Contacts of the strand formed by residues 269 - 274 (chain B) in PDB entry 2XMR
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 THR 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B VAL* 3.3 12.7 - - + +
245B LEU* 4.1 14.4 - - + -
261B ASN* 3.4 27.0 - - - +
264B LEU* 3.5 29.1 - - + +
265B ASP* 2.8 21.0 + - - +
266B PRO* 3.5 14.5 + - - +
267B THR 3.7 0.2 - - - -
268B GLN* 1.3 81.4 + - - +
270B SER* 1.3 69.9 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL 2.9 12.3 + - - +
244B MET* 3.6 17.8 - - - +
245B LEU* 2.8 28.3 + - - +
268B GLN 4.2 0.2 + - - -
269B THR* 1.3 79.2 - - - +
271B PHE* 1.3 62.8 + - - +
272B LEU 4.2 0.4 - - - -
296B PHE* 4.3 4.2 - - - -
169C ALA* 6.2 2.2 - - - -
172C LEU* 3.7 31.2 - - - +
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.5 20.6 - - + -
247B VAL* 4.1 11.7 - - + -
257B VAL* 3.6 25.1 - - + -
258B VAL* 3.7 31.6 - - + -
261B ASN* 3.7 32.5 - - + +
270B SER* 1.3 76.8 - - - +
272B LEU* 1.3 63.9 + - - +
273B LYS* 3.8 36.1 + - + -
176C THR* 4.4 6.4 + - - -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B MET* 4.6 6.5 - - + -
245B LEU 2.8 15.2 + - - +
246B VAL* 3.5 19.8 - - + -
247B VAL 3.3 23.8 + - - +
270B SER 4.2 0.2 - - - -
271B PHE* 1.3 73.9 - - - +
273B LYS* 1.3 61.0 + - - +
274B MET* 3.5 29.0 + - + +
288B LYS* 5.2 2.2 - - + +
289B LEU* 4.2 6.3 - - + -
292B ALA* 3.6 33.4 - - + -
172C LEU* 4.1 17.5 - - + +
175C LEU* 4.0 16.2 - - + -
176C THR* 3.9 23.8 - - + +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B VAL* 3.4 24.5 - - + +
249B ASP* 3.7 34.2 + - - +
254B GLU* 3.3 25.0 + - - +
258B VAL* 4.3 7.4 - - - +
271B PHE* 3.8 34.2 + - + -
272B LEU* 1.3 70.4 - - - +
274B MET* 1.3 62.0 + - - +
275B ALA 3.7 1.7 + - - -
176C THR* 3.3 24.5 + - - +
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.1 5.8 - - - -
247B VAL 2.9 10.2 + - - +
249B ASP* 2.7 29.0 + - - -
272B LEU* 3.8 37.2 - - + +
273B LYS* 1.3 72.5 - - - +
275B ALA* 1.3 61.6 + - - +
276B ASP 3.9 0.3 + - - -
277B SER* 3.3 19.2 + - - +
281B PRO* 3.8 21.8 - - + -
285B GLN* 3.5 41.1 - - + +
288B LYS* 3.6 30.7 - - + -
289B LEU* 4.2 8.5 - - - +
176C THR* 4.3 7.0 - - + -
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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