Contacts of the strand formed by residues 254 - 260 (chain B) in PDB entry 2C0O
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 GLU 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B LYS* 3.9 17.4 + - + +
248B GLY 3.4 8.3 - - - +
249B ALA* 3.8 21.0 - - + +
250B GLY 4.5 0.4 - - - +
253B GLY* 1.3 76.8 - - - -
255B VAL* 1.3 65.7 + - - +
256B TRP* 2.7 44.1 + - - +
268B VAL 3.7 0.2 - - - +
269B LYS* 3.2 6.4 - - - +
270B THR* 2.9 38.6 + - - +
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Residues in contact with VAL 255 (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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246B LYS* 3.7 2.3 - - - -
247B LEU* 2.7 39.2 + - + +
248B GLY 2.8 16.6 + - - +
254B GLU* 1.3 78.2 - - - +
256B TRP* 1.3 63.3 + - - +
267B ALA* 4.7 1.6 - - + -
268B VAL 3.3 7.2 - - - +
269B LYS* 3.9 29.2 - - + +
1506B L2G 3.7 61.9 - - + +
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Residues in contact with TRP 256 (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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243B LEU* 3.6 48.0 - - + +
244B GLU 4.5 1.3 - - - -
245B LYS* 3.3 11.7 - - - -
246B LYS* 3.3 45.3 - - + +
247B LEU* 3.9 4.3 - - - -
254B GLU* 2.7 40.6 + - + +
255B VAL* 1.3 82.0 - - - +
257B MET* 1.3 65.1 + - - +
267B ALA* 3.4 4.3 - - - +
268B VAL* 2.7 42.6 + - + +
270B THR* 3.9 20.7 - - + +
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Residues in contact with MET 257 (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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243B LEU 3.8 0.5 - - - -
244B GLU* 2.9 50.8 + - + +
245B LYS* 2.8 37.3 + - + +
247B LEU* 3.5 16.9 - - + +
256B TRP* 1.3 72.5 - - - +
258B ALA* 1.3 69.1 + - - +
259B THR* 5.2 0.4 - - - -
265B LYS* 3.6 28.7 - - - +
266B VAL 3.8 3.4 - - - +
314B PHE* 3.5 31.0 - - + -
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Residues in contact with ALA 258 (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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241B LEU* 5.2 0.2 - - + -
242B LYS 3.3 13.9 - - - +
243B LEU* 3.7 12.1 - - + -
244B GLU* 4.1 2.2 - - - +
257B MET* 1.3 81.2 - - - +
259B THR* 1.3 69.1 + - - +
265B LYS* 3.6 6.8 - - - +
266B VAL* 2.7 38.4 + - + +
268B VAL* 3.4 33.7 - - + -
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Residues in contact with THR 259 (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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240B SER 3.3 4.5 - - - +
241B LEU* 3.4 5.7 - - - -
242B LYS* 2.8 40.5 + - + +
244B GLU* 2.9 29.8 + - - +
257B MET* 5.2 0.3 - - - -
258B ALA* 1.3 78.6 + - - +
260B TYR* 1.3 60.6 + - - +
261B ASN 4.0 0.2 + - - -
262B LYS* 3.1 41.9 + - - +
264B THR 3.5 8.2 + - - +
265B LYS* 4.7 5.4 - - - +
266B VAL* 4.4 0.2 - - - -
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Residues in contact with TYR 260 (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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72B HIS* 4.9 6.3 - + - -
229B TRP* 3.5 41.5 - + + -
230B GLU* 2.5 37.5 + - + -
233B ALA* 4.0 12.6 - - - +
236B ILE* 3.7 18.4 - - + +
237B PRO* 5.6 1.1 - - + +
240B SER* 3.3 34.3 - - - -
241B LEU* 3.8 14.4 - - + -
259B THR* 1.3 71.2 - - - +
261B ASN* 1.3 84.2 + - + +
262B LYS 3.3 0.3 + - - -
264B THR* 3.0 37.1 + - - +
266B VAL* 4.2 7.8 - - + +
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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