Contacts of the strand formed by residues 246 - 251 (chain A) in PDB entry 4J2X
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 PHE 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS* 3.2 3.0 - - - -
213A VAL* 2.7 52.7 + - + +
214A ALA* 4.9 1.6 - - - -
215A LEU* 4.7 7.4 - - + -
229A LEU* 3.5 57.0 - - + -
230A HIS* 3.8 9.4 - - - -
231A VAL* 4.1 2.7 - - + -
236A PHE* 3.5 28.5 - + - -
244A GLY* 3.5 21.8 - - - -
245A ALA* 1.3 74.1 - - - +
247A TYR* 1.3 69.8 + - - +
276A LEU* 4.3 13.9 - - + -
277A VAL 3.3 9.0 - - - +
278A CYS* 3.6 32.3 - - + -
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Residues in contact with TYR 247 (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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210A GLY 3.3 26.9 - - - +
211A THR 3.3 4.0 - - - +
212A LYS* 2.9 37.5 + - + +
246A PHE* 1.3 73.5 - - - +
248A ILE* 1.3 58.8 + - - +
249A HIS* 3.4 29.2 - + + +
275A LYS 3.2 5.2 - - - +
276A LEU* 3.3 3.5 - - - -
277A VAL* 2.8 45.7 + - + +
278A CYS 4.7 0.9 - - - -
279A SER* 3.4 27.7 + - - -
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Residues in contact with ILE 248 (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 ILE* 3.6 26.7 - - + -
208A ALA 4.5 0.9 - - - +
209A SER* 3.4 4.6 - - - -
210A GLY 2.7 30.4 + - - -
211A THR* 2.9 15.2 + - - +
213A VAL* 3.8 14.8 - - + -
247A TYR* 1.3 73.3 - - - +
249A HIS* 1.3 53.5 + - - +
268A ILE* 4.1 13.2 - - + -
274A VAL* 4.0 33.7 - - + -
275A LYS 3.5 3.4 - - - -
276A LEU* 3.9 21.8 - - + -
290A ILE* 4.5 9.0 - - + -
314A PHE* 5.0 0.7 - - + -
356A ILE* 4.1 20.6 - - + -
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Residues in contact with HIS 249 (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* 3.9 2.9 + - - -
210A GLY* 3.8 19.0 - - - -
247A TYR* 3.4 32.9 - + + +
248A ILE* 1.3 71.8 - - - +
250A LEU* 1.3 61.4 + - - +
251A LEU* 3.7 1.5 - - + +
261A PHE* 4.1 16.4 - + + -
263A VAL* 3.4 34.7 - - + +
268A ILE* 4.4 2.0 - - - -
274A VAL* 3.1 6.0 - - - -
275A LYS* 2.8 36.9 + - + +
277A VAL* 3.8 28.8 - - + +
186B VAL* 4.2 15.2 - - + +
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Residues in contact with LEU 250 (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* 3.1 20.2 + - - +
249A HIS* 1.3 73.0 - - - +
251A LEU* 1.3 65.9 + - - +
263A VAL* 3.5 4.9 - - - -
264A ARG* 2.7 43.2 + - + +
265A ASP 3.8 23.1 - - - +
266A GLY 5.0 0.9 - - - +
267A TYR 4.8 6.1 - - - +
268A ILE* 3.7 14.8 - - + +
272A GLN* 3.4 49.1 - - + +
273A THR 3.5 16.8 - - - +
274A VAL* 4.6 0.2 - - - +
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Residues in contact with LEU 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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249A HIS* 3.7 13.9 - - + +
250A LEU* 1.3 90.4 - - - +
252A ASP* 1.3 71.5 + - - +
253A ASP* 3.7 0.9 + - - -
255A GLU* 4.0 22.0 - - + -
256A SER 5.1 0.7 - - - +
261A PHE* 3.6 32.5 - - + -
262A THR 4.1 11.0 - - - +
264A ARG* 4.6 2.2 - - - -
273A THR* 2.9 39.2 + - + +
274A VAL 4.4 1.6 - - - -
275A LYS* 3.7 17.3 - - + -
287A ARG* 3.9 30.1 - - + -
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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