Contacts of the helix formed by residues 244 - 251 (chain A) in PDB entry 1B3U
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 MET 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LEU 3.0 8.1 + - - +
240A GLU* 3.7 34.1 - - - +
243A VAL* 1.3 79.1 - - - +
245A PRO* 1.3 69.8 - - + +
247A LEU* 3.7 31.4 - - + -
248A ARG* 2.9 54.7 + - + +
273A VAL* 3.9 20.4 - - + -
277A ILE* 3.8 12.1 - - + -
281A ASP* 3.7 33.4 - - + +
282A LEU* 5.0 3.1 - - + -
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Residues in contact with PRO 245 (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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240A GLU* 3.2 20.4 - - - +
241A ALA* 4.2 11.2 - - - +
242A LEU 4.5 0.9 - - - -
243A VAL 3.3 10.1 - - - +
244A MET* 1.3 90.8 - - + +
246A THR* 1.3 63.1 + - - +
248A ARG* 3.4 13.7 + - + +
249A GLN* 3.1 23.5 + - - +
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Residues in contact with THR 246 (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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208A PHE* 3.6 35.3 - - + -
209A SER* 4.4 16.0 + - - -
212A ALA* 3.5 33.0 - - + -
242A LEU 5.0 3.5 + - - -
243A VAL 3.0 8.1 + - - -
245A PRO* 1.3 75.4 - - - +
247A LEU* 1.3 66.6 + - - +
249A GLN* 3.1 16.9 + - - +
250A ALA* 3.0 22.3 + - + +
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Residues in contact with LEU 247 (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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224A VAL* 5.7 2.9 - - + -
227A CYS* 4.1 20.1 - - + -
243A VAL* 3.1 13.2 + - + +
244A MET* 3.7 37.5 - - + +
246A THR* 1.3 75.9 - - - +
248A ARG* 1.3 63.0 + - - +
250A ALA* 3.0 9.7 + - + +
251A ALA* 3.0 22.3 + - + +
262A VAL* 4.8 14.8 - - + -
269A LEU* 3.9 41.5 - - + -
273A VAL* 5.5 5.4 - - + -
282A LEU* 4.4 17.3 - - + -
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Residues in contact with ARG 248 (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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240A GLU* 2.9 32.9 + - - -
244A MET* 2.9 46.9 + - + +
245A PRO* 3.7 14.1 - - - +
247A LEU* 1.3 76.5 - - - +
249A GLN* 1.3 63.2 + - - +
251A ALA* 3.4 8.2 + - - +
252A GLU* 3.2 27.6 + - - +
280A THR* 5.6 1.0 - - - +
281A ASP* 2.9 44.8 + - + +
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Residues in contact with GLN 249 (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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209A SER* 5.5 4.8 + - - -
212A ALA* 3.2 28.5 - - + +
213A SER* 3.6 18.0 - - - -
220A ARG* 5.6 0.2 - - - -
245A PRO 3.1 12.2 + - - +
246A THR* 3.1 24.3 + - - +
248A ARG* 1.3 76.7 - - - +
250A ALA* 1.3 58.6 + - - +
252A GLU* 3.6 4.2 + - - -
253A ASP* 3.1 28.4 + - - +
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Residues in contact with ALA 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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212A ALA* 6.2 2.5 - - + -
224A VAL* 4.5 9.6 - - + -
246A THR* 3.0 13.1 + - + +
247A LEU* 3.0 13.7 + - + +
249A GLN* 1.3 76.6 - - - +
251A ALA* 1.3 65.3 + - - +
252A GLU 3.1 1.8 - - - -
253A ASP* 3.1 18.5 + - - +
258A VAL* 3.8 21.5 - - + +
259A ARG* 4.0 4.7 - - - +
262A VAL* 3.8 20.3 - - + +
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Residues in contact with ALA 251 (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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247A LEU* 3.0 13.8 + - + +
248A ARG* 3.4 11.6 + - - +
250A ALA* 1.3 75.8 - - - +
252A GLU* 1.3 62.3 + - + +
259A ARG* 3.3 21.8 - - - +
262A VAL* 3.9 23.8 - - + +
285A ALA* 5.0 16.8 - - + -
289A LEU* 4.7 11.0 - - + +
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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