Contacts of the strand formed by residues 225 - 229 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A MET* 3.4 14.7 - - - +
150A LEU* 3.9 19.5 - - + -
181A LEU* 4.7 2.1 - - - +
186A ASP 3.2 3.9 + - - +
187A TYR* 3.2 39.7 - - + -
188A MET 3.3 4.2 + - - -
209A MET* 4.6 3.1 - - - +
213A ILE* 3.9 11.3 - - - +
224A LYS* 1.3 76.4 - - - +
226A TRP* 1.3 69.1 + - - +
227A PHE* 3.6 16.8 - - + -
250A LYS* 4.0 4.9 + - - +
251A HIS* 2.6 31.2 + - + +
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Residues in contact with TRP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 4.4 4.0 - - - -
188A MET* 3.1 38.4 - - + -
189A KCX 4.3 0.4 - - - -
190A ASP* 3.0 42.9 + - - +
202A PHE* 4.5 7.6 - + - -
205A ARG* 3.7 16.4 - - + -
206A ALA* 3.6 38.1 - - + -
209A MET* 3.5 38.2 - - + +
213A ILE* 4.4 5.5 - - + +
225A THR* 1.3 84.0 + - - +
227A PHE* 1.3 64.3 + - - +
228A ALA* 3.1 33.9 + - + -
244A LEU* 3.9 1.1 - - + -
249A LEU* 3.8 25.2 - - + +
250A LYS 6.0 0.4 - - - +
251A HIS* 3.1 19.5 + - - +
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Residues in contact with PHE 227 (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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150A LEU* 6.0 1.3 - - + -
157A ILE* 5.8 1.6 - - + -
187A TYR* 3.0 52.0 - + - -
188A MET 2.9 7.5 + - - -
189A KCX 3.9 17.5 - - + -
190A ASP* 3.1 24.6 + - - +
225A THR* 3.6 16.2 - - + -
226A TRP* 1.3 70.3 - - - +
228A ALA* 1.3 62.2 + - - +
229A ASN 3.5 1.2 + - - -
251A HIS* 3.4 42.2 - + - -
253A MET* 3.8 16.9 - - + +
279A HIS* 3.6 35.2 - + + -
312A GLN* 3.6 13.2 - - - -
387A VAL* 4.6 5.4 - - + -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP* 3.5 6.3 - - - -
202A PHE* 3.8 7.0 - - + -
226A TRP* 3.1 45.5 + - + -
227A PHE* 1.3 70.9 - - - +
229A ASN* 1.3 59.5 + - - +
230A ILE* 3.3 5.5 + - - +
244A LEU* 3.7 19.3 - - + -
251A HIS 3.8 8.0 + - - +
252A ALA* 3.6 0.5 - - - -
253A MET* 2.5 29.8 + - - +
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Residues in contact with ASN 229 (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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190A ASP* 3.0 25.3 + - + +
191A ASP 3.2 13.7 + - - -
192A GLU* 3.3 19.2 + - - +
194A LEU 3.0 30.0 + - - +
195A THR* 4.5 7.9 - - - +
202A PHE* 3.3 18.2 - - - -
205A ARG* 4.4 0.5 + - - -
227A PHE 3.5 1.8 + - - -
228A ALA* 1.3 69.6 - - - +
230A ILE* 1.3 59.6 + - - +
231A THR* 2.6 32.2 + - - -
240A ARG* 5.0 0.9 + - - -
253A MET* 3.6 22.8 - - - +
255A ASP* 3.9 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