Contacts of the helix formed by residues 242 - 259 (chain B) in PDB entry 3SAJ
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B ASN* 2.5 49.5 + - - +
241B THR* 1.3 81.0 + - - +
243B THR* 1.3 57.2 + - - +
244B ILE 3.5 0.9 - - - -
245B PRO* 3.3 22.3 - - + +
246B ALA* 2.7 32.6 + - - +
349B HIS* 5.3 4.0 + - - -
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Residues in contact with THR 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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241B THR 3.7 2.1 + - - -
242B ASP* 1.3 73.2 - - - +
244B ILE* 1.3 71.6 + - + +
246B ALA* 3.0 6.2 + - - +
247B ARG* 2.9 37.1 + - + +
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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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243B THR* 1.3 82.2 - - + +
245B PRO* 1.3 74.8 - - + +
247B ARG* 3.1 21.3 + - - +
248B ILE* 3.1 39.9 + - + +
329B GLU* 4.1 43.7 - - + +
330B GLY 4.4 4.9 - - - +
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Residues in contact with PRO 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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238B VAL* 4.9 1.8 - - + -
239B ASN 2.9 30.7 - - - +
240B TYR* 4.4 4.0 - - - -
242B ASP* 3.3 22.0 - - + +
244B ILE* 1.3 98.5 - - + +
246B ALA* 1.3 62.5 + - - +
248B ILE* 3.2 3.3 + - - +
249B MET* 3.1 28.9 + - + +
329B GLU* 5.7 3.1 - - + +
330B GLY 4.6 4.5 - - - +
331B LEU* 3.9 35.6 - - + +
333B GLY* 5.9 0.9 - - - +
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Residues in contact with ALA 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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240B TYR 4.1 14.3 + - - +
241B THR* 4.1 11.9 - - - +
242B ASP 2.7 22.3 + - - +
243B THR* 3.3 6.7 - - - +
245B PRO* 1.3 71.7 - - - +
247B ARG* 1.3 62.5 + - - +
249B MET* 3.2 7.3 + - - +
250B GLN* 3.1 20.3 + - - +
253B ARG* 3.6 8.9 + - - +
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Residues in contact with ARG 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 THR* 2.9 22.7 + - + +
244B ILE* 3.1 33.4 + - - +
246B ALA* 1.3 75.8 - - - +
248B ILE* 1.3 58.1 + - - +
250B GLN* 3.3 9.5 + - - +
251B GLN* 2.7 51.2 + - + +
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Residues in contact with ILE 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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26B PHE* 4.2 0.8 - - + -
244B ILE* 3.1 35.3 + - + +
245B PRO 3.5 1.3 - - - +
247B ARG* 1.3 81.2 - - + +
249B MET* 1.3 61.5 + - - +
251B GLN* 3.0 25.2 + - - +
252B TRP* 2.9 33.0 - - + +
276B TYR* 3.5 39.9 - - + +
280B LYS* 4.6 2.7 - - - +
329B GLU 5.7 0.2 - - - +
330B GLY* 4.8 0.4 - - - -
331B LEU* 3.3 52.9 - - + +
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Residues in contact with MET 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 VAL* 4.8 2.0 - - + -
240B TYR* 3.0 50.3 - - + +
245B PRO 3.1 16.6 + - - +
246B ALA* 3.5 6.5 - - - +
247B ARG 3.2 0.2 - - - -
248B ILE* 1.3 71.3 - - - +
250B GLN* 1.3 64.3 + - - +
251B GLN 3.0 1.5 + - - -
252B TRP* 3.3 14.6 + - - +
253B ARG* 2.3 63.6 + - - +
267B ARG* 4.9 5.4 - - - +
268B PRO* 3.5 33.2 - - + -
273B ALA* 6.0 0.9 - - + -
331B LEU* 4.3 22.4 - - + -
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Residues in contact with GLN 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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246B ALA 3.1 5.4 + - - +
247B ARG* 3.5 11.9 - - - +
249B MET* 1.3 74.4 - - - +
251B GLN* 1.3 62.1 + - + +
253B ARG* 2.8 38.2 + - - +
254B THR* 2.8 61.6 + - + +
