Contacts of the helix formed by residues 5288 - 5293 (chain c) in PDB entry 3A0B
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 CYS5288 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5163a ILE* 3.8 21.5 - - - -
5295a PHE* 5.7 4.9 - - - -
5225c VAL* 3.5 10.9 - - + +
5284c PHE 3.1 8.4 + - - +
5285c ILE 4.7 0.7 - - - +
5286c ALA 2.6 5.5 + - - -
5287c THR* 1.3 80.0 - - - +
5289c PHE* 1.3 57.6 + - - +
5291c TRP* 3.8 4.7 - - - -
5292c PHE* 3.0 39.1 + - + -
6055c DGD 2.8 59.2 - - + -
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Residues in contact with PHE5289 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5224c ILE* 3.1 41.3 - - + -
5225c VAL* 3.1 24.2 - - + +
5285c ILE* 2.8 27.3 + - + -
5286c ALA 2.4 23.7 + - - +
5288c CYS* 1.3 65.3 - - - +
5290c VAL* 1.3 65.0 + - - +
5291c TRP 3.0 2.3 + - - -
5293c ASN* 3.1 51.6 + - + +
5296c VAL* 4.4 0.9 - - + -
5297c TYR* 3.1 18.5 - + + -
6025c CLA 2.9 67.3 - + + +
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Residues in contact with VAL5290 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5286c ALA 3.2 3.8 + - - +
5287c THR* 3.6 10.8 - - - +
5289c PHE* 1.3 80.3 - - - +
5291c TRP* 1.3 60.0 + - - +
5297c TYR* 3.8 24.1 - - + -
5302c TYR* 5.7 1.3 - - + -
5423c ARG* 3.1 45.9 + - + +
5426c LEU* 3.2 42.4 - - + +
5427c ALA* 3.5 33.2 - - + +
6026c CLA 4.1 6.7 - - - -
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Residues in contact with TRP5291 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5163a ILE 4.2 0.4 - - - -
5164a GLY 3.1 22.3 + - - -
5165a GLN* 6.0 0.2 - - - -
5294a ALA 4.1 2.5 - - - -
5295a PHE* 3.2 66.9 - + + -
5296a ASN* 4.0 7.9 - - - -
5287c THR 3.5 18.4 - - - +
5288c CYS* 3.5 6.2 + - - +
5289c PHE 3.0 0.6 - - - -
5290c VAL* 1.3 83.0 - - + +
5292c PHE* 1.3 83.8 + + - +
5305c THR* 2.4 31.4 + - - -
5306c GLY* 4.1 14.4 + - - -
5307c PRO* 4.4 2.2 - - + +
5400c PRO* 3.7 26.9 - - + -
5401c LEU* 6.2 0.2 - - + -
5423c ARG* 3.2 32.9 + - + -
5424c SER* 3.7 7.0 - - - -
5427c ALA* 3.7 0.4 - - + -
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Residues in contact with PHE5292 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5091a LEU* 4.3 4.5 - - + -
5163a ILE* 3.2 39.9 - - + -
5164a GLY 4.9 1.6 - - - -
5165a GLN 5.5 1.3 - - - -
5225c VAL* 3.6 13.2 - - + -
5288c CYS* 3.0 32.5 + - + -
5291c TRP* 1.3 96.5 - + - +
5293c ASN* 1.3 66.6 + - - +
5294c ASN 3.2 0.2 + - - -
5305c THR* 3.2 10.6 + - - -
5307c PRO* 4.2 24.9 - - + -
5358c PHE* 5.5 2.7 - + - -
5423c ARG* 4.1 0.2 - - - -
6055c DGD 2.7 86.7 + - - +
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Residues in contact with ASN5293 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5225c VAL* 3.5 14.4 + - + +
5227c VAL* 3.0 24.6 - - - +
5289c PHE* 3.1 40.0 + - + +
5292c PHE* 1.3 75.2 - - - +
5294c ASN* 1.3 57.6 + - - +
5295c THR* 2.4 25.5 + - - -
5296c VAL* 2.8 28.6 - - - +
5297c TYR* 2.8 20.6 - - + +
5423c ARG* 2.5 25.4 + - - -
6055c DGD 4.1 3.1 - - - -
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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