Contacts of the helix formed by residues 485 - 489 (chain D) in PDB entry 2W93
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 ALA 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ASP* 4.8 2.2 - - - +
38C TYR* 5.2 2.5 - - + -
482D GLY* 3.0 18.9 + - - +
484D LYS* 1.3 79.5 - - - +
486D GLN* 1.3 61.4 + - - +
487D TYR* 3.4 41.7 - - + +
488D ASN* 3.0 23.4 + - - +
489D GLU* 3.7 5.9 - - - +
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Residues in contact with GLN 486 (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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38C TYR* 3.5 31.8 + - + +
45C TRP* 5.1 2.2 - - + -
459C ARG* 4.3 6.6 + - - -
460C TRP* 5.3 10.0 - - - -
484D LYS 3.5 5.1 + - - +
485D ALA* 1.3 72.1 - - - +
487D TYR* 1.3 61.4 + - - +
489D GLU* 3.1 31.0 + - + +
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Residues in contact with TYR 487 (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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26C PRO* 3.5 23.8 - - + +
31C LEU* 3.5 28.2 + - + -
34C LEU* 3.6 31.0 - - + -
35C ASP* 2.7 31.7 + - - -
38C TYR* 3.1 23.2 + + - +
45C TRP* 3.4 32.2 + + + +
47C GLY* 6.0 0.8 - - - -
474D TYR* 3.6 7.1 - - - -
481D HIS* 3.2 23.1 - - - -
482D GLY* 4.0 2.3 - - - -
485D ALA* 3.4 22.7 - - + +
486D GLN* 1.3 76.9 - - - +
488D ASN* 1.3 82.5 + - - +
489D GLU 3.3 3.5 + - - +
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Residues in contact with ASN 488 (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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31C LEU* 4.5 0.4 - - - +
474D TYR* 3.0 33.5 + - - +
477D GLN* 2.8 38.2 + - - +
478D LYS* 3.5 33.1 - - + +
481D HIS 3.0 19.4 + - - -
482D GLY 2.9 22.7 + - - +
485D ALA 3.0 11.3 + - - +
487D TYR* 1.3 94.5 - - - +
489D GLU* 1.3 60.1 + - - +
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Residues in contact with GLU 489 (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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47C GLY* 6.0 0.2 - - - -
459C ARG* 3.2 20.3 + - - +
472D ASP* 3.3 12.6 - - - +
473D GLY* 4.7 0.7 - - - -
474D TYR* 4.8 0.9 - - - -
478D LYS* 2.8 35.6 + - - -
483D PRO 4.6 0.5 - - - +
484D LYS* 4.4 16.7 - - - +
485D ALA 3.7 13.2 - - - +
486D GLN* 3.1 21.6 + - + +
487D TYR 4.1 4.9 - - - +
488D ASN* 1.3 81.0 - - - +
490D ILE* 1.3 69.2 + - - +
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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