Contacts of the helix formed by residues 244 - 255 (chain B) in PDB entry 1U0O
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 SER 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.2 16.4 - - - -
209B TYR* 4.3 3.6 + - - -
210B GLU* 5.8 1.2 + - - -
242B PHE 4.4 0.5 - - - -
243B GLN* 1.3 79.7 + - - +
245B LYS* 1.3 63.8 + - - +
246B GLU* 3.5 17.6 + - - +
247B GLU* 3.4 25.7 + - - +
248B ALA 3.4 6.9 + - - -
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Residues in contact with LYS 245 (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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92A TYR* 3.1 28.9 - - + +
244B SER* 1.3 71.3 - - - +
246B GLU* 1.3 69.9 + - - +
248B ALA* 3.0 7.4 + - + +
249B ASP* 2.9 51.3 + - - +
252B ARG* 5.8 2.2 - - - +
306B ASN* 5.1 2.9 - - + +
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Residues in contact with GLU 246 (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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209B TYR* 3.0 23.0 + - + +
244B SER* 3.5 19.0 - - - +
245B LYS* 1.3 83.2 + - - +
247B GLU* 1.3 60.1 - - - +
249B ASP* 3.3 12.0 + - - +
250B PHE* 2.9 22.9 + - - +
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Residues in contact with GLU 247 (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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209B TYR* 3.3 20.7 + - + -
212B HIS* 4.7 1.9 - - - -
214B TYR* 3.0 33.5 + - + +
241B SER* 2.5 25.0 + - - +
242B PHE* 3.9 9.0 - - + -
243B GLN* 2.7 41.7 + - - +
244B SER* 3.4 16.1 + - - +
245B LYS 3.2 0.4 - - - -
246B GLU* 1.3 77.1 - - - +
248B ALA* 1.3 64.5 + - - +
250B PHE* 3.0 6.8 + - - +
251B VAL* 2.9 22.0 + - - +
322B GLU* 3.1 11.3 - - - +
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Residues in contact with ALA 248 (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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92A TYR* 4.3 1.3 - - - +
242B PHE* 3.9 26.6 - - + -
244B SER 3.4 6.1 + - - +
245B LYS* 3.0 14.3 + - + +
247B GLU* 1.3 79.1 - - - +
249B ASP* 1.3 59.8 + - - +
251B VAL* 2.9 5.7 + - - +
252B ARG* 2.8 28.3 + - - +
306B ASN* 3.2 35.2 + - - +
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Residues in contact with ASP 249 (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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245B LYS* 2.9 50.0 + - - +
246B GLU* 3.5 11.3 - - - +
248B ALA* 1.3 75.2 - - - +
250B PHE* 1.3 60.6 + - - +
252B ARG* 3.1 52.1 + - - +
253B SER* 3.4 8.3 + - - -
306B ASN* 5.3 6.2 - - - +
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Residues in contact with PHE 250 (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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207B SER* 3.6 24.7 - - - -
208B SER 2.9 23.1 - - - -
209B TYR* 3.2 42.6 - + + -
214B TYR* 3.5 29.8 - + + -
246B GLU 2.9 13.4 + - - +
247B GLU 3.2 10.3 - - - +
249B ASP* 1.3 74.5 - - - +
251B VAL* 1.3 65.0 + - + +
252B ARG 3.1 1.8 - - - -
253B SER* 3.1 30.0 + - - -
254B LEU* 3.8 8.9 - - + +
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Residues in contact with VAL 251 (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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214B TYR* 3.6 35.2 - - + -
240B VAL* 3.8 2.5 - - + -
242B PHE* 3.3 36.3 - - + -
247B GLU 2.9 10.0 + - - +
248B ALA 2.9 8.8 + - - +
250B PHE* 1.3 75.9 - - + +
252B ARG* 1.3 64.7 + - - +
253B SER 3.3 0.2 - - - -
254B LEU* 3.3 17.0 + - - +
255B THR* 3.2 14.5 + - + +
264B VAL* 5.7 2.7 - - + -
303B PRO* 5.9 1.6 - - + -
320B VAL* 3.9 32.5 - - + -
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Residues in contact with ARG 252 (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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245B LYS* 5.8 2.4 - - - +
248B ALA 2.8 11.2 + - - +
249B ASP* 3.1 46.4 + - - +
251B VAL* 1.3 80.7 - - - +
253B SER* 1.3 60.7 + - - +
255B THR* 3.0 30.8 + - - +
256B SER* 4.6 1.6 - - - -
303B PRO* 3.4 37.5 + - + +
304B THR* 3.9 13.9 + - - +
306B ASN* 6.2 1.4 - - - +
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Residues in contact with SER 253 (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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249B ASP 3.4 8.1 + - - -
250B PHE* 3.1 21.1 + - - -
251B VAL 3.3 0.4 - - - -
252B ARG* 1.3 81.5 - - - +
254B LEU* 1.3 71.8 + - - +
255B THR* 4.5 0.2 - - - -
256B SER* 3.6 18.2 + - - -
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Residues in contact with LEU 254 (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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207B SER* 3.5 31.0 - - - +
214B TYR* 3.7 32.1 - - + +
215B ARG* 4.2 13.7 - - - +
216B PHE* 3.7 29.2 - - + +
250B PHE* 3.8 19.3 - - + +
251B VAL* 3.5 11.4 - - + +
252B ARG 3.1 0.8 - - - -
253B SER* 1.3 91.2 + - - +
255B THR* 1.3 60.4 + - + +
256B SER* 3.5 5.0 + - - -
257B GLU* 4.8 4.2 + - - +
320B VAL* 5.0 3.8 - - + -
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Residues in contact with THR 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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216B PHE* 3.3 34.8 - - + -
251B VAL* 3.2 15.1 + - + +
252B ARG* 3.0 14.7 + - - +
254B LEU* 1.3 76.5 - - + +
256B SER* 1.3 56.9 - - - +
257B GLU 3.8 0.9 - - - +
258B MET* 3.5 26.2 - - - +
264B VAL* 4.0 12.1 - - + -
303B PRO* 2.9 32.4 - - + +
320B VAL* 4.1 10.5 - - + -
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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