Contacts of the strand formed by residues 246 - 250 (chain A) in PDB entry 2XLR
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 TRP 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A LEU* 4.2 9.2 - - + -
214A ALA 4.4 2.0 - - - -
215A GLU 3.8 4.9 - - - -
218A GLY* 3.3 45.3 - - - -
219A SER* 3.4 10.1 - - - -
222A TYR* 4.6 3.6 - - + -
229A LEU* 3.2 34.7 - - + +
231A SER* 3.6 21.7 + - - +
238A MET* 4.3 8.3 - - + -
242A TRP* 3.2 74.9 - + + +
243A PRO* 3.5 24.1 - - + +
244A GLU 3.2 5.0 + - - +
245A ASN* 1.3 79.7 - - - +
247A ASP* 1.3 76.2 + - - +
414A MET* 4.2 4.0 - - + -
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Residues in contact with ASP 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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228A LYS* 3.0 33.2 + - - -
229A LEU 3.0 5.8 + - - -
230A ILE* 3.4 7.3 - - + +
231A SER 3.0 24.6 + - - -
242A TRP* 5.3 0.4 - - - -
244A GLU 4.9 2.4 - - - +
245A ASN 4.3 0.5 - - - -
246A TRP* 1.3 90.7 + - - +
248A GLU* 1.3 64.3 + - - +
249A ARG* 3.0 35.2 + - + +
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Residues in contact with GLU 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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231A SER* 3.1 24.0 + - - +
233A TYR* 4.2 13.5 - - + +
237A PRO* 3.2 15.1 - - + +
238A MET* 2.5 40.6 + - - +
239A GLY* 3.3 15.8 + - - -
240A TYR 4.5 0.5 - - - +
242A TRP* 2.9 33.5 + - + +
247A ASP* 1.3 74.2 - - - +
249A ARG* 1.3 65.2 + - - +
250A PRO* 4.8 0.5 - - - +
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Residues in contact with ARG 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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228A LYS* 4.1 2.6 - - - +
230A ILE* 3.8 18.4 - - + +
231A SER 2.9 9.7 + - - +
232A CYS* 3.0 14.6 - - + -
233A TYR* 2.8 28.1 - - - -
247A ASP* 3.0 24.9 + - + +
248A GLU* 1.3 79.9 - - - +
250A PRO* 1.3 70.4 - - + +
262A PHE* 3.6 22.8 - - + -
264A ASP* 3.8 9.4 + - - +
266A SER* 3.3 36.9 + - - -
268A GLU* 2.3 33.8 + - - -
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Residues in contact with PRO 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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232A CYS* 3.4 6.1 - - - +
233A TYR* 3.8 27.6 - - + +
248A GLU 4.8 0.2 - - - +
249A ARG* 1.3 94.8 - - + +
251A ASN* 1.3 71.1 + - - +
262A PHE* 3.5 11.8 - - - +
263A ALA* 4.1 17.5 - - + -
264A ASP* 3.8 32.5 - - + +
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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