Contacts of the helix formed by residues 238 - 246 (chain B) in PDB entry 2AG1
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 ASP 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B VAL* 4.7 0.8 - - - +
211B LEU 3.1 14.1 + - - +
212B GLY* 3.6 15.4 - - - -
213B SER* 4.1 4.1 + - - -
237B ALA* 1.3 78.2 - - - +
239B TYR* 1.3 67.0 + - - +
240B GLU* 3.3 7.2 + - - +
241B GLY 3.0 22.9 + - - -
242B LEU 3.1 7.1 + - - -
256B LEU* 3.8 5.9 - - - +
257B VAL* 3.7 12.0 - - + +
277B GLY 5.1 0.5 - - - +
278B ALA* 4.8 6.7 - - + -
279B ARG 5.5 0.9 + - - -
283B ASN* 3.8 33.7 + - + +
284B THR* 5.4 5.4 - - + +
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Residues in contact with TYR 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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238B ASP* 1.3 76.1 - - - +
240B GLU* 1.3 63.7 + - + +
242B LEU* 3.1 16.1 + - - +
243B SER 4.9 0.2 + - - -
256B LEU* 3.9 13.0 - - + -
258B GLN* 3.8 26.7 + - - -
282B LEU* 6.1 1.6 - - + -
283B ASN* 3.6 25.9 - - - +
397B TYR* 3.5 32.3 - + - -
398B LEU* 4.3 8.1 - - - +
401B SER* 4.3 15.4 + - - -
412B PHE* 3.6 32.7 - + + +
414B CYS* 3.8 25.4 - - + +
415B HIS 3.7 22.2 - - - +
552B GLU* 5.3 2.1 + - - -
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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
----------------------------------------------------------
62B ARG* 2.7 48.5 + - - +
91B ASP* 5.1 4.7 - - - +
213B SER* 3.6 31.4 - - - +
216B SER* 3.4 18.7 + - - -
217B ARG* 3.0 31.7 + - - +
238B ASP* 3.2 9.4 + - - +
239B TYR* 1.3 79.6 - - - +
241B GLY* 1.3 59.7 + - - +
243B SER* 4.9 3.8 + - - -
412B PHE 3.9 11.7 - - - +
413B LEU* 4.3 3.9 - - - -
414B CYS 4.4 1.2 + - - -
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Residues in contact with GLY 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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211B LEU* 4.3 6.7 - - - +
212B GLY 4.1 15.0 - - - -
216B SER* 4.6 4.7 - - - -
237B ALA* 3.4 15.5 - - - +
238B ASP* 3.0 17.5 + - - -
240B GLU* 1.3 76.0 - - - +
242B LEU* 1.3 64.9 + - - +
243B SER 3.4 1.8 - - - -
244B MSE 3.0 24.8 + - - +
245B LEU* 4.1 1.0 + - - +
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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* 3.7 7.0 - - + -
238B ASP 3.1 8.3 + - - +
239B TYR 3.1 15.8 + - - +
240B GLU 3.3 0.2 - - - -
241B GLY* 1.3 76.7 - - - +
243B SER* 1.3 53.2 + - - +
245B LEU* 2.8 51.1 + - + +
246B SER* 4.0 2.1 + - - -
253B ARG* 4.5 10.2 + - - +
255B GLY* 4.5 7.0 - - - -
256B LEU* 4.1 22.9 - - + +
404B MSE 3.8 44.4 - - + +
409B PRO* 4.4 7.4 - - + +
412B PHE* 3.7 26.0 - - + -
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Residues in contact with SER 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 SER* 4.4 12.0 + - - -
221B LYS* 5.7 3.9 - - - -
239B TYR 4.9 0.6 + - - -
240B GLU 4.9 3.0 + - - -
241B GLY 3.2 0.6 + - - -
242B LEU* 1.3 77.6 - - - +
244B MSE 1.3 59.7 + - - +
245B LEU 3.1 0.9 - - - -
246B SER* 3.0 32.6 + - - -
247B GLY 4.7 0.7 + - - -
409B PRO* 3.6 16.3 - - - +
410B GLY* 3.7 17.8 + - - +
411B GLY* 3.8 14.2 - - - -
412B PHE* 4.1 7.7 + - - +
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Residues in contact with MSE 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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211B LEU* 3.8 14.1 - - + -
215B ALA* 3.9 16.8 - - + +
216B SER* 3.8 28.3 - - - +
219B ALA* 3.8 19.3 - - - -
220B ARG* 3.7 37.5 - - + +
221B LYS* 4.0 26.5 - - + +
224B LEU* 3.5 35.2 - - + +
241B GLY 3.0 15.3 + - - +
243B SER* 1.3 78.7 + - - +
245B LEU* 1.3 59.6 + - - +
246B SER 3.3 0.6 + - - -
247B GLY* 4.4 3.7 + - - -
248B LEU* 4.2 4.0 - - - +
326B ILE* 5.4 2.0 - - + -
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Residues in contact with LEU 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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211B LEU* 3.8 16.4 - - + -
235B VAL* 3.5 47.6 - - + +
236B PHE 4.0 4.7 - - - +
237B ALA* 4.1 10.3 - - + -
241B GLY 4.7 0.2 - - - +
242B LEU* 2.8 25.5 + - + +
244B MSE 1.3 74.9 - - - +
246B SER* 1.3 63.9 + - - +
247B GLY 3.2 4.1 + - - -
248B LEU* 3.2 20.5 + - + +
253B ARG* 2.9 37.1 + - + +
254B GLY 4.9 0.7 - - - +
255B GLY* 3.5 38.1 - - - +
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Residues in contact with SER 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 4.0 0.7 + - - -
243B SER* 3.0 17.9 + - - -
245B LEU* 1.3 78.6 - - - +
247B GLY* 1.3 57.9 + - - +
248B LEU 3.5 2.2 + - - +
253B ARG* 4.4 1.0 + - - +
385B ALA* 5.7 4.7 - - - -
408B LYS* 3.3 49.0 - - - +
409B PRO* 2.6 31.8 + - - +
410B GLY* 5.5 1.1 - - - -
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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