Contacts of the helix formed by residues 493 - 500 (chain A) in PDB entry 2W8D
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 THR 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A GLU* 5.2 2.2 - - - -
491A GLU* 3.9 27.6 - - + +
492A ILE* 1.3 78.7 - - - +
494A ASP* 1.3 65.7 + - - +
495A TYR* 3.6 10.7 + - - +
496A ASP* 3.0 32.8 + - - +
497A ASN* 3.0 20.7 + - - +
577A TYR* 6.4 1.1 - - - -
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Residues in contact with ASP 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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477A GLU* 4.3 14.1 - - - +
493A THR* 1.3 73.5 - - - +
495A TYR* 1.3 62.4 + - - +
497A ASN* 3.5 7.4 + - - +
498A ALA* 3.1 22.0 + - - +
572A ILE* 4.1 30.7 - - + +
573A SER* 5.1 5.5 + - - -
575A LYS* 5.3 4.7 - - - +
577A TYR* 4.0 19.4 + - - +
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Residues in contact with TYR 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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493A THR* 3.6 8.2 + - - +
494A ASP* 1.3 80.5 - - - +
496A ASP* 1.3 79.7 + - - +
498A ALA* 3.1 15.8 + - - +
499A GLN* 3.2 49.5 + - + +
570A THR* 3.8 9.0 - - + -
572A ILE* 5.2 0.4 - - - -
577A TYR* 3.8 40.6 - - + -
578A ASP 3.7 10.1 - - - -
579A THR 2.7 21.2 + - - -
580A LYS 3.9 5.5 + - - -
581A THR 4.2 1.6 - - - -
582A GLY* 3.5 36.6 + - - +
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Residues in contact with ASP 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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487A LEU* 5.6 0.9 - - + -
489A LYS* 3.7 26.2 - - - +
491A GLU 3.4 14.0 - - - +
492A ILE* 3.7 15.0 - - + -
493A THR* 3.0 36.4 + - - +
495A TYR* 1.3 94.0 - - - +
497A ASN* 1.3 64.6 + - - +
499A GLN* 3.0 19.0 + - - +
500A LEU* 3.0 18.9 + - + +
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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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475A ILE 4.9 6.1 - - - +
476A SER 5.1 0.5 - - - -
477A GLU* 3.3 49.2 + - - +
480A ASN* 4.7 3.5 - - - +
492A ILE* 4.0 5.9 - - + +
493A THR 3.0 16.0 + - - +
494A ASP* 3.7 5.4 - - - +
496A ASP* 1.3 77.9 - - - +
498A ALA* 1.3 60.4 + - - +
500A LEU* 3.1 19.8 + - - +
501A GLN* 3.0 43.6 + - - +
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Residues in contact with ALA 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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289A PHE* 3.9 10.7 - - - -
494A ASP 3.1 10.6 + - - +
495A TYR 3.1 9.6 + - - +
497A ASN* 1.3 75.8 - - - +
499A GLN* 1.3 68.4 + - - +
501A GLN* 3.1 25.2 + - - +
559A PHE* 4.4 9.1 - - + -
565A ILE* 5.1 2.7 - - + -
570A THR* 4.0 12.8 - - - +
572A ILE* 3.6 34.1 - - + -
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Residues in contact with GLN 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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495A TYR* 3.2 59.4 + - + +
496A ASP* 3.0 10.4 + - - +
498A ALA* 1.3 76.9 - - - +
500A LEU* 1.3 60.2 + - + +
501A GLN 3.2 4.0 + - - -
502A ARG* 2.8 63.2 + - - +
565A ILE* 3.7 10.8 - - - +
570A THR* 3.3 22.0 + - - +
579A THR* 4.6 4.4 - - - +
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Residues in contact with LEU 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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256A GLN* 2.9 27.4 - - - +
258A PHE* 3.8 37.2 - - + -
473A TYR* 4.9 0.2 - - - +
483A MSE 3.9 20.6 - - + -
487A LEU* 3.9 28.9 - - + -
492A ILE* 4.4 14.4 - - + -
496A ASP 3.0 21.9 + - - +
497A ASN* 3.1 19.6 + - - +
499A GLN* 1.3 75.2 - - + +
501A GLN* 1.3 64.7 + - - +
502A ARG* 3.2 12.5 + - - +
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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