Contacts of the helix formed by residues 242 - 253 (chain D) in PDB entry 3E8C
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D ALA* 4.0 0.2 - - - +
241D ASP* 1.3 82.2 - - + +
243D PRO* 1.3 74.9 - - + +
244D ILE* 3.2 25.8 - - + +
245D GLN* 3.1 46.2 + - - +
246D ILE* 3.4 15.1 + - - +
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Residues in contact with PRO 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D PRO* 4.3 10.8 - - + -
241D ASP 4.6 0.7 - - - +
242D GLN* 1.3 87.1 - - + +
244D ILE* 1.3 67.5 + - + +
246D ILE* 2.9 25.3 + - + +
247D TYR* 3.0 43.5 + - + +
15J ARG* 4.1 24.7 - - - +
22J ILE* 5.5 2.9 - - + -
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Residues in contact with ILE 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLN* 3.2 37.9 - - + +
243D PRO* 1.3 80.9 - - + +
245D GLN* 1.3 62.6 + - + +
247D TYR* 3.5 16.6 + - + +
248D GLU* 3.3 32.9 + - + +
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Residues in contact with GLN 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D ALA* 3.7 13.0 - - + +
241D ASP* 3.8 12.5 + - - +
242D GLN* 3.1 49.3 + - + +
244D ILE* 1.3 77.8 - - + +
246D ILE* 1.3 63.6 + - - +
247D TYR 3.3 0.2 - - - -
248D GLU* 3.6 20.7 + - - +
249D LYS* 3.4 29.7 + - - +
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Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D PRO* 4.0 15.0 - - + +
203D GLU* 3.8 28.9 - - - +
238D PHE 3.6 19.7 - - - +
239D PHE* 3.8 2.2 - - - -
240D ALA* 3.4 29.6 - - - +
242D GLN 3.7 8.5 - - - +
243D PRO* 2.9 18.0 + - + +
245D GLN* 1.3 76.9 - - - +
247D TYR* 1.3 58.3 + - + +
249D LYS* 3.3 9.2 + - - +
250D ILE* 3.0 42.5 + - + +
15J ARG* 3.9 16.8 - - - +
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Residues in contact with TYR 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 6.3 0.9 - - + -
202D PRO* 3.7 21.7 - - + +
205D LEU* 3.5 22.4 - - + -
210D ILE* 3.4 42.2 - - + -
243D PRO* 3.0 40.5 + - + +
244D ILE* 3.7 18.2 - - + +
245D GLN 3.3 0.2 - - - -
246D ILE* 1.3 74.9 - - - +
248D GLU* 1.3 65.7 + - - +
250D ILE* 3.3 4.3 + - + +
251D VAL* 3.1 31.4 + - - +
22J ILE* 3.7 24.6 - - + +
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE* 3.3 23.7 + - + +
245D GLN* 3.6 22.9 - - - +
247D TYR* 1.3 78.5 - - + +
249D LYS* 1.3 62.3 + - + +
251D VAL* 3.3 10.4 - - - +
252D SER* 3.2 24.0 + - - -
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Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D PRO 5.4 1.3 - - - +
238D PHE* 3.8 26.5 - - + -
239D PHE 3.7 33.3 + - - +
240D ALA* 4.4 7.9 - - - +
245D GLN* 3.4 15.6 + - - +
246D ILE* 3.3 9.1 + - - +
247D TYR 3.3 0.6 - - - -
248D GLU* 1.3 78.4 - - + +
250D ILE* 1.3 65.2 + - - +
252D SER* 3.0 24.1 + - - -
253D GLY 4.1 0.9 + - - -
254D LYS 4.1 2.5 - - - +
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Residues in contact with ILE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D PRO 3.2 26.9 - - - +
203D GLU 4.5 5.8 - - - +
205D LEU 3.4 25.4 - - - +
207D PRO* 4.0 12.1 - - + +
210D ILE* 3.8 21.1 - - + -
222D TRP* 3.8 21.0 - - + +
238D PHE* 3.7 29.7 - - + -
246D ILE* 3.0 29.1 + - + +
247D TYR* 3.3 6.0 + - + +
249D LYS* 1.3 78.2 - - - +
251D VAL* 1.3 61.4 + - - +
252D SER 3.4 0.3 + - - -
253D GLY 3.8 1.6 + - - -
275D VAL* 3.8 16.6 - - - +
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D PRO* 4.4 14.4 - - + -
210D ILE* 4.1 30.1 - - + -
211D LEU* 4.2 24.5 - - + -
247D TYR 3.1 19.0 + - - +
248D GLU* 3.3 16.4 - - - +
250D ILE* 1.3 75.5 - - - +
252D SER* 1.3 63.9 + - - +
253D GLY 3.2 1.3 + - - -
275D VAL* 4.1 14.2 - - + +
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D GLU 3.2 18.2 + - - -
249D LYS* 3.0 18.1 + - - -
250D ILE 3.3 0.4 - - - -
251D VAL* 1.3 79.0 - - - +
253D GLY* 1.3 59.2 + - - +
254D LYS* 3.2 43.6 + - - +
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Residues in contact with GLY 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D PHE* 6.4 0.2 - - - -
250D ILE 3.8 4.6 + - - -
251D VAL 3.2 4.6 - - - -
252D SER* 1.3 79.5 + - - +
254D LYS* 1.3 59.4 + - - +
255D VAL* 4.2 5.1 + - - +
273D LEU 6.0 0.4 - - - -
275D VAL* 3.6 24.0 - - - -
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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