Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 2WIN
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 LEU 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A PRO* 4.1 22.9 - - + -
217A THR* 5.7 0.7 - - - +
218A GLU* 4.9 2.0 - - + +
220A PHE 4.1 18.8 - - - +
221A TYR* 3.4 19.5 - - + -
228A GLY* 1.3 68.4 - - - -
230A GLU* 1.3 61.8 + - - +
231A VAL* 3.7 10.7 + - + +
251A PHE* 4.2 21.1 - - + -
279A VAL* 3.7 1.7 - - - -
280A LEU* 2.9 43.4 + - + +
285A LEU* 6.5 0.4 - - + -
302A LEU* 3.7 28.7 - - + -
324A ILE* 4.0 24.5 - - + -
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Residues in contact with GLU 230 (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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216A PRO* 3.2 7.1 - - - +
217A THR* 3.0 57.6 + - + +
227A LYS* 3.1 37.3 - - + +
228A GLY 3.3 11.7 + - - +
229A LEU* 1.3 74.6 - - - +
231A VAL* 1.3 59.9 + - - +
277A GLU* 4.2 11.6 - - - +
278A VAL 3.9 4.7 - - - +
279A VAL* 4.3 21.7 - - + +
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Residues in contact with VAL 231 (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 VAL* 4.5 4.0 - - + -
215A GLU 4.0 14.1 - - - +
216A PRO* 4.3 9.0 - - + -
229A LEU* 4.0 13.2 - - + +
230A GLU* 1.3 78.8 - - - +
232A THR* 1.3 68.8 + - - +
233A ILE* 3.9 21.1 - - + -
251A PHE* 3.8 26.5 - - + -
277A GLU* 4.0 4.1 - - - +
278A VAL* 2.8 46.2 + - + +
304A VAL* 3.9 21.8 - - + -
321A ARG* 6.5 0.2 - - + -
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Residues in contact with THR 232 (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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213A ILE 3.4 4.9 - - - +
214A VAL* 3.6 2.3 - - - -
215A GLU* 3.0 42.9 + - - +
217A THR* 5.0 7.8 - - - +
231A VAL* 1.3 73.0 - - - +
233A ILE* 1.3 62.7 + - - +
234A THR* 3.7 17.4 + - - +
275A SER* 4.1 11.7 - - - +
276A GLY 3.4 12.8 - - - +
277A GLU* 3.3 18.8 + - - +
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Residues in contact with ILE 233 (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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212A VAL* 4.1 23.3 - - + -
213A ILE 3.6 1.8 - - - +
214A VAL* 3.5 24.5 - - + -
231A VAL* 3.9 14.1 - - + -
232A THR* 1.3 75.6 - - - +
234A THR* 1.3 62.4 + - - +
235A ALA* 3.9 1.5 + - + +
247A ALA* 4.4 10.3 - - + -
249A VAL* 4.7 8.5 - - + -
269A ILE* 4.0 24.0 - - + -
271A ILE* 4.3 11.8 - - + +
274A GLY 4.7 0.2 - - - -
275A SER* 3.4 2.8 - - - -
276A GLY 2.8 35.3 + - - +
278A VAL* 3.9 10.5 - - + -
306A ALA* 4.3 11.9 - - + -
308A VAL* 4.3 14.6 - - + -
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Residues in contact with THR 234 (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 GLU 3.9 0.3 - - - +
212A VAL* 3.5 2.2 - - - -
213A ILE* 2.7 59.0 + - + +
215A GLU* 5.3 5.2 + - - +
232A THR* 4.0 15.8 + - - +
233A ILE* 1.3 73.1 - - - +
235A ALA* 1.3 64.7 + - - +
236A ARG* 4.3 28.4 + - + +
274A GLY 3.7 12.1 - - - +
275A SER* 4.6 4.6 + - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A PHE* 4.4 3.1 - - + -
211A GLU 3.4 10.3 - - - +
212A VAL* 4.3 13.7 - - + -
233A ILE* 3.9 2.5 + - + +
234A THR* 1.3 75.0 - - - +
236A ARG* 1.3 62.7 + - - +
243A VAL* 3.2 37.0 + - + +
271A ILE* 4.5 9.4 - - + -
274A GLY* 3.1 18.6 + - - +
308A VAL* 4.4 15.5 - - + -
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Residues in contact with ARG 236 (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 GLU* 2.9 50.4 + - + +
213A ILE* 4.7 13.6 - - + +
234A THR* 4.3 22.1 - - + +
235A ALA* 1.3 75.3 - - - +
237A PHE* 1.3 69.8 + - - +
240A GLY* 3.6 21.4 + - - +
241A LYS 3.5 14.4 - - - +
242A LYS* 4.4 17.4 - - + +
243A VAL* 3.5 8.0 - - - +
274A GLY 5.8 0.2 - - - +
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Residues in contact with PHE 237 (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 SER* 3.2 29.6 - - - -
210A PHE* 3.5 6.1 - - + -
211A GLU* 5.1 1.4 - - - +
236A ARG* 1.3 81.8 - - - +
238A LEU* 1.3 59.9 - - - +
239A TYR* 3.1 31.6 - + + -
240A GLY* 3.0 18.8 + - - -
241A LYS 2.7 17.7 + - - +
242A LYS 3.2 28.0 - - - -
243A VAL* 3.3 20.5 - - + +
244A GLU 5.0 2.0 - - - -
310A LEU* 4.4 18.4 - - + -
830B TYR* 3.5 33.9 - + - -
832B TYR* 3.5 19.1 - + - -
871B SER* 5.6 2.0 - - - -
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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