Contacts of the helix formed by residues 242 - 253 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241L ASP* 1.3 89.1 - - + +
243L PRO* 1.4 81.6 - - + +
244L ILE* 3.1 16.4 + - + +
245L GLN* 3.1 27.7 + - - +
246L ILE* 3.4 15.1 + - - +
15N ARG* 4.7 0.8 + - - +
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Residues in contact with PRO 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L PRO* 4.2 9.4 - - + -
242L GLN* 1.4 98.7 - - + +
244L ILE* 1.3 59.1 + - + +
246L ILE* 3.0 16.6 + - + +
247L TYR* 2.8 59.3 + - + +
15N ARG* 3.4 28.9 - - - +
22N ILE* 5.1 5.4 - - + -
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Residues in contact with ILE 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L GLN* 3.1 14.4 + - + +
243L PRO* 1.3 77.8 - - + +
245L GLN* 1.3 63.5 + - + +
247L TYR* 3.3 16.9 + - + +
248L GLU* 3.0 41.6 + - + +
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Residues in contact with GLN 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L ALA* 3.6 14.7 - - + +
241L ASP* 3.8 12.7 + - - +
242L GLN* 3.1 34.5 + - - +
244L ILE* 1.3 77.2 - - + +
246L ILE* 1.3 64.1 + - - +
248L GLU* 3.6 23.3 - - - +
249L LYS* 3.3 30.4 + - - +
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Residues in contact with ILE 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L PRO* 4.2 13.5 - - + +
203L GLU* 3.7 32.1 - - + +
238L PHE 3.7 20.4 - - - +
239L PHE 3.9 1.1 - - - -
240L ALA* 3.4 26.7 - - - +
242L GLN 3.4 8.9 + - - +
243L PRO* 3.0 16.1 + - + +
245L GLN* 1.3 76.7 - - - +
247L TYR* 1.3 60.7 + - + +
249L LYS* 3.2 9.0 + - - +
250L ILE* 3.0 43.6 + - + +
15N ARG* 3.8 21.8 - - - +
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Residues in contact with TYR 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L LEU* 5.8 3.2 - - + +
202L PRO* 3.6 23.2 - - + +
205L LEU* 3.6 22.6 - - + +
210L ILE* 3.7 42.6 - - + -
243L PRO* 2.8 35.4 + - + +
244L ILE* 3.3 15.7 + - + +
246L ILE* 1.3 75.0 - - + +
248L GLU* 1.3 65.1 + - - +
250L ILE* 3.3 6.2 + - + +
251L VAL* 3.1 29.5 + - - +
22N ILE* 3.1 34.7 - - - +
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Residues in contact with GLU 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L ILE* 3.0 34.1 + - + +
245L GLN* 3.6 22.8 - - - +
247L TYR* 1.3 77.1 - - - +
249L LYS* 1.3 57.8 + - + +
251L VAL* 3.1 11.9 - - - +
252L SER* 3.1 27.7 + - - -
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Residues in contact with LYS 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238L PHE* 3.8 27.3 - - + -
239L PHE* 2.8 36.6 + - - +
240L ALA* 3.9 10.3 - - - +
245L GLN* 3.3 16.5 + - - +
246L ILE* 3.2 8.1 + - - +
248L GLU* 1.3 73.9 - - + +
250L ILE* 1.3 65.5 + - - +
252L SER* 2.5 26.2 + - - -
253L GLY 3.9 0.7 + - - -
254L LYS 4.5 1.7 - - - +
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Residues in contact with ILE 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L PRO 3.3 25.8 - - - +
203L GLU 4.4 5.8 - - - +
205L LEU 3.4 25.1 - - - +
207L PRO* 3.9 11.0 - - + +
210L ILE* 3.8 21.1 - - + -
222L TRP* 3.7 19.8 - - + -
238L PHE* 3.6 29.7 - - + -
246L ILE* 3.0 29.5 + - + +
247L TYR* 3.3 7.6 + - + +
249L LYS* 1.3 78.4 - - - +
251L VAL* 1.3 61.1 + - - +
253L GLY* 3.8 5.9 + - - -
275L VAL* 3.9 12.5 - - - +
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Residues in contact with VAL 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207L PRO* 4.5 19.5 - - + -
210L ILE* 4.6 11.7 - - + -
211L LEU* 4.1 37.7 - - + -
247L TYR 3.1 13.4 + - - +
248L GLU* 3.1 21.3 - - - +
250L ILE* 1.3 75.6 - - - +
252L SER* 1.3 66.2 + - - +
253L GLY* 3.1 2.9 + - - -
275L VAL* 4.0 12.4 - - - +
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Residues in contact with SER 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L GLU 3.1 17.2 + - - -
249L LYS* 2.5 25.5 + - - +
251L VAL* 1.3 77.2 - - - +
253L GLY* 1.3 59.7 + - - +
254L LYS* 3.5 41.8 + - - +
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Residues in contact with GLY 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L TRP* 6.3 0.2 - - - -
238L PHE* 6.1 0.9 - - - -
250L ILE 3.8 4.9 + - - -
251L VAL 3.1 4.4 + - - -
252L SER* 1.3 78.8 + - - +
254L LYS* 1.3 61.0 + - - +
255L VAL* 4.2 3.4 + - - -
275L VAL* 3.8 23.6 - - - -
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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