Contacts of the strand formed by residues 223 - 228 (chain C) in PDB entry 3P9K
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 LYS 223 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLY* 2.6 16.2 + - - +
200C THR* 3.3 23.6 - - + +
201C LEU 3.0 22.5 + - - -
221C THR 4.7 4.9 - - - +
222C ILE* 1.3 74.3 - - - +
224C GLY* 1.3 63.9 + - - +
225C VAL* 5.2 0.9 - - + -
241C GLY* 4.3 3.4 - - - -
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Residues in contact with GLY 224 (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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201C LEU 3.5 6.7 - - - -
212C VAL* 3.7 16.6 - - - -
216C ALA* 4.9 3.0 - - - +
222C ILE* 3.8 9.0 - - - +
223C LYS* 1.3 74.6 - - - +
225C VAL* 1.3 63.5 + - - +
241C GLY 3.0 17.6 + - - +
242C VAL* 3.4 4.6 - - - -
243C THR* 2.9 27.1 + - - -
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C THR* 4.2 21.3 - - + -
201C LEU 2.9 11.1 + - - +
202C VAL* 4.1 13.2 - - + -
203C ASP 2.9 26.5 + - - -
212C VAL* 3.8 7.4 - - - +
223C LYS* 4.7 1.8 - - + +
224C GLY* 1.3 78.8 - - - +
226C ASN* 1.3 66.8 + - - +
243C THR* 3.3 18.4 - - + +
245C VAL* 3.8 21.5 - - + -
254C PRO* 4.2 21.3 - - + -
255C SER 5.3 1.6 - - - +
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Residues in contact with ASN 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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203C ASP* 4.1 5.6 - - - +
206C GLY* 3.1 30.1 - - - -
207C GLY 2.9 26.0 + - - +
209C GLY* 3.5 17.3 - - - +
212C VAL* 3.9 14.6 - - + +
225C VAL* 1.3 73.3 - - - +
227C PHE* 1.3 59.0 + - - +
228C ASP* 5.0 0.2 - - - +
233C ILE* 4.2 8.0 - - - +
242C VAL* 4.0 3.3 - - + +
243C THR 2.8 9.7 + - - -
244C HIS* 3.2 33.2 + - + +
245C VAL 2.8 28.4 + - - +
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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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202C VAL* 4.4 5.8 - - + -
203C ASP 3.0 14.7 + - - +
204C VAL* 4.1 18.4 - - + -
205C GLY 2.7 31.0 + - - -
206C GLY 3.0 6.8 + - - -
225C VAL* 3.9 1.3 + - + -
226C ASN* 1.3 73.8 - - - +
228C ASP* 1.3 57.8 + - - +
245C VAL* 3.3 17.7 - - + -
246C GLY 3.9 4.0 - - - -
247C GLY* 3.7 21.1 - - - -
248C ASP 3.6 18.2 - - - -
249C MET* 3.6 28.3 - - + -
252C GLU* 3.4 22.0 - - + -
253C VAL* 4.2 1.8 - - + -
254C PRO* 3.3 42.4 - - + -
403C SAH 4.3 4.9 - + - -
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Residues in contact with ASP 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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205C GLY 3.4 6.6 - - - -
207C GLY 2.7 22.0 + - - +
226C ASN* 5.0 0.2 - - - +
227C PHE* 1.3 75.2 - - - +
229C LEU* 1.3 77.7 + - - +
232C VAL* 3.5 15.5 - - + +
233C ILE* 3.7 16.7 - - + +
245C VAL 3.2 5.9 + - - -
246C GLY* 3.2 3.8 - - - -
247C GLY* 3.0 25.3 + - - +
403C SAH 2.6 66.5 + - - -
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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