Contacts of the strand formed by residues 249 - 253 (chain A) in PDB entry 1XR2
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 ARG 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 4.9 3.3 - - - +
4A TYR* 3.7 8.5 - - - -
195A GLU* 3.4 17.7 + - - +
226A PRO* 3.7 22.4 + - - +
227A LEU 3.0 27.9 + - - +
228A THR* 2.8 39.9 + - + +
229A VAL 3.3 22.0 + - - -
247A VAL* 3.3 3.9 - - - +
248A LYS* 1.3 106.1 - - - +
250A LEU* 1.3 66.3 + - - +
273A LYS* 5.0 0.2 - - - -
274A LYS* 3.4 24.6 - - + +
276A VAL* 4.6 6.1 - - + -
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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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229A VAL* 3.7 33.9 - - + +
231A THR* 5.8 1.1 - - + -
242A CYS* 3.6 37.9 - - - +
243A VAL* 3.8 15.9 - - + -
245A LEU* 5.4 2.9 - - + -
247A VAL* 3.6 23.1 - - + -
249A ARG* 1.3 73.1 - - - +
251A HIS* 1.3 61.9 + - - +
252A PHE* 4.0 21.5 - - + -
269A PHE* 4.4 9.8 - - + -
273A LYS* 4.5 11.2 - - + +
274A LYS 3.1 7.1 + - - -
275A LEU* 3.5 10.6 - - - +
276A VAL* 2.8 26.2 + - - -
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Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.1 0.8 - - - -
228A THR* 5.0 0.6 - - + +
229A VAL 2.8 15.1 + - - +
230A PHE* 3.2 37.2 - + + -
231A THR* 3.0 50.4 + - - +
232A TYR* 4.3 3.4 - + - -
249A ARG 4.3 0.4 - - - -
250A LEU* 1.3 76.0 - - - +
252A PHE* 1.3 79.1 + - - +
276A VAL* 3.2 21.7 - - + +
278A GLY* 3.8 2.3 - - - -
306A SER* 3.2 21.1 - - - -
307A ASN 3.3 20.0 + - - -
308A SER 3.4 15.8 + - - -
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Residues in contact with PHE 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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231A THR* 3.8 5.2 - - + -
236A VAL* 3.4 38.6 - - + -
239A TYR* 4.1 16.2 - + - -
242A CYS* 4.0 15.7 - - - -
243A VAL* 4.0 20.2 - - + -
250A LEU* 4.0 21.3 - - + -
251A HIS* 1.3 83.9 + - - +
253A ASP* 1.3 60.6 + - - +
254A PHE* 3.5 25.4 + + + -
260A ASN* 3.8 21.8 - - + +
264A LEU* 6.1 0.4 - - + -
269A PHE* 4.1 15.5 - + - -
275A LEU* 3.7 17.9 - - + -
276A VAL 3.2 4.8 + - - -
278A GLY* 3.0 27.0 + - - -
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Residues in contact with ASP 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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231A THR* 3.4 18.9 + - - +
232A TYR* 3.6 8.8 - - - +
233A TYR* 2.9 18.4 + - - -
234A ASP 4.4 3.4 - - - +
251A HIS* 4.3 0.2 - - - -
252A PHE* 1.3 69.9 - - - +
254A PHE* 1.3 58.9 + - - +
255A VAL* 2.8 17.8 + - - -
256A SER* 2.5 35.9 + - - -
257A ASN* 2.9 29.6 + - - +
260A ASN* 3.0 13.0 + - - +
278A GLY 4.2 2.7 - - - -
308A SER* 3.5 23.7 - - - +
309A CYS* 4.8 2.4 - - - +
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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