Contacts of the helix formed by residues 242 - 253 (chain B) in PDB entry 3AG9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B ALA* 3.6 4.3 - - - +
241B ASP* 1.3 100.0 + - + +
243B PRO* 1.3 77.5 - - + +
244B ILE* 4.3 11.0 - - + -
245B GLN* 3.0 48.0 + - + +
246B ILE* 3.5 5.9 + - - +
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Residues in contact with PRO 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PRO* 5.4 6.2 - - + +
241B ASP 3.9 6.3 - - - +
242B GLN* 1.3 88.8 - - + +
244B ILE* 1.3 62.2 + - + +
246B ILE* 3.1 32.1 + - + +
247B TYR* 3.5 18.7 + - + -
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLN* 4.3 13.2 - - + -
243B PRO* 1.3 79.0 - - + +
245B GLN* 1.3 66.3 + - + +
247B TYR* 3.2 20.3 + - + +
248B GLU* 3.0 47.4 + - + +
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ALA* 3.4 17.0 - - + +
241B ASP* 4.1 4.2 + - - +
242B GLN* 3.0 45.4 + - + +
244B ILE* 1.3 78.7 - - + +
246B ILE* 1.3 66.6 + - - +
248B GLU* 3.8 18.4 - - - +
249B LYS* 3.0 37.3 + - - +
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PRO* 4.2 28.0 - - + -
203B GLU* 4.1 22.2 - - + +
238B PHE* 3.6 21.5 - - - +
239B PHE* 4.8 1.6 - - + -
240B ALA* 3.7 33.2 - - - +
242B GLN 3.8 4.9 - - - +
243B PRO* 3.1 24.3 + - + +
245B GLN* 1.3 77.1 - - - +
247B TYR* 1.3 57.8 + - - +
249B LYS* 3.3 8.0 + - - +
250B ILE* 3.0 46.5 + - + +
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 5.4 8.2 - - + +
200B GLY 5.2 1.2 + - - -
202B PRO* 3.4 43.4 - - + +
205B LEU* 4.1 12.6 - - + +
210B ILE* 3.4 48.0 - - + -
243B PRO* 3.5 16.1 + - + -
244B ILE* 3.2 22.7 + - + +
246B ILE* 1.3 79.0 - - - +
248B GLU* 1.3 56.7 + - - +
250B ILE* 3.2 4.6 + - + +
251B VAL* 2.9 35.7 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ILE* 3.0 39.9 + - + +
245B GLN* 3.8 22.0 - - - +
247B TYR* 1.3 74.8 - - - +
249B LYS* 1.3 59.4 + - + +
251B VAL* 3.6 5.3 + - - +
252B SER* 3.0 30.7 + - - -
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B PHE* 3.7 22.9 - - + -
239B PHE 2.8 34.7 + - - +
240B ALA* 3.8 11.1 - - - +
245B GLN* 3.0 29.7 + - - +
246B ILE 3.7 4.3 - - - +
247B TYR 3.3 0.2 - - - -
248B GLU* 1.3 74.6 - - + +
250B ILE* 1.3 61.2 + - - +
252B SER* 3.4 7.6 + - - -
253B GLY* 2.8 26.7 + - - -
254B LYS 4.1 3.1 + - - +
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PRO 3.1 28.0 - - - +
203B GLU 4.5 4.3 - - - +
205B LEU 3.4 23.1 - - - +
207B PRO* 3.8 13.5 - - + +
210B ILE* 3.7 20.6 - - + -
222B TRP* 3.7 16.5 - - + -
238B PHE* 3.6 29.8 - - + -
246B ILE* 3.0 29.7 + - + +
247B TYR* 3.6 6.1 - - + +
249B LYS* 1.3 76.1 - - - +
251B VAL* 1.3 59.6 + - - +
253B GLY* 2.8 21.0 + - - -
275B VAL* 3.8 6.9 - - - +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B PRO* 4.2 12.4 - - + +
210B ILE* 4.0 20.9 - - + -
211B LEU* 3.9 42.6 - - + -
247B TYR 2.9 21.0 + - - +
248B GLU* 4.0 5.4 - - - +
250B ILE* 1.3 74.6 - - - +
252B SER* 1.3 63.3 + - - +
253B GLY 3.4 0.5 + - - -
275B VAL* 3.6 14.2 - - - +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLU 3.0 19.9 + - - -
249B LYS* 3.6 6.1 + - - -
251B VAL* 1.3 77.5 - - - +
253B GLY* 1.3 57.3 + - - +
254B LYS* 3.1 40.4 + - - +
275B VAL* 4.3 6.8 - - - +
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B TRP* 4.6 2.7 - - - -
238B PHE* 4.1 12.3 - - - -
249B LYS 2.8 10.8 + - - -
250B ILE 2.8 14.4 + - - -
252B SER* 1.3 75.1 - - - +
254B LYS* 1.3 64.9 + - - +
255B VAL* 3.2 13.9 + - - +
273B LEU 4.6 7.7 - - - +
275B VAL* 3.6 14.8 - - - -
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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