Contacts of the helix formed by residues 236 - 248 (chain A) in PDB entry 3EDY
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 HIS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A TYR* 3.7 13.3 + - + -
235A PHE* 1.3 93.9 - - - +
237A ASP* 1.3 64.2 + - - +
238A SER* 3.7 14.6 + - - +
239A ASP* 3.2 40.1 + - - +
240A LEU 3.3 9.2 + - - -
263A GLN* 5.3 0.2 - - - -
267A GLY 2.6 30.2 + - - -
268A ARG* 4.5 0.9 - - - -
269A ALA* 3.6 6.3 + - + +
464A ASN* 3.8 23.4 + - - -
465A ARG* 5.4 5.3 + - - -
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Residues in contact with ASP 237 (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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235A PHE* 3.1 33.3 - - - -
236A HIS* 1.3 73.6 - - - +
238A SER* 1.3 57.4 + - - +
240A LEU* 3.3 5.0 + - - +
241A ALA* 2.9 27.9 + - - +
255A ALA 3.9 3.1 - - - +
256A SER* 3.5 20.4 + - - +
257A VAL* 3.3 24.8 + - - +
260A VAL* 5.1 2.3 - - - +
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Residues in contact with SER 238 (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 HIS* 3.7 16.1 + - - +
237A ASP* 1.3 80.1 - - - +
239A ASP* 1.3 61.1 + - - +
241A ALA* 3.4 7.7 + - - +
242A GLN* 3.0 28.2 + - - +
465A ARG* 3.3 41.6 + - - -
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 3.2 28.7 + - + +
238A SER* 1.3 80.1 + - - +
240A LEU* 1.3 55.0 + - - +
242A GLN* 3.4 2.2 + - - +
243A PHE* 2.8 35.3 + - - +
269A ALA* 3.5 9.7 - - - +
274A SER* 4.6 2.2 + - - +
278A GLN* 3.9 6.1 - - - +
462A VAL* 3.4 25.5 - - + +
463A SER* 3.5 2.4 - - - -
464A ASN* 2.8 25.3 + - - -
465A ARG* 2.8 33.9 + - - +
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Residues in contact with LEU 240 (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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235A PHE* 4.4 6.1 - - + -
236A HIS 3.3 9.5 + - - +
237A ASP* 3.3 11.2 + - - +
239A ASP* 1.3 79.1 - - - +
241A ALA* 1.3 56.5 + - - +
243A PHE* 3.3 5.4 + - + +
244A MET* 2.9 55.1 + - + +
255A ALA* 3.5 27.4 - - - +
256A SER* 3.8 11.7 - - - +
257A VAL* 4.0 9.6 - - + +
277A VAL* 4.4 4.3 - - + -
278A GLN* 4.1 29.3 - - + +
281A MET* 3.6 28.5 - - + -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP 2.9 17.6 + - - +
238A SER* 3.6 8.7 - - - +
239A ASP 3.3 0.2 - - - -
240A LEU* 1.3 76.5 - - - +
242A GLN* 1.3 57.9 + - - +
244A MET* 3.3 2.9 + - - +
245A ARG* 3.0 37.5 + - - +
255A ALA* 3.8 24.2 + - + +
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Residues in contact with GLN 242 (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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238A SER 3.0 16.2 + - - +
239A ASP 3.7 4.0 - - - +
241A ALA* 1.3 72.5 - - - +
243A PHE* 1.3 67.0 + - - +
245A ARG* 3.2 11.3 + - + +
246A LEU* 2.9 33.4 + - + +
462A VAL* 3.8 19.0 - - + +
465A ARG* 3.2 50.2 + - - +
467A PRO* 4.7 10.1 - - - +
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Residues in contact with PHE 243 (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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202A PRO* 3.3 29.6 - - + -
239A ASP 2.8 21.3 + - - +
240A LEU* 3.4 4.7 - - + +
242A GLN* 1.3 72.7 - - - +
244A MET* 1.3 74.8 + - + +
246A LEU* 3.2 2.0 + - - -
247A PHE* 2.9 46.3 + + + +
278A GLN* 3.0 67.5 - - + -
279A TYR* 3.7 20.0 - + - -
282A SER* 3.4 9.6 - - - -
460A TRP 3.8 4.9 - - - -
462A VAL* 3.8 17.4 - - + +
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Residues in contact with MET 244 (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 LEU* 2.9 29.4 + - + +
241A ALA 3.8 4.0 - - - +
242A GLN 3.2 0.2 - - - -
243A PHE* 1.3 83.9 - - + +
245A ARG* 1.3 62.7 + - - +
248A GLY* 2.9 39.5 + - - +
249A GLY* 5.0 0.2 - - - -
251A PHE* 4.4 3.4 - - + -
253A HIS* 3.6 39.2 + - + +
254A GLN 3.7 22.0 - - - +
255A ALA* 4.4 7.2 - - + -
278A GLN 4.0 6.1 - - - +
281A MET* 3.6 38.6 - - + +
282A SER* 3.8 15.3 - - - +
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Residues in contact with ARG 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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241A ALA* 3.0 24.9 + - - +
242A GLN* 3.6 9.0 - - + +
244A MET* 1.3 77.6 - - - +
246A LEU* 1.3 61.7 + - - +
247A PHE 3.7 0.2 + - - -
248A GLY 4.6 0.5 + - - -
249A GLY* 5.1 4.9 + - - -
253A HIS* 5.7 1.1 - - - +
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Residues in contact with LEU 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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242A GLN* 2.9 26.1 + - + +
243A PHE 3.2 5.6 + - - +
245A ARG* 1.3 79.6 - - - +
247A PHE* 1.3 90.2 + - + +
249A GLY 5.2 0.7 + - - -
462A VAL* 4.1 19.1 - - + -
467A PRO* 4.5 18.4 - - + -
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Residues in contact with PHE 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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201A THR* 3.5 29.6 - - + -
202A PRO* 3.7 26.1 - - + +
203A SER* 4.6 9.7 + - - -
243A PHE* 2.9 47.6 + + + +
246A LEU* 1.3 108.5 - - + +
248A GLY* 1.3 58.3 + - - +
249A GLY 3.4 6.6 + - - -
250A ASN 5.1 0.3 + - - -
251A PHE* 3.7 13.5 - - - -
460A TRP* 3.7 39.0 - + + -
461A VAL 5.4 0.4 - - - -
462A VAL* 4.7 4.7 - - + -
467A PRO* 5.7 0.7 - - + -
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Residues in contact with GLY 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 PHE 4.2 0.2 + - - -
244A MET* 2.9 24.3 + - - -
246A LEU 3.7 0.2 - - - -
247A PHE* 1.3 78.1 - - - +
249A GLY* 1.3 64.1 + - - +
250A ASN 3.1 3.1 - - - -
251A PHE* 3.1 28.6 - - - +
253A HIS* 2.9 28.0 + - - -
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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