Contacts of the strand formed by residues 250 - 257 (chain A) in PDB entry 4OI9
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 ALA 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A THR* 5.3 1.6 - - - +
220A LEU 3.2 13.5 - - - +
221A ASP* 3.2 23.3 + - + +
226A ALA* 5.2 0.2 - - - -
246A LEU* 3.6 5.1 - - - +
247A GLU* 2.8 45.9 + - + +
248A GLY 4.4 0.3 - - - +
249A ASP* 1.3 80.6 - - - +
251A PHE* 1.3 60.4 + - - +
252A VAL* 5.3 3.6 - - + -
2335A EDO 5.5 2.0 - - - +
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Residues in contact with PHE 251 (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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200A PRO* 5.1 0.2 - - + -
218A CYS* 3.8 11.2 - - - -
219A THR* 2.7 40.3 + - - -
220A LEU* 3.0 40.2 + - + -
223A LEU* 3.9 17.5 - - + -
226A ALA* 5.4 1.3 - - + +
229A ALA* 5.7 2.2 - - + -
231A VAL* 3.7 22.2 - - + -
244A VAL* 3.8 19.3 - - + -
245A THR 3.3 5.2 - - - +
246A LEU* 3.7 21.8 - - + -
249A ASP 4.1 1.6 + - - -
250A ALA* 1.3 72.8 - - - +
252A VAL* 1.3 61.9 + - - +
253A ALA* 3.7 20.2 - - + -
273A VAL* 3.8 31.0 - - + -
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Residues in contact with VAL 252 (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 SER* 5.5 4.9 - - - +
218A CYS 3.9 4.0 - - - +
219A THR* 4.2 10.8 - - - +
243A ASP 3.0 5.9 - - - +
245A THR* 2.8 49.6 + - + +
247A GLU* 5.5 7.6 - - + -
250A ALA* 5.3 5.4 - - + +
251A PHE* 1.3 83.1 - - - +
253A ALA* 1.3 61.3 + - - +
254A THR* 3.8 21.0 + - + -
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Residues in contact with ALA 253 (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 VAL 4.0 0.3 - - - +
217A SER* 3.1 7.1 - - - -
218A CYS* 2.8 50.7 + - + +
231A VAL* 4.2 9.4 - - + -
233A LEU* 4.5 2.3 - - + +
242A PRO* 3.9 22.7 - - + -
243A ASP 3.6 4.9 - - - -
244A VAL* 4.4 4.7 - - + -
251A PHE* 3.7 16.8 - - + -
252A VAL* 1.3 71.2 - - - +
254A THR* 1.3 61.3 + - - +
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Residues in contact with THR 254 (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 VAL 3.6 4.9 - - - -
217A SER* 4.5 7.2 - - - +
242A PRO* 3.2 3.0 - - - +
243A ASP* 3.0 41.2 + - - +
245A THR* 5.4 4.1 - - + +
252A VAL* 3.8 24.0 - - + +
253A ALA* 1.3 78.2 - - - +
255A ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 255 (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 PRO* 3.6 4.2 - - - +
216A VAL* 2.8 33.4 + - - +
233A LEU* 5.0 3.6 - - + -
240A LEU* 3.7 28.0 - - + -
241A SER 4.7 1.3 - - - +
242A PRO* 3.7 21.8 - - + -
254A THR* 1.3 75.8 - - - +
256A THR* 1.3 65.9 + - - +
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Residues in contact with THR 256 (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 GLU* 3.6 41.7 + - + +
214A ARG 3.5 14.4 + - - +
215A PRO* 4.3 3.8 - - - +
216A VAL 4.8 0.2 - - - +
240A LEU* 3.9 14.8 - - - +
255A ALA* 1.3 77.3 + - - +
257A ALA* 1.3 65.2 + - - +
258A THR* 4.7 2.7 - - + -
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Residues in contact with ALA 257 (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 LEU* 3.7 19.1 - - + +
212A SER 3.1 12.5 - - - +
214A ARG 3.1 21.2 + - - +
216A VAL* 4.2 14.1 - - + +
235A LEU* 4.8 14.1 - - + -
240A LEU* 4.0 24.5 - - + -
256A THR* 1.3 75.0 - - - +
258A THR* 1.3 64.3 + - - +
269A LEU* 5.8 1.1 - - + -
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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