Contacts of the helix formed by residues 239 - 248 (chain B) in PDB entry 3C3A
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 MET 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.8 36.1 - - + +
212B GLY 4.0 4.9 - - - +
213B GLY* 3.9 10.7 + - - +
214B ALA 3.5 10.1 + - - +
215B LYS 4.2 1.6 - - - +
216B VAL* 3.6 28.7 - - + +
219B LYS* 3.2 38.6 - - + -
223B ILE* 3.9 15.5 - - + -
235B ILE* 3.8 20.0 - - + -
236B GLY 3.4 14.8 - - - +
237B GLY 4.4 0.2 - - - -
238B GLY* 1.3 75.2 - - - +
240B ALA* 1.3 62.2 + - - +
241B PHE 3.2 1.4 + - - -
242B THR* 3.2 19.9 + - - -
243B PHE* 3.8 7.0 - - - -
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Residues in contact with ALA 240 (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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235B ILE* 3.7 12.1 - - - +
236B GLY 4.1 0.2 + - - -
237B GLY 3.4 11.3 + - - +
238B GLY 3.2 1.4 - - - -
239B MET* 1.3 78.4 - - - +
241B PHE* 1.3 59.1 + - + +
242B THR 3.2 0.4 - - - -
243B PHE* 3.3 5.5 + - - +
244B LEU* 2.8 34.1 + - + +
281B LEU* 4.0 8.7 - - + -
282B PRO* 3.3 42.4 - - + -
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Residues in contact with PHE 241 (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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237B GLY 4.4 4.9 - - - -
238B GLY* 3.2 31.6 - - - +
239B MET 3.2 1.2 + - - -
240B ALA* 1.3 76.1 - - + +
242B THR* 1.3 58.1 + - - +
244B LEU* 4.4 2.7 - - + +
245B LYS* 2.8 36.0 + - - +
250B MET* 4.1 5.8 - - + -
252B ILE* 3.8 28.6 - - + +
255B SER* 3.6 23.1 - - - -
256B LEU 3.4 18.4 - - - +
257B PHE* 4.1 2.4 - - - -
282B PRO* 6.1 0.2 - - + -
285B PHE* 3.6 31.0 - + - -
306B ILE* 3.6 20.9 - - + -
312B GLY* 3.6 33.0 - - - -
419B ADP 4.8 0.4 - - - -
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Residues in contact with THR 242 (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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216B VAL* 3.5 21.8 - - + +
238B GLY 5.2 0.5 + - - -
239B MET 3.2 11.2 + - - -
240B ALA 3.2 0.4 - - - -
241B PHE* 1.3 79.7 - - - +
243B PHE* 1.3 62.4 + - + +
245B LYS* 4.1 0.5 - - - +
246B VAL* 3.1 30.3 + - - +
256B LEU 4.3 1.4 + - - -
257B PHE* 3.6 13.6 - - - -
258B ASP 3.3 24.0 + - - +
261B GLY 4.0 3.1 - - - -
262B ALA* 3.5 38.1 - - + +
265B VAL* 3.8 9.6 - - + -
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Residues in contact with PHE 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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216B VAL* 3.9 23.8 - - + -
223B ILE* 4.4 12.3 - - + -
235B ILE* 4.0 27.1 - - + -
239B MET 3.8 13.0 - - - -
240B ALA 3.3 7.8 + - - +
242B THR* 1.3 80.0 - - - +
244B LEU* 1.3 52.4 + - - +
246B VAL* 3.3 1.6 + - - +
247B LEU* 2.8 43.6 + - + +
265B VAL* 3.8 31.9 - - + -
268B LEU* 3.8 30.7 - - + -
269B MET* 3.9 28.5 - - + -
279B ILE* 5.6 0.9 - - + -
281B LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 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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240B ALA* 2.8 28.2 + - + +
241B PHE* 4.3 3.8 - - + +
243B PHE* 1.3 69.3 - - - +
245B LYS* 1.3 68.2 + - - +
246B VAL 3.1 1.1 - - - -
248B ASN* 3.0 52.0 + - + +
249B ASN 3.3 4.7 + - - -
250B MET* 3.3 22.2 + - + -
281B LEU* 4.2 16.8 - - + -
282B PRO* 3.4 43.5 - - + +
283B VAL* 6.1 0.7 - - + -
285B PHE* 3.9 15.0 - - + -
302B VAL* 4.0 13.5 - - + -
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Residues in contact with LYS 245 (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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241B PHE 2.8 23.9 + - - +
244B LEU* 1.3 72.8 - - - +
246B VAL* 1.3 59.0 + - + +
249B ASN* 3.1 28.2 + - - +
250B MET* 3.7 24.1 - - - +
251B GLU* 6.3 0.2 - - - +
252B ILE* 4.4 18.2 - - + +
257B PHE* 3.4 50.5 - - + +
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Residues in contact with VAL 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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242B THR 3.1 19.1 + - - +
243B PHE 3.8 2.2 - - - +
244B LEU 3.1 0.2 - - - -
245B LYS* 1.3 80.1 - - + +
247B LEU* 1.3 67.9 + - + +
248B ASN 3.6 0.2 + - - -
249B ASN* 4.0 11.7 + - - +
257B PHE* 4.5 6.1 - - + -
262B ALA* 3.8 37.7 - - + +
265B VAL* 4.3 17.7 - - + -
266B LYS* 5.6 4.0 - - + +
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Residues in contact with LEU 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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243B PHE* 2.8 28.8 + - + +
246B VAL* 1.3 76.3 - - + +
248B ASN* 1.3 74.5 + - - +
249B ASN* 3.6 1.3 - - - +
265B VAL* 4.1 11.0 - - + -
266B LYS* 6.0 2.2 - - - -
269B MET* 3.7 50.0 - - + -
281B LEU* 3.9 19.7 - - + -
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Residues in contact with ASN 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 LEU* 3.0 42.1 + - - +
247B LEU* 1.3 92.9 - - - +
249B ASN* 1.3 73.0 + - - +
250B MET* 3.3 1.5 + - - +
281B LEU* 5.3 2.8 - - - +
302B VAL* 3.9 26.1 - - + +
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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