Contacts of the strand formed by residues 212 - 219 (chain A) in PDB entry 2OA2
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 ASP 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU* 1.3 78.7 - - - +
213A GLN* 1.3 61.7 + - - +
246A LEU* 6.3 2.2 - - + -
247A ILE 3.5 5.8 - - - +
248A PRO* 3.5 10.0 - - + +
249A ALA* 2.9 27.9 + - - +
268A ILE 3.8 0.3 - - - +
269A TYR* 3.7 0.5 - - - -
270A ALA* 2.9 38.7 + - + +
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Residues in contact with GLN 213 (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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195A MSE 5.4 3.0 - - - -
203A ILE* 5.7 1.4 - - - +
208A HIS* 4.4 5.2 + - - -
211A LEU* 4.5 7.2 - - + -
212A ASP* 1.3 78.5 - - - +
214A PHE* 1.3 59.7 + - - +
215A LEU* 3.4 28.8 - - + +
245A ILE 3.7 0.5 - - - +
246A LEU* 3.6 7.3 - - - +
247A ILE* 2.8 46.9 + - + +
253A HIS* 3.9 21.8 + - + -
267A SER* 2.7 33.2 + - - +
268A ILE 3.2 6.7 - - - +
269A TYR* 3.7 28.6 + - + -
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Residues in contact with PHE 214 (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 GLN* 1.3 74.0 - - - +
215A LEU* 1.3 63.9 + - - +
216A ARG* 3.8 26.7 - - + -
244A ALA* 3.6 28.3 - - + -
245A ILE 3.4 4.0 - - - -
246A LEU* 3.9 29.8 - - + -
266A TYR* 4.0 13.7 - + - -
267A SER* 3.3 2.3 - - - -
268A ILE* 2.7 64.0 + - + +
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Residues in contact with LEU 215 (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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195A MSE 5.1 0.2 - - - -
203A ILE* 4.3 16.2 - - + -
213A GLN* 3.4 34.8 - - + +
214A PHE* 1.3 77.9 - - - +
216A ARG* 1.3 61.0 + - - +
217A VAL 4.2 0.2 - - - -
243A TYR 4.0 0.2 - - - +
244A ALA* 3.1 6.6 - - - +
245A ILE* 2.8 50.2 + - + +
247A ILE* 3.4 34.8 - - + -
255A VAL* 4.7 9.4 - - + -
265A LEU* 3.8 32.8 - - + -
266A TYR 3.2 5.6 - - - +
267A SER* 4.1 5.4 - - - -
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Residues in contact with ARG 216 (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* 3.8 17.7 - - + -
215A LEU* 1.3 74.1 - - - +
217A VAL* 1.3 85.6 + - - +
218A GLU* 3.5 36.1 + - - +
242A ASP* 3.1 42.6 + - - +
243A TYR 3.4 12.8 - - - +
244A ALA* 4.5 2.5 - - + -
265A LEU* 3.1 6.7 - - - +
266A TYR* 2.9 66.2 + - + +
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Residues in contact with VAL 217 (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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215A LEU 5.8 0.2 - - - -
216A ARG* 1.3 91.7 + - - +
218A GLU* 1.3 61.2 + - - +
219A GLU 3.8 12.3 - - - +
220A GLY 4.0 2.0 - - - +
239A VAL* 4.0 27.1 - - + -
240A PHE* 3.3 30.5 - - - +
241A ASP 3.8 1.1 - - - +
242A ASP* 3.0 11.6 + - - -
243A TYR 2.9 15.0 + - - +
245A ILE* 4.7 11.7 - - + -
255A VAL* 6.2 0.2 - - + -
263A LEU* 3.8 28.3 - - + -
264A LYS 3.7 4.7 - - - +
265A LEU* 4.0 10.5 - - + -
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Residues in contact with GLU 218 (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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170A ILE* 4.6 2.6 - - - +
171A GLU* 3.5 33.9 + - - +
174A THR* 3.8 35.7 - - + -
175A LYS* 3.4 26.7 + - + -
216A ARG* 3.5 27.5 + - - +
217A VAL* 1.3 76.1 - - - +
219A GLU* 1.4 62.1 + - - +
241A ASP* 4.0 12.1 - - - +
242A ASP* 5.7 0.2 - - - +
264A LYS 2.8 6.4 + - - +
266A TYR* 3.6 27.6 + - + -
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Residues in contact with GLU 219 (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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175A LYS* 4.2 24.6 + - + +
217A VAL* 3.6 3.9 - - - -
218A GLU* 1.4 79.9 - - - +
220A GLY* 1.3 64.3 + - - +
241A ASP* 3.3 10.3 - - - +
261A ARG* 3.9 33.7 + - - +
262A PRO 4.5 2.1 - - - +
263A LEU* 3.5 7.6 - - - +
264A LYS* 2.9 57.5 + - + +
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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