Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 2O0L
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 VAL 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A PHE* 3.9 0.5 - - - +
229A PRO* 1.3 88.5 - - - +
231A VAL* 1.3 69.0 + - - +
232A ALA* 5.7 0.4 - - + -
251A CYS* 3.4 2.6 - - - -
252A SER* 2.8 39.5 + - - +
254A ASN 3.5 21.1 - - - +
255A PRO* 3.6 18.8 - - + +
257A THR* 3.5 23.1 - - - +
259A PHE* 3.7 24.5 - - + +
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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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221A ARG* 3.8 28.3 + - + +
224A CYS* 3.5 44.4 - - + +
225A GLN* 3.1 40.7 + - + +
228A PHE* 3.9 9.2 - - + +
230A VAL* 1.3 83.4 - - - +
232A ALA* 1.3 62.4 + - - +
249A MET* 5.1 3.6 - - + -
250A LEU 3.2 8.5 - - - +
251A CYS* 4.1 2.5 - - - -
260A GLN* 5.6 0.2 + - - -
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Residues in contact with ALA 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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221A ARG* 4.0 8.3 - - - +
230A VAL* 5.7 0.4 - - + -
231A VAL* 1.3 76.3 - - - +
233A TYR* 1.3 61.5 + - - +
234A ALA 4.3 0.2 - - - -
248A PHE 3.8 0.7 - - - +
249A MET* 3.8 8.3 - - - +
250A LEU* 2.8 34.4 + - + +
259A PHE* 3.9 17.9 - - + -
260A GLN* 3.9 18.4 - - - +
288A PHE* 3.6 25.1 - - + -
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Residues in contact with TYR 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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207A GLY* 5.0 0.4 - - - -
208A GLU 2.8 31.9 + - - -
209A CYS* 4.2 0.2 - - - -
210A GLN* 3.4 38.5 + - + +
217A ILE* 3.5 33.2 - - + -
221A ARG* 3.5 20.9 + - - +
232A ALA* 1.3 74.9 - - - +
234A ALA* 1.3 64.5 + - - +
235A TYR* 4.1 6.1 - - + +
246A ILE 4.5 0.2 - - - -
247A GLY* 3.4 22.9 + - - -
248A PHE 3.3 17.3 - - - -
249A MET* 4.2 9.4 - - + -
288A PHE* 3.7 20.6 - - - +
290A LEU* 3.7 29.1 - - + +
298A LEU* 4.1 8.3 - - + -
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Residues in contact with ALA 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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86A LEU* 4.2 14.4 - - + -
233A TYR* 1.3 80.3 - - - +
235A TYR* 1.3 60.2 + - - +
247A GLY* 3.1 3.8 - - - -
248A PHE* 2.6 39.8 + - + +
250A LEU* 4.2 3.7 - - + +
287A ALA* 3.2 24.9 - - + +
288A PHE* 3.8 28.0 - - + -
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Residues in contact with TYR 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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82A MET* 3.9 1.4 - - - +
210A GLN* 3.6 21.3 - - - +
233A TYR* 4.1 9.6 - - + +
234A ALA* 1.3 76.2 - - - +
236A CYS* 1.3 70.2 + - - +
237A THR* 4.5 7.6 - - + -
245A GLN* 3.4 28.3 - - - +
246A ILE 3.1 16.4 - - - +
247A GLY* 3.9 4.7 - - - -
248A PHE* 4.0 5.6 - - - -
278A TYR* 4.9 0.5 + - - -
286A ALA 4.6 3.7 + - - -
287A ALA* 3.1 54.9 + - - +
289A VAL 3.5 26.0 + - - -
290A LEU* 3.8 10.8 - - + -
291A PRO* 4.5 6.9 - - + +
235B TYR* 5.3 6.1 + - - -
237B THR* 4.4 16.0 + - + +
278B TYR* 5.0 4.5 + - - -
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Residues in contact with CYS 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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78A SER 4.1 4.0 - - - -
79A TYR* 4.0 24.2 - - - -
82A MET* 3.8 14.6 - - + -
235A TYR* 1.3 77.6 - - - +
237A THR* 1.3 70.7 + - - +
238A ILE* 4.3 8.5 - - - -
245A GLN* 3.1 6.7 - - - +
246A ILE* 2.9 33.8 + - - -
248A PHE* 3.8 23.3 - - + -
278A TYR* 3.4 21.1 - - + +
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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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78A SER* 3.1 24.3 + - - -
235A TYR* 4.5 9.2 - - + -
236A CYS* 1.3 76.4 - - - +
238A ILE* 1.3 61.8 + - - +
244A GLY 3.5 11.2 - - - +
245A GLN* 4.5 1.3 - - + -
278A TYR* 2.9 18.7 + - - +
211B TRP* 3.2 22.9 + - - -
235B TYR* 4.3 12.3 + - + +
237B THR* 3.7 26.5 - - + -
245B GLN* 3.2 22.5 + - + +
291B PRO* 4.9 3.5 - - - +
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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