Contacts of the strand formed by residues 224 - 229 (chain A) in PDB entry 1WKB
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 TYR 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS* 3.7 38.8 - - + -
214A PHE 3.4 6.1 - - - +
215A GLU* 4.3 16.8 - - + -
217A ARG* 6.2 1.3 - - - -
222A VAL* 4.6 20.6 - - + +
223A ILE* 1.3 81.0 - - - +
225A LEU* 1.3 60.3 + - - +
226A PRO* 3.2 7.2 - - + +
261A GLU* 3.4 45.3 + - + +
262A THR 2.9 19.9 + - - -
263A TRP* 3.2 14.6 - + + +
264A ILE* 3.0 26.3 + - - +
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Residues in contact with LEU 225 (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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214A PHE* 2.9 36.5 + - + +
216A LEU* 5.2 10.1 - - + -
223A ILE 4.1 0.6 + - - -
224A TYR* 1.3 71.9 - - - +
226A PRO* 1.4 64.2 - - - +
227A ALA* 3.2 3.6 + - - +
241A MET* 4.4 14.1 - - + -
243A VAL* 5.3 2.5 - - + -
264A ILE* 3.6 31.9 - - + +
291A LEU* 4.9 12.1 - - + -
296A VAL* 4.6 11.7 - - + -
307A ILE* 3.8 34.3 - - + -
321A VAL* 3.6 32.5 - - + -
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Residues in contact with PRO 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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211A ILE* 4.0 23.8 - - + +
212A ILE 3.2 12.3 - - - +
213A LYS* 4.1 5.2 - - + -
224A TYR* 3.2 17.3 - - + +
225A LEU* 1.4 80.0 - - - +
227A ALA* 1.3 61.9 + - - +
263A TRP* 3.6 36.1 - - + -
264A ILE 3.7 12.8 - - - +
265A VAL* 3.8 7.0 - - + -
319A THR* 2.8 32.0 + - + +
321A VAL* 3.6 5.6 - - - +
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Residues in contact with ALA 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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210A ILE 3.4 1.7 - - - +
211A ILE* 4.1 0.7 - - - -
212A ILE* 2.9 41.3 + - - +
214A PHE* 4.4 11.9 - - + -
225A LEU 3.2 2.0 + - - +
226A PRO* 1.3 72.3 - - - +
228A ALA* 1.3 61.2 + - - +
229A THR* 3.7 1.6 + - - +
241A MET* 5.2 2.2 - - - -
321A VAL* 3.2 26.0 - - + +
322A VAL 4.1 0.4 - - - -
323A MET* 4.0 31.9 - - + +
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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
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209A TYR* 3.6 13.3 - - + -
210A ILE 3.3 5.8 - - - -
211A ILE* 3.8 15.7 - - + -
227A ALA* 1.3 73.2 - - - +
229A THR* 1.3 61.2 + - - +
318A ALA* 3.3 34.3 - - + -
319A THR* 3.3 10.6 + - - +
321A VAL 3.1 12.6 + - - +
322A VAL* 4.8 9.4 - - - +
323A MET* 5.3 0.7 + - - +
907A SO4 4.2 4.9 + - - -
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Residues in contact with THR 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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209A TYR* 3.9 3.9 - - - -
210A ILE* 2.9 43.6 + - + +
212A ILE* 3.9 11.4 - - + -
227A ALA 4.5 0.2 - - - +
228A ALA* 1.3 75.7 - - - +
230A LEU* 1.3 64.7 + - - +
231A ARG 2.8 24.3 + - - -
232A PRO* 3.9 19.1 - - + -
323A MET* 3.8 26.9 - - + +
907A SO4 2.4 29.9 + - - -
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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