Contacts of the helix formed by residues 246 - 253 (chain C) in PDB entry 5AYR
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 GLY 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C GLN* 6.1 0.9 - - - -
245C TRP* 1.3 76.2 - - - +
247C SER* 1.3 61.2 + - - -
248C TYR* 3.3 3.1 - - - -
249C ALA 3.2 1.5 + - - -
250C GLN* 3.0 34.1 + - - +
266C THR 3.0 14.4 + - - -
267C ALA* 4.3 1.6 - - - -
268C HIS* 3.4 17.4 - - - +
30D GLU* 3.2 14.4 - - - -
34D ASP* 5.6 1.1 - - - -
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLY* 1.3 69.0 - - - -
248C TYR* 1.3 67.9 + - - +
250C GLN* 3.2 16.3 + - - +
251C LYS* 2.9 36.8 + - - +
30D GLU* 2.9 32.1 + - - -
31D ILE* 3.2 24.9 + - - +
34D ASP* 5.3 4.2 + - - -
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Residues in contact with TYR 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLY 4.3 6.5 - - - -
144C GLN* 3.7 37.9 - - + +
205C ALA* 3.6 31.7 - - + +
206C VAL* 4.7 3.8 - - - +
218C LYS* 4.6 7.3 + - - -
223C GLU* 3.7 21.7 + - - +
246C GLY 3.3 0.6 - - - -
247C SER* 1.3 82.8 + - - +
249C ALA* 1.3 69.0 + - + +
251C LYS* 3.2 10.7 + - - +
252C LYS* 3.1 28.9 + - + +
29D GLU* 3.5 43.7 + - + +
30D GLU* 4.6 1.8 + - - -
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 3.7 31.8 - - + +
143C GLY* 5.7 0.7 - - - -
144C GLN* 5.3 2.4 - - + +
244C LEU* 3.5 13.9 - - - +
245C TRP 3.4 32.5 + - - +
246C GLY 3.2 3.7 + - - +
248C TYR* 1.3 86.8 - - + +
250C GLN* 1.3 56.7 - - - +
252C LYS* 3.3 8.6 + - - +
253C GLY 3.1 20.8 + - - -
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Residues in contact with GLN 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C LEU* 3.3 23.2 + - + +
246C GLY* 3.0 23.0 + - - +
247C SER* 3.4 16.3 - - - +
249C ALA* 1.3 76.6 - - - +
251C LYS* 1.3 64.9 + - + +
253C GLY 3.0 10.6 + - - -
254C SER* 3.1 15.4 + - - -
265C GLN* 3.2 30.4 - - - +
266C THR* 3.1 32.3 + - - +
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C SER* 2.9 30.3 + - - +
248C TYR* 3.2 8.1 + - - +
250C GLN* 1.3 72.3 - - - +
252C LYS* 1.3 60.1 + - - +
254C SER* 2.7 28.8 + - - -
31D ILE* 4.1 19.3 - - - +
50D ILE* 4.0 24.5 - - - +
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.0 22.9 - - + -
143C GLY 5.3 0.4 - - - +
203C LEU* 5.9 0.4 - - - -
205C ALA* 3.7 25.6 - - + +
223C GLU* 3.3 13.7 + - - +
226C THR* 2.8 38.3 + - - -
227C ASP* 2.7 37.8 + - - +
230C VAL* 4.5 21.1 - - + +
248C TYR* 3.1 20.9 + - + +
249C ALA* 3.4 11.2 - - - +
250C GLN 3.2 0.2 - - - -
251C LYS* 1.3 78.9 - - - +
253C GLY* 1.3 57.2 + - - +
254C SER 3.3 1.2 + - - -
255C ALA* 4.8 3.3 + - - +
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Residues in contact with GLY 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.5 1.8 - - - -
244C LEU* 3.8 17.2 - - - +
249C ALA 3.1 6.8 + - - -
250C GLN 3.0 9.0 + - - -
252C LYS* 1.3 75.3 - - - +
254C SER* 1.3 55.9 + - - +
255C ALA 2.9 12.2 + - - -
256C ILE* 3.1 31.8 + - - +
258C ARG* 2.9 18.4 + - - -
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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