Contacts of the helix formed by residues 247 - 256 (chain B) in PDB entry 2F37
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 THR 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLY* 6.3 0.2 - - - -
214B SER* 4.5 2.2 - - - -
238B LEU 4.3 8.3 - - - +
239B GLN 4.2 2.5 - - - +
240B ALA 3.4 14.1 - - - +
241B THR* 3.7 13.7 - - + -
246B ASN* 1.3 75.7 - - - +
248B VAL* 1.3 65.9 + - - +
249B LEU* 3.1 20.6 + - - +
250B HIS* 2.9 23.9 + - + +
251B ALA* 2.9 21.5 + - - +
286B LEU* 5.1 2.5 + - + +
289B ILE* 3.7 41.7 - - + -
297B PRO* 4.7 0.5 - - - +
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Residues in contact with VAL 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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213B LEU* 4.6 10.1 - - + +
214B SER* 3.5 31.0 + - - +
217B ALA* 3.4 33.0 - - + -
238B LEU* 4.4 28.2 + - + +
240B ALA 4.3 3.4 + - - -
247B THR* 1.3 74.4 - - - +
249B LEU* 1.3 67.7 + - + +
251B ALA* 3.2 4.2 + - + +
252B LEU* 2.9 30.0 + - + +
273B LEU* 3.6 24.7 - - + -
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Residues in contact with LEU 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 LEU 6.1 0.4 - - - +
247B THR* 3.1 10.6 + - - +
248B VAL* 1.3 87.5 - - + +
250B HIS* 1.3 65.0 + - - +
252B LEU* 3.3 5.3 + - + +
253B VAL* 3.0 25.6 + - - +
270B TYR* 3.7 49.1 - - + +
273B LEU* 4.3 22.0 - - + -
274B LEU* 3.8 25.8 - - + -
286B LEU* 3.8 28.0 - - + +
287B GLU* 4.0 9.4 - - + -
297B PRO* 3.9 7.9 - - + -
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Residues in contact with HIS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLY 4.2 2.5 - - - -
246B ASN* 3.4 29.6 - - + +
247B THR* 2.9 44.7 + - + +
249B LEU* 1.3 76.8 - - - +
251B ALA* 1.3 63.3 + - - +
253B VAL* 3.2 7.3 + - - +
254B MSE 2.9 27.3 + - - +
289B ILE* 3.0 26.5 + - + -
291B ASN* 3.7 9.6 + - - -
295B LEU 2.8 28.6 + - - -
296B THR 3.9 1.1 - - - -
297B PRO* 3.5 22.3 - - + +
300B LEU* 3.6 17.4 - - + +
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Residues in contact with ALA 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 TYR* 4.1 11.4 - - + +
208B PHE 3.7 29.2 - - - +
209B GLY* 4.0 8.5 - - - -
214B SER* 4.4 2.0 - - - -
218B CYS* 3.9 10.5 - - - -
246B ASN* 4.7 0.2 - - - +
247B THR 2.9 12.9 + - - +
248B VAL* 3.5 12.6 - - - +
249B LEU 3.2 0.2 - - - -
250B HIS* 1.3 78.5 - - - +
252B LEU* 1.3 57.0 + - - +
254B MSE 3.1 4.2 + - - +
255B ILE* 3.0 32.2 + - - +
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Residues in contact with LEU 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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217B ALA 3.9 26.2 - - - +
218B CYS* 4.2 4.0 - - - -
220B LYS* 4.9 1.8 - - - -
248B VAL* 2.9 23.8 + - + +
249B LEU* 3.6 5.4 - - + +
251B ALA* 1.3 71.0 - - - +
253B VAL* 1.3 65.2 + - - +
255B ILE* 3.4 22.0 + - + +
256B SER* 3.1 24.3 + - - -
266B VAL* 3.8 13.9 - - + +
269B MSE 4.0 7.6 - - + -
270B TYR* 3.9 37.0 - - + +
273B LEU* 3.6 30.5 - - + -
309B ILE* 4.2 2.7 - - - -
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Residues in contact with VAL 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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249B LEU 3.0 18.2 + - - +
250B HIS 3.2 8.5 + - - +
252B LEU* 1.3 76.1 - - - +
254B MSE 1.3 63.4 + - - +
256B SER* 2.7 21.6 + - - -
270B TYR* 4.4 0.7 - - + -
297B PRO* 3.7 22.4 - - + +
300B LEU* 4.0 13.7 - - + +
301B ALA* 3.5 35.9 - - + +
306B LYS* 3.3 14.7 - - + +
309B ILE* 4.0 14.1 - - + -
313B ILE* 3.9 20.9 - - + -
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Residues in contact with MSE 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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200B LYS* 3.1 51.3 + - + +
207B TYR* 3.6 29.8 - - + +
246B ASN* 5.6 2.5 - - - +
250B HIS* 2.9 17.9 + - + +
251B ALA 3.1 8.0 + - - +
253B VAL* 1.3 79.6 - - - +
255B ILE* 1.3 59.4 + - - +
256B SER 3.5 0.7 + - - -
300B LEU* 3.7 22.2 - - + -
304B GLU* 3.7 42.6 - - + +
306B LYS* 3.6 19.3 + - - +
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Residues in contact with ILE 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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200B LYS* 4.6 5.2 - - - +
207B TYR* 3.5 31.2 - - + +
218B CYS* 3.9 28.0 - - + +
220B LYS* 3.8 25.4 - - - +
251B ALA 3.0 21.9 + - - +
252B LEU* 3.5 20.9 - - + +
254B MSE 1.3 74.8 - - - +
256B SER* 1.3 66.5 + - - +
257B ASP* 5.1 2.3 - - - +
266B VAL* 4.1 14.8 - - + +
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Residues in contact with SER 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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252B LEU 3.1 16.0 + - - -
253B VAL 2.7 17.3 + - - -
255B ILE* 1.3 82.7 - - - +
257B ASP* 1.3 66.7 + - - +
263B ILE* 4.7 3.8 - - - -
266B VAL* 4.1 23.6 - - - -
306B LYS* 2.9 32.1 + - - +
309B ILE* 3.6 24.3 - - - +
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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