Contacts of the strand formed by residues 223 - 228 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY* 2.5 17.1 + - - +
200A THR* 3.2 20.0 - - + +
201A LEU 2.9 23.7 + - - +
220A PRO 4.2 7.5 + - - -
221A THR* 3.4 25.9 + - - +
222A ILE* 1.3 75.3 + - - +
224A GLY* 1.3 63.1 + - - +
225A VAL* 4.9 1.8 - - + -
241A GLY 4.4 2.0 - - - -
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Residues in contact with GLY 224 (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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201A LEU 3.4 6.5 - - - -
212A VAL* 3.8 16.6 - - - -
216A ALA* 5.0 3.5 - - - +
222A ILE* 3.7 10.8 - - - +
223A LYS* 1.3 75.5 - - - +
225A VAL* 1.3 63.2 + - - +
241A GLY 3.1 18.4 + - - +
242A VAL* 4.3 2.5 - - - -
243A THR* 3.0 25.7 + - - -
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 4.2 22.2 - - + -
201A LEU 2.8 10.3 + - - +
202A VAL* 4.0 19.1 - - + -
203A ASP* 2.9 29.3 + - - +
212A VAL* 3.9 4.9 - - - +
223A LYS* 4.4 2.5 - - + +
224A GLY* 1.3 78.6 - - - +
226A ASN* 1.3 67.1 + - - +
243A THR* 3.3 19.1 - - + +
245A VAL* 3.9 23.1 - - + -
254A PRO* 4.4 10.8 - - + -
255A SER 5.4 1.1 - - - +
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Residues in contact with ASN 226 (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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203A ASP* 4.2 2.1 - - - +
206A GLY* 3.1 28.4 - - - -
207A GLY 2.9 25.0 + - - +
209A GLY* 3.3 16.1 - - - -
212A VAL* 4.0 8.2 - - + +
224A GLY 4.3 0.2 - - - -
225A VAL* 1.3 73.5 - - - +
227A PHE* 1.3 55.2 + - - +
233A ILE* 3.5 13.3 - - - +
242A VAL* 4.0 9.8 - - + +
243A THR 2.8 9.9 + - - -
244A HIS* 3.0 38.1 + - + +
245A VAL 2.7 33.3 + - - +
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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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202A VAL* 4.3 6.7 - - + -
203A ASP 3.0 14.7 + - - +
204A VAL* 4.1 18.6 - - + -
205A GLY 2.6 30.8 + - - -
206A GLY 3.0 6.6 + - - -
225A VAL* 3.8 1.1 + - + -
226A ASN* 1.3 72.9 - - - +
228A ASP* 1.3 58.9 + - - +
245A VAL* 3.2 20.4 - - + +
246A GLY 4.0 4.3 - - - -
247A GLY* 3.9 18.6 - - - -
248A ASP 3.7 18.2 - - - -
249A MET* 3.6 29.8 - - + -
252A GLU 3.4 20.4 - - - -
253A VAL* 3.9 3.4 - - + -
254A PRO* 3.3 38.6 - - + -
401A SAH 4.2 5.6 - + - -
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Residues in contact with ASP 228 (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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205A GLY 3.4 5.9 - - - -
207A GLY 2.8 21.8 + - - +
227A PHE* 1.3 74.9 - - - +
229A LEU* 1.3 78.4 + - - +
232A VAL* 3.5 15.1 - - + +
233A ILE* 3.8 18.0 - - + +
245A VAL 3.2 5.3 + - - -
246A GLY* 3.1 3.8 - - - -
247A GLY 2.9 24.9 + - - +
401A SAH 2.7 67.0 + - - -
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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