Contacts of the strand formed by residues 231 - 240 (chain A) in PDB entry 2A3K
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A CYS* 2.8 53.8 + - + +
229A PRO* 3.4 10.3 - - + -
230A GLU* 1.3 80.6 - - + +
232A THR* 1.3 60.1 + - - +
233A VAL* 3.5 25.6 - - + -
250A ILE* 3.7 19.3 - - + -
251A LEU 3.0 21.5 - - - +
252A PHE* 3.8 12.8 - + + +
253A SER* 4.8 1.1 - - - -
266A PRO* 4.5 4.5 - - + -
269A ARG* 3.8 21.6 + - + +
270A LEU* 4.1 28.9 - - + -
273A GLU* 2.5 33.0 + - + -
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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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225A MET* 3.9 24.2 - - + -
226A LYS 3.6 10.8 - - - +
227A GLU* 3.9 24.5 - - + +
228A CYS 5.2 0.7 + - - -
231A TYR* 1.3 76.0 + - - +
233A VAL* 1.3 63.0 + - - +
234A ARG* 3.7 27.7 + - - +
249A HIS 3.6 2.1 - - - +
250A ILE* 3.5 2.4 - - - -
251A LEU* 2.9 39.1 + - - +
253A SER* 5.7 1.2 + - - -
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Residues in contact with VAL 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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224A ASP 3.6 1.7 - - - +
225A MET* 3.5 3.5 - - - -
226A LYS* 2.9 47.3 + - + +
228A CYS* 4.9 4.9 - - - -
231A TYR* 3.5 31.6 - - + -
232A THR* 1.3 70.2 - - - +
234A ARG* 1.3 63.3 + - - +
235A GLN* 4.0 11.8 + - + +
248A LYS* 4.0 26.7 - - + -
249A HIS 3.6 6.3 - - - +
250A ILE* 4.5 3.4 - - + +
273A GLU* 4.3 16.4 - - + +
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Residues in contact with ARG 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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208A TRP* 3.3 42.9 - - - +
209A PRO 5.2 0.6 + - - -
222A ILE* 3.8 19.1 - - + +
224A ASP 3.4 2.0 - - - +
225A MET* 3.6 39.3 - - + -
232A THR* 3.7 24.9 + - - +
233A VAL* 1.3 71.7 - - - +
235A GLN* 1.3 62.7 + - - +
236A LEU* 3.8 8.7 + - + +
247A VAL 3.8 0.2 - - - +
248A LYS* 3.7 0.3 - - - -
249A HIS* 2.7 60.5 + - + +
251A LEU* 4.2 23.8 - - - +
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Residues in contact with GLN 235 (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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222A ILE* 3.5 3.1 - - - +
223A GLN* 2.5 39.1 + - + -
224A ASP* 2.7 39.6 + - + +
233A VAL* 4.0 11.0 + - + +
234A ARG* 1.3 72.4 - - - +
236A LEU* 1.3 56.2 + - - +
246A SER* 5.2 8.3 - - - -
247A VAL 3.5 19.2 + - - +
248A LYS* 3.7 30.0 - - - +
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Residues in contact with LEU 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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180A TRP* 4.5 18.2 - - + -
191A ILE* 6.1 0.2 - - + -
208A TRP* 5.2 9.2 - - + -
209A PRO* 6.1 0.2 - - + -
220A ILE* 4.2 21.3 - - + -
221A ARG 3.2 14.8 - - - +
222A ILE* 4.0 9.0 - - + -
223A GLN* 3.9 3.5 - - - +
234A ARG* 4.3 9.2 - - + +
235A GLN* 1.3 76.6 + - - +
237A THR* 1.3 77.9 + - - +
238A ILE* 4.5 0.7 - - + +
246A SER* 3.4 6.8 - - - -
247A VAL* 2.8 62.1 + - + +
249A HIS* 4.0 27.4 - - + -
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Residues in contact with THR 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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219A GLN 4.5 0.2 - - - -
220A ILE* 3.5 4.9 - - - -
221A ARG* 2.9 45.8 + - - +
223A GLN* 3.6 31.8 + - + +
236A LEU* 1.3 87.2 - - - +
238A ILE* 1.3 60.9 + - - +
239A GLN* 6.1 0.3 - - - +
244A ARG* 3.9 34.0 + - - +
245A ARG 3.1 10.8 - - - +
246A SER* 4.5 9.4 - - - -
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Residues in contact with ILE 238 (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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180A TRP* 4.0 26.5 - - + +
183A VAL* 4.8 7.0 - - + -
184A TRP* 3.7 23.3 - - + -
188A VAL 5.8 0.4 - - - +
218A PHE* 4.0 32.5 - - + -
219A GLN 3.4 8.7 - - - +
220A ILE* 4.0 16.4 - - + -
236A LEU* 4.9 0.9 - - + -
237A THR* 1.3 75.8 - - - +
239A GLN* 1.3 65.2 + - - +
244A ARG* 3.3 5.0 - - - -
245A ARG* 2.7 56.0 + - + +
247A VAL* 3.9 19.3 - - + -
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Residues in contact with GLN 239 (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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217A PRO 3.7 1.4 - - - +
218A PHE* 3.2 8.7 - - - -
219A GLN* 3.0 55.6 + - + +
221A ARG* 5.9 2.2 - - + -
238A ILE* 1.3 77.9 - - - +
240A TYR* 1.3 61.2 + - - +
241A GLN 3.2 22.8 + - - +
242A GLU* 4.4 12.7 + - - +
243A GLU 3.0 20.9 - - - +
244A ARG* 4.5 12.9 + - + +
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Residues in contact with TYR 240 (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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184A TRP* 3.7 37.4 - + + -
217A PRO* 3.8 33.0 - - + -
218A PHE* 3.5 32.5 - + + -
239A GLN* 1.3 74.1 - - - +
241A GLN* 1.3 102.7 + - + +
242A GLU 3.0 4.0 + - - -
243A GLU* 3.0 21.5 + - - +
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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