Contacts of the strand formed by residues 246 - 250 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D LEU* 4.3 7.4 - - + -
214D ALA 4.4 4.3 - - - -
215D GLU 3.8 5.8 - - - -
218D GLY* 3.4 27.6 - - - -
219D SER* 3.4 24.7 - - - -
222D TYR* 4.5 4.7 - - + -
229D LEU* 3.1 35.0 - - + +
231D SER* 3.5 21.3 + - - +
238D MET* 4.5 6.1 - - + -
242D TRP* 3.3 71.4 - + + +
243D PRO* 3.4 24.3 - - + +
244D GLU 3.2 5.0 + - - +
245D ASN* 1.3 80.5 - - - +
247D ASP* 1.3 76.0 + - - +
414D MET* 4.2 4.7 - - + -
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Residues in contact with ASP 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LYS* 3.0 40.9 + - - -
229D LEU 3.1 5.2 + - - -
230D ILE* 3.3 9.2 - - + +
231D SER 2.9 24.8 + - - +
242D TRP* 5.4 0.4 - - - -
244D GLU 4.9 2.1 - - - +
245D ASN 4.2 0.3 - - - -
246D TRP* 1.3 87.0 + - - +
248D GLU* 1.3 64.7 + - - +
249D ARG* 3.1 29.3 + - + +
268D GLU* 3.9 0.9 - - - +
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D SER* 5.0 0.2 - - - -
231D SER* 3.3 21.8 - - - +
232D CYS 5.9 0.2 - - - -
233D TYR* 4.1 14.4 - - + +
237D PRO* 3.1 15.5 - - + +
238D MET* 2.4 41.6 + - - +
239D GLY* 3.4 14.7 + - - -
240D TYR 4.6 0.9 - - - +
242D TRP* 3.1 30.8 + - + +
247D ASP* 1.3 75.1 - - - +
249D ARG* 1.3 64.5 + - - +
250D PRO* 4.8 0.5 - - - +
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Residues in contact with ARG 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LYS* 4.4 2.0 - - - +
230D ILE* 3.8 20.1 - - + +
231D SER 2.9 10.9 + - - +
232D CYS* 3.2 2.4 - - + -
233D TYR* 2.7 41.5 + - - -
247D ASP* 3.1 21.4 + - + +
248D GLU* 1.3 76.4 - - - +
250D PRO* 1.3 72.7 - - + +
262D PHE* 3.8 23.0 - - + -
264D ASP* 3.5 13.8 + - - +
266D SER* 3.1 32.7 + - - -
268D GLU* 2.3 31.0 + - - -
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Residues in contact with PRO 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D CYS* 3.3 8.2 - - - +
233D TYR* 3.6 28.0 - - + +
248D GLU 4.8 0.7 - - - +
249D ARG* 1.3 95.0 - - + +
251D ASN* 1.3 67.2 + - - +
262D PHE* 3.5 11.3 - - - +
263D ALA* 4.1 18.8 - - + -
264D ASP* 3.7 33.2 - - + +
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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