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Residues in contact with GLN 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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26B PHE* 4.0 2.6 - - + -
30B GLN* 2.9 33.8 + - - +
247B ARG* 2.7 40.6 - - + +
248B ILE* 3.1 26.0 + - - +
249B MET 3.0 1.0 - - - -
250B GLN* 1.3 79.1 - - + +
252B TRP* 1.3 55.2 + - - +
254B THR* 3.1 6.6 + - - -
255B SER* 2.8 25.9 + - - -
258B ARG* 4.8 2.1 + - - -
276B TYR* 4.6 0.3 + - - -
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Residues in contact with TRP 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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19B GLN* 5.5 4.0 - - + -
22B ALA* 4.4 6.7 - - + -
23B ALA* 3.9 37.0 - - + -
26B PHE* 3.0 51.1 - + + -
248B ILE* 2.9 33.3 + - + +
249B MET* 3.4 27.0 - - - +
251B GLN* 1.3 73.7 - - - +
253B ARG* 1.3 58.7 + - + +
254B THR 3.5 0.2 - - - -
255B SER* 3.3 7.6 - - - +
256B ASP* 2.5 54.4 + - - +
268B PRO* 3.3 36.8 - - + -
272B SER* 5.1 4.7 - - - -
276B TYR* 5.2 2.9 - + - -
331B LEU* 4.7 13.2 - - + -
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Residues in contact with ARG 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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240B TYR 5.7 1.4 + - - -
246B ALA* 3.6 7.5 + - - +
249B MET* 2.3 56.1 + - + +
250B GLN* 2.8 54.9 + - - +
252B TRP* 1.3 79.9 - - + +
254B THR* 1.3 63.1 + - + +
256B ASP* 4.1 3.2 - - - +
257B SER* 3.3 23.6 + - - -
266B LYS* 6.3 4.7 - - + -
267B ARG* 5.1 15.2 - - - +
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Residues in contact with THR 254 (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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250B GLN* 2.8 47.5 + - + +
251B GLN* 3.1 7.8 + - - -
253B ARG* 1.3 75.4 - - + +
255B SER* 1.3 60.1 + - - +
257B SER* 3.1 15.9 + - - -
258B ARG* 2.8 36.4 + - - +
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Residues in contact with SER 255 (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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26B PHE* 4.2 14.3 - - - -
251B GLN 2.8 19.6 + - - -
252B TRP* 3.3 11.1 - - - +
254B THR* 1.3 80.5 + - - +
256B ASP* 1.3 64.7 + - - +
258B ARG* 3.0 42.4 - - - +
259B ASP* 3.6 5.4 + - - +
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Residues in contact with ASP 256 (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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26B PHE* 5.8 1.6 - - - +
252B TRP* 2.5 45.5 + - - +
253B ARG* 4.1 4.2 - - - +
255B SER* 1.3 72.8 + - - +
257B SER* 1.3 65.6 + - - +
259B ASP* 3.2 22.8 + - - +
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Residues in contact with SER 257 (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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253B ARG 3.3 11.7 + - - -
254B THR* 3.1 17.8 + - - -
256B ASP* 1.3 79.2 - - - +
258B ARG* 1.3 62.9 + - - +
259B ASP 4.4 2.4 - - - -
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Residues in contact with ARG 258 (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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251B GLN 4.8 1.2 + - - -
254B THR* 2.8 35.4 + - - +
255B SER* 3.0 32.1 - - - +
256B ASP 3.0 0.2 - - - -
257B SER* 1.3 81.3 + - - +
259B ASP* 1.3 56.4 + - + +
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Residues in contact with ASP 259 (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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25B ARG* 5.3 6.8 + - - -
255B SER 3.6 5.1 + - - +
256B ASP* 3.2 18.2 + - - +
257B SER 4.4 2.9 - - - -
258B ARG* 1.3 81.4 - - + +
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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