Contacts of the helix formed by residues 242 - 252 (chain A) in PDB entry 3E8E
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 GLN 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ALA* 3.8 0.2 - - - +
241A ASP* 1.3 87.2 - - + +
243A PRO* 1.3 81.1 - - + +
244A ILE* 4.4 4.0 - - + +
245A GLN* 3.2 40.4 + - - +
246A ILE* 3.4 15.8 + - - +
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Residues in contact with PRO 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* 4.5 6.5 - - + -
241A ASP 4.4 0.2 - - - +
242A GLN* 1.3 97.5 - - + +
244A ILE* 1.3 65.2 + - + +
246A ILE* 2.9 25.0 + - + +
247A TYR* 3.0 42.7 + - + +
15G ARG* 3.5 30.1 - - - +
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Residues in contact with ILE 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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242A GLN* 3.3 3.0 + - + +
243A PRO* 1.3 80.8 - - + +
245A GLN* 1.3 77.7 + - + +
247A TYR* 3.4 15.5 + - + +
248A GLU* 3.4 36.6 + - + +
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Residues in contact with GLN 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 ALA* 3.5 19.2 - - + +
241A ASP* 4.5 6.6 + - - +
242A GLN* 3.2 39.5 + - - +
244A ILE* 1.3 87.3 - - + +
246A ILE* 1.3 65.7 + - - +
248A GLU* 3.5 16.5 + - - +
249A LYS* 3.3 27.9 + - - +
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Residues in contact with ILE 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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202A PRO* 4.0 13.9 - - + +
203A GLU* 3.8 32.1 - - + +
238A PHE* 3.7 18.6 - - + +
239A PHE* 4.0 1.6 - - - -
240A ALA* 3.5 28.7 - - - +
242A GLN 3.4 12.1 + - - +
243A PRO* 2.9 16.9 + - + +
245A GLN* 1.3 76.9 - - - +
247A TYR* 1.3 58.4 + - + +
249A LYS* 3.2 10.7 + - - +
250A ILE* 3.0 40.9 + - + +
15G ARG* 3.9 16.8 - - - +
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Residues in contact with TYR 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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198A LEU* 6.1 2.5 - - + -
202A PRO* 3.5 42.8 - - + +
205A LEU* 3.6 21.1 - - + -
210A ILE* 3.6 39.5 - - + -
243A PRO* 3.0 33.7 + - + +
244A ILE* 3.8 14.8 - - + +
245A GLN 3.3 0.4 - - - -
246A ILE* 1.3 76.6 - - - +
248A GLU* 1.3 62.1 + - + +
250A ILE* 3.1 4.2 + - + +
251A VAL* 3.0 29.1 + - - +
22G ILE* 3.8 17.2 - - - +
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Residues in contact with GLU 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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244A ILE* 3.4 29.1 + - + +
245A GLN* 3.7 18.8 - - - +
246A ILE 3.3 0.2 - - - -
247A TYR* 1.3 76.6 - - + +
249A LYS* 1.3 62.3 + - + +
251A VAL* 3.5 11.6 - - - +
252A SER* 3.3 22.2 + - - -
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Residues in contact with LYS 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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237A PRO 5.9 0.2 - - - +
238A PHE* 3.7 26.5 - - + -
239A PHE* 2.7 39.8 + - - +
240A ALA* 4.3 8.2 - - - +
245A GLN* 3.3 15.4 + - - +
246A ILE* 3.2 9.5 + - - +
248A GLU* 1.3 77.3 - - + +
250A ILE* 1.3 63.8 + - - +
252A SER* 2.5 26.6 + - - -
254A LYS 4.2 0.5 - - - +
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Residues in contact with ILE 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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202A PRO 3.3 23.6 - - - +
203A GLU 4.2 6.5 - - - +
205A LEU 3.3 28.9 - - - +
207A PRO* 3.9 11.9 - - + -
210A ILE* 3.7 21.3 - - + -
222A TRP* 3.6 20.8 - - + -
238A PHE* 3.7 30.0 - - + -
246A ILE* 3.0 24.8 + - + +
247A TYR* 3.1 8.9 + - + +
249A LYS* 1.3 77.5 - - - +
251A VAL* 1.3 61.0 + - - +
252A SER 3.4 0.2 + - - -
253A GLY 4.0 1.4 + - - -
275A VAL* 3.4 17.3 - - - +
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Residues in contact with VAL 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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207A PRO* 4.3 15.0 - - + -
210A ILE* 3.9 30.5 - - + -
211A LEU* 4.4 21.5 - - + -
247A TYR 3.0 19.4 + - - +
248A GLU* 3.5 15.5 - - - +
250A ILE* 1.3 76.1 - - - +
252A SER* 1.3 63.5 + - - +
253A GLY 3.3 1.5 + - - -
275A VAL* 4.2 16.1 - - + +
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Residues in contact with SER 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 GLU 3.3 14.2 + - - -
249A LYS* 2.5 25.7 + - - -
251A VAL* 1.3 79.1 - - - +
253A GLY* 1.3 59.7 + - - +
254A LYS* 3.2 46.2 + - - +
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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