Contacts of the helix formed by residues 244 - 254 (chain A) in PDB entry 4UAL
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A TYR 3.6 2.2 + - - -
243A ILE* 1.3 77.6 - - - +
245A PRO* 1.4 75.3 - - - +
246A GLU* 3.0 31.1 + - - -
247A ILE* 3.2 28.1 + - - +
248A LEU* 3.3 13.3 + - - +
262A CYS* 3.4 9.6 + - - +
265A TRP* 3.6 23.6 - - - -
266A SER* 5.4 0.2 + - - -
293A ILE* 4.1 2.0 - - - -
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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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244A SER* 1.4 85.4 - - - +
246A GLU* 1.3 63.0 + - - +
248A LEU* 3.3 5.4 + - + +
249A GLN* 2.9 30.9 + - - +
265A TRP* 3.4 31.2 - - + -
293A ILE* 3.6 17.9 - - + +
294A MET* 4.7 10.7 - - + +
296A HIS* 3.5 34.8 - - + +
327A ARG* 4.3 1.3 - - - +
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Residues in contact with GLU 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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244A SER* 3.0 24.0 + - - +
245A PRO* 1.3 78.0 - - - +
247A ILE* 1.3 60.4 + - + +
249A GLN* 3.7 6.9 - - - +
250A ALA* 3.1 25.8 + - - +
257A LYS 4.7 2.6 + - - +
258A TYR* 3.8 14.4 - - + +
261A GLU* 3.2 23.5 - - - +
262A CYS* 3.4 5.6 - - + -
324A ARG* 3.5 37.8 - - - +
327A ARG* 2.8 44.1 + - - -
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Residues in contact with ILE 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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199A ARG* 5.1 12.1 - - + +
236A ALA* 4.3 9.2 - - + -
237A VAL* 5.0 7.2 - - + +
243A ILE* 3.5 31.0 - - + -
244A SER* 3.2 14.3 + - - +
245A PRO 3.2 0.6 - - - -
246A GLU* 1.3 77.7 - - - +
248A LEU* 1.3 65.6 + - - +
250A ALA* 3.1 4.0 + - - +
251A MET* 3.1 30.7 + - + +
258A TYR* 3.8 46.7 - - + +
262A CYS* 3.6 25.4 - - + -
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Residues in contact with LEU 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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243A ILE* 3.1 31.6 - - + -
244A SER 3.3 6.2 + - - +
245A PRO 3.8 5.8 - - - +
247A ILE* 1.3 77.1 - - - +
249A GLN* 1.3 62.9 + - - +
251A MET* 3.4 19.5 + - + +
252A GLU* 3.2 22.5 + - - +
290A TYR* 3.8 48.5 - - + -
293A ILE* 3.7 29.6 - - + -
294A MET* 3.8 28.1 - - + +
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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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245A PRO 2.9 18.1 + - - +
246A GLU* 3.7 9.4 - - - +
248A LEU* 1.3 76.9 - - - +
250A ALA* 1.3 58.3 + - - +
252A GLU* 3.0 14.7 + - - +
253A ASP* 2.8 67.4 + - - +
294A MET* 3.9 18.5 - - + +
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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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246A GLU 3.1 16.7 + - - +
247A ILE 3.1 4.9 + - - +
249A GLN* 1.3 80.0 - - - +
251A MET* 1.3 60.9 + - - +
253A ASP* 4.4 5.6 - - - -
254A GLY* 3.1 24.6 + - - -
257A LYS* 4.7 15.3 - - - +
258A TYR* 4.1 22.0 - - + -
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Residues in contact with MET 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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236A ALA* 2.9 38.4 - - + -
237A VAL 4.8 2.7 - - - +
243A ILE* 3.2 35.4 - - + -
247A ILE* 3.1 14.8 + - + +
248A LEU* 3.5 17.9 - - + +
249A GLN 3.3 0.2 - - - -
250A ALA* 1.3 78.7 - - - +
252A GLU* 1.3 64.7 + - + +
254A GLY 4.1 2.8 + - - -
290A TYR* 5.4 8.7 - - - +
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Residues in contact with GLU 252 (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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248A LEU 3.2 5.2 + - - +
249A GLN* 3.0 17.9 + - - +
251A MET* 1.3 82.8 - - + +
253A ASP* 1.3 63.6 + - - +
294A MET* 3.6 35.6 - - - +
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Residues in contact with ASP 253 (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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249A GLN* 2.8 46.0 + - - +
250A ALA* 4.2 2.7 - - - +
252A GLU* 1.3 81.8 - - - +
254A GLY* 1.3 70.0 + - - +
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Residues in contact with GLY 254 (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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250A ALA* 3.1 19.4 + - - -
251A MET 4.1 2.4 + - - -
252A GLU 3.7 1.6 - - - -
253A ASP* 1.3 88.9 - - - +
257A LYS 6.3 1.1 - - - -
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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