
492A ASN* 1.4 77.5 + - - +
494A PRO* 1.3 58.0 - - + +
496A ILE* 3.2 20.2 + - - +
497A ASN* 2.9 59.1 + - - +
500A GLU* 5.6 0.3 - - - +
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Residues in contact with PRO 494 (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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491A ASP* 3.3 22.2 - - - +
492A ASN* 3.6 4.3 - - - +
493A GLN* 1.3 89.5 - - + +
495A CYS* 1.4 56.1 + - - +
497A ASN* 3.8 8.3 - - + +
498A LEU* 3.1 26.2 + - - +
535A CYS* 5.5 2.8 - - - -
537A LEU* 3.7 18.3 - - + +
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Residues in contact with CYS 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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459A GLU* 3.5 33.7 - - - +
492A ASN* 3.2 14.5 + - + +
494A PRO* 1.4 75.6 - - - +
496A ILE* 1.4 65.7 + - - +
498A LEU* 3.2 7.0 + - - +
499A ILE* 3.2 28.4 + - - +
537A LEU* 3.5 18.8 - - + +
550A ILE* 4.2 12.6 - - - -
551A LYS 3.9 18.6 - - - +
552A HIS* 3.9 12.8 - - - -
553A PHE 5.9 0.2 - - - +
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Residues in contact with ILE 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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456A TYR* 5.1 4.7 - - + -
459A GLU* 3.8 29.8 - - + +
460A LYS* 4.0 33.2 - - + +
463A GLN* 3.5 27.8 - - + +
492A ASN* 3.3 30.3 + - - +
493A GLN* 3.2 25.7 + - - +
495A CYS* 1.4 74.5 - - - +
497A ASN* 1.3 56.4 + - - +
499A ILE* 3.4 10.3 + - - +
500A GLU* 2.9 35.5 + - + +
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Residues in contact with ASN 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 GLN* 2.9 48.4 + - - +
494A PRO* 3.8 8.6 - - + +
496A ILE* 1.3 74.4 - - - +
498A LEU* 1.3 61.4 + - - +
500A GLU* 5.1 3.2 - - - +
501A ALA* 2.9 46.3 + - + +
504A GLY* 4.6 1.4 - - - -
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Residues in contact with LEU 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 PRO 3.1 15.3 + - - +
495A CYS* 3.2 10.3 + - - +
497A ASN* 1.3 74.3 - - - +
499A ILE* 1.3 59.5 + - + +
504A GLY* 3.2 7.7 - - - -
505A VAL* 2.9 34.0 + - + +
531A HIS* 4.1 33.9 - - + +
535A CYS* 4.3 16.6 - - + -
537A LEU* 3.9 38.8 - - + +
538A PHE* 4.1 5.8 - - + -
550A ILE* 3.9 23.3 - - + -
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Residues in contact with ILE 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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452A PHE* 3.8 35.2 - - + +
456A TYR* 3.6 41.1 - - + -
459A GLU* 4.8 4.7 - - + -
495A CYS* 3.2 22.1 + - - +
496A ILE* 3.7 7.4 - - - +
498A LEU* 1.3 82.5 - - + +
500A GLU* 1.4 59.0 + - - +
501A ALA 3.9 0.2 - - - -
504A GLY 4.2 0.5 - - - -
505A VAL* 3.7 7.4 + - + +
506A LEU* 3.2 36.0 + - + +
507A ASP 4.7 0.2 + - - -
550A ILE* 5.3 5.2 - - + -
552A HIS* 3.9 28.0 - - + +
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Residues in contact with GLU 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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456A TYR* 2.6 42.3 + - + +
460A LYS* 2.6 37.0 + - - -
493A GLN* 5.6 0.3 - - - +
496A ILE* 2.9 26.9 + - + +
497A ASN* 5.1 3.1 - - - +
499A ILE* 1.4 72.4 - - - +
501A ALA* 1.3 66.0 + - - +
506A LEU* 4.7 5.4 - - + -
507A ASP* 5.7 1.4 - - - +
641A ARG* 2.6 48.5 + - - +
645A HIS* 3.5 1.2 + - - -
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Residues in contact with ALA 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 ASN* 2.9 34.4 + - + +
500A GLU* 1.3 84.0 - - - +
502A LYS* 1.4 65.4 + - - +
503A MET 3.5 0.2 + - - -
504A GLY* 3.0 20.9 + - - +
507A ASP* 3.6 8.2 - - - +
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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