Contacts of the helix formed by residues 226 - 230 (chain C) in PDB entry 5D0A
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 PRO 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C LEU* 4.9 4.9 - - + -
221C THR* 6.0 0.4 - - - +
224C PHE 3.3 8.7 - - - +
225C LEU* 1.3 94.2 - - + +
227C ASP* 1.3 67.3 + - - +
228C GLU* 4.6 7.0 - - + +
229C PHE* 3.1 38.0 + - + +
230C ARG* 3.7 5.4 + - - +
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Residues in contact with ASP 227 (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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42A SER* 3.0 47.9 + - - +
225C LEU 4.2 0.2 - - - +
226C PRO* 1.3 72.8 - - - +
228C GLU* 1.3 64.5 + - - +
229C PHE 3.0 1.4 + - - -
230C ARG* 3.0 38.3 + - - +
231C THR* 4.3 4.3 + - - +
338C TRP* 4.2 9.6 + - + +
370C LYS* 2.8 36.0 + - - +
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Residues in contact with GLU 228 (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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42A SER 4.7 2.7 + - - +
213C ARG* 3.4 27.2 + - - -
226C PRO* 4.6 6.9 - - + +
227C ASP* 1.3 78.1 - - - +
229C PHE* 1.3 93.2 + - + +
231C THR* 3.8 13.0 + - - -
232C LYS* 3.8 11.3 - - - +
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Residues in contact with PHE 229 (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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200C THR* 3.9 20.6 - - + -
212C GLN 4.2 4.3 - - - -
213C ARG* 4.0 41.5 - - + -
215C ILE* 6.3 0.7 - - + -
218C LEU* 3.4 41.1 - - + -
225C LEU* 4.0 13.9 - - + -
226C PRO* 3.1 27.9 + - + +
227C ASP 3.1 0.8 - - - -
228C GLU* 1.3 111.7 - - + +
230C ARG* 1.3 65.0 + - - +
231C THR 3.1 3.6 - - - -
232C LYS* 3.0 17.4 + - + +
233C ILE* 3.2 17.3 + - + +
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Residues in contact with ARG 230 (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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224C PHE* 4.1 13.9 - - - +
225C LEU* 2.7 41.4 + - + +
226C PRO 3.7 6.5 - - - +
227C ASP* 3.0 31.8 + - - +
229C PHE* 1.3 77.4 - - - +
231C THR* 1.3 60.1 + - + +
232C LYS 3.5 0.2 - - - -
233C ILE* 3.6 15.3 - - - +
234C GLY 5.2 0.2 + - - -
306C LEU* 4.1 26.0 - - + +
310C HIS* 5.5 4.3 - - - +
335C THR* 5.3 6.4 + - - +
338C TRP* 3.1 62.7 - - + +
367C GLU* 2.7 45.2 + - - -
370C LYS* 3.8 1.0 - - - +
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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