Contacts of the strand formed by residues 225 - 229 (chain C) in PDB entry 3KDO
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 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C MET* 3.3 15.8 - - - +
150C LEU* 3.8 20.4 - - + -
181C LEU* 4.6 3.5 - - - +
186C ASP 3.3 3.9 + - - +
187C TYR* 3.2 38.7 - - + -
188C MET 3.3 3.8 + - - -
209C MET* 4.6 2.1 - - - +
213C ILE* 3.7 12.3 - - - +
224C LYS* 1.3 76.6 - - - +
226C TRP* 1.3 69.3 + - - +
227C PHE* 3.9 6.7 - - + -
250C LYS* 3.8 7.8 + - - +
251C HIS* 2.8 35.7 + - + +
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Residues in contact with TRP 226 (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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173C PHE* 4.5 3.4 - + - -
188C MET* 3.1 36.1 - - + +
190C ASP* 3.0 33.5 + - - -
202C PHE* 4.4 5.8 - + - -
205C ARG* 3.8 18.6 - - + -
206C ALA* 3.2 43.1 - - + -
209C MET* 3.5 40.7 - - + +
213C ILE* 4.1 5.9 - - + +
225C THR* 1.3 84.2 + - - +
227C PHE* 1.3 64.9 + - - +
228C ALA* 3.1 38.6 + - + -
244C LEU* 3.7 2.0 - - + -
249C LEU* 3.5 25.0 - - + +
251C HIS* 3.4 17.8 + - - +
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Residues in contact with PHE 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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150C LEU* 6.1 1.1 - - + -
157C ILE* 5.7 1.6 - - + -
187C TYR* 3.3 51.4 - + + -
188C MET 2.8 9.3 + - - -
189C KCX 3.8 17.5 - - + -
190C ASP* 3.2 24.1 + - - +
225C THR* 3.9 10.8 - - + -
226C TRP* 1.3 71.4 - - - +
228C ALA* 1.3 62.9 + - - +
229C ASN 3.4 1.6 + - - -
251C HIS* 3.4 46.9 - + + -
253C MET* 3.8 17.1 - - + +
279C HIS* 3.7 35.0 - + + -
312C GLN* 3.4 13.9 - - - -
387C VAL* 4.7 4.7 - - + -
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Residues in contact with ALA 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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190C ASP* 3.5 6.3 - - - -
202C PHE* 3.6 7.9 - - + -
226C TRP* 3.1 44.1 + - + -
227C PHE* 1.3 69.2 - - - +
229C ASN* 1.3 58.7 + - - +
230C ILE* 3.1 10.9 + - - +
244C LEU* 3.6 22.2 - - + -
251C HIS 4.0 3.4 + - - +
252C ALA 3.7 0.2 - - - -
253C MET* 2.7 28.5 + - - +
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Residues in contact with ASN 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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190C ASP* 3.0 23.0 + - + -
191C ASP 3.3 6.1 + - - -
192C GLU 3.0 27.7 + - - -
194C LEU 3.0 32.2 + - - +
195C THR* 4.3 7.1 - - - +
202C PHE* 3.5 15.7 - - - -
205C ARG* 4.1 1.7 + - - -
227C PHE 3.4 3.0 + - - -
228C ALA* 1.3 69.0 - - - +
230C ILE* 1.3 58.6 + - - +
231C THR* 2.5 33.2 + - - -
240C ARG* 5.1 0.7 + - - -
253C MET* 3.6 23.9 - - - +
255C ASP* 3.7 2.8 - - - +
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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