Contacts of the helix formed by residues 238 - 248 (chain B) in PDB entry 3GA5
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 LEU 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN* 3.7 27.8 - - + +
16B PHE* 4.1 30.1 - - + +
19B VAL* 4.4 16.4 - - + -
212B ASP* 2.9 30.4 + - + +
213B ALA* 4.3 4.5 - - + +
216B MET* 4.1 16.4 - - - -
236B ASP* 3.3 14.0 + - + +
237B ALA* 1.3 80.3 - - - +
239B PRO* 1.3 75.5 - - + +
240B GLU* 3.7 12.3 - - - +
241B ALA 2.9 15.3 + - - +
242B LEU* 3.1 8.8 + - - +
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Residues in contact with PRO 239 (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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19B VAL* 5.5 7.0 - - + -
237B ALA 3.6 2.9 - - - +
238B LEU* 1.3 85.8 - - + +
240B GLU* 1.3 75.8 + - + +
242B LEU* 3.1 13.8 + - + +
243B ALA* 3.0 21.4 + - - +
307B THR* 5.5 1.2 - - + +
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Residues in contact with GLU 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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15B ASN* 5.1 5.5 + - - -
216B MET* 3.7 32.4 - - + +
238B LEU* 3.7 11.2 - - + +
239B PRO* 1.3 91.4 - - + +
241B ALA* 1.3 60.5 + - - +
243B ALA* 3.4 9.4 - - - +
244B LEU* 3.2 27.1 + - + +
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Residues in contact with ALA 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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212B ASP* 3.1 43.3 - - + +
216B MET* 4.7 3.3 - - - -
238B LEU* 2.9 7.8 + - + +
240B GLU* 1.3 79.3 - - - +
242B LEU* 1.3 54.3 + - - +
243B ALA 3.1 0.2 - - - -
244B LEU* 3.0 7.4 + - - +
245B VAL* 2.7 38.8 + - - +
250B MET* 4.0 19.4 - - + +
253B THR* 4.7 5.2 - - + -
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Residues in contact with LEU 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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237B ALA* 3.9 29.4 - - + +
238B LEU 3.1 11.2 + - - +
239B PRO* 3.1 11.0 + - + +
241B ALA* 1.3 76.9 - - - +
243B ALA* 1.3 56.4 + - - +
245B VAL* 3.3 6.4 + - + +
246B LYS* 2.9 28.8 + - - +
253B THR* 4.0 9.9 - - + -
298B VAL* 3.6 31.0 - - + -
303B LEU* 3.8 10.6 - - + +
306B PHE* 4.0 18.6 - - + +
307B THR* 3.2 35.9 - - + -
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Residues in contact with ALA 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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239B PRO 3.0 11.2 + - - +
240B GLU* 3.4 14.1 - - - +
242B LEU* 1.3 77.7 - - - +
244B LEU* 1.3 61.5 + - + +
246B LYS* 3.3 11.9 + - - +
247B SER* 3.1 25.8 + - - -
307B THR* 5.4 0.2 - - - +
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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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216B MET* 3.8 28.0 - - + -
219B VAL* 4.2 22.0 - - + -
223B LYS* 5.4 4.7 - - - -
240B GLU* 3.3 15.3 - - + +
241B ALA 3.0 6.4 + - - +
243B ALA* 1.3 76.9 - - + +
245B VAL* 1.3 64.7 + - - +
246B LYS 3.1 1.1 - - - -
247B SER* 3.2 6.4 + - - +
248B GLY 2.8 19.9 + - - -
249B ALA* 3.0 25.3 + - + -
250B MET* 3.2 31.6 + - + +
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Residues in contact with VAL 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 ALA 2.7 21.9 + - - +
242B LEU* 3.6 11.2 - - + +
244B LEU* 1.3 71.9 - - - +
246B LYS* 1.3 62.3 + - - +
248B GLY* 3.3 8.8 + - - -
250B MET* 3.3 28.4 - - + +
251B ALA 4.8 3.1 - - - +
252B GLY* 4.2 10.8 - - - -
253B THR* 4.2 23.8 - - + -
298B VAL* 4.9 1.3 - - + +
299B ASP* 3.7 11.9 - - - +
300B LYS* 3.7 38.7 - - - +
303B LEU* 4.3 11.2 - - + -
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Residues in contact with LYS 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 LEU 2.9 13.2 + - - +
243B ALA* 3.4 14.1 - - - +
244B LEU 3.1 0.2 - - - -
245B VAL* 1.3 78.3 - - - +
247B SER* 1.3 55.9 + - - +
300B LYS* 2.6 31.7 + - + +
303B LEU* 3.5 21.5 - - + +
307B THR* 6.1 1.1 - - - +
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Residues in contact with SER 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 ALA 3.1 8.7 + - - -
244B LEU* 3.2 17.2 + - - +
246B LYS* 1.3 79.3 - - - +
248B GLY* 1.3 59.0 + - - +
249B ALA* 3.3 18.0 + - - +
300B LYS* 4.5 2.6 + - - -
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Residues in contact with GLY 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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228B SER 5.2 5.2 - - - +
244B LEU 2.8 5.8 + - - -
245B VAL 3.3 4.7 + - - -
246B LYS 3.2 4.6 - - - -
247B SER* 1.3 79.7 - - - +
249B ALA* 1.3 62.1 + - - +
250B MET 3.2 13.7 + - - +
251B ALA* 5.9 0.2 - - - -
300B LYS* 4.8 4.9 - - - -
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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