Contacts of the helix formed by residues 244 - 255 (chain B) in PDB entry 1FBU
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 ASN 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.5 34.0 - - - -
220A GLY 4.6 0.6 + - - -
221A GLU* 3.6 30.8 - - + +
232B VAL* 5.3 4.0 - - + -
236B LEU* 3.7 8.2 - - - +
243B SER* 1.3 78.6 + - - +
245B PHE* 1.3 64.4 + - - +
246B ALA* 3.1 9.2 + - - +
247B SER* 2.7 35.9 + - - -
248B PHE* 3.1 18.9 + - - +
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Residues in contact with PHE 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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225B VAL* 4.9 5.6 - - + -
228B ARG* 3.6 29.2 - - + -
231B PHE* 4.1 26.7 - + - -
232B VAL* 3.8 29.2 - - + +
236B LEU* 4.0 3.0 - - - +
244B ASN* 1.3 74.8 - - - +
246B ALA* 1.3 59.0 + - - +
248B PHE* 3.2 11.9 + + - +
249B VAL* 2.9 54.4 + - + +
276B TRP* 3.5 53.8 - + + -
278B PHE* 4.3 5.8 - + - -
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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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206A ASN* 4.5 5.6 - - - +
216A TRP* 3.4 40.2 - - + +
244B ASN* 3.1 7.7 + - - +
245B PHE* 1.3 79.3 - - - +
247B SER* 1.3 58.3 + - - +
249B VAL* 3.4 7.6 + - - +
250B ARG* 2.9 29.5 + - - +
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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
----------------------------------------------------------
216A TRP* 4.3 10.3 - - - +
217A SER 2.8 26.3 + - - -
218A THR* 3.3 14.4 + - - -
220A GLY 3.9 8.9 + - - -
243B SER* 3.7 11.8 + - - -
244B ASN* 2.7 25.7 + - - -
246B ALA* 1.3 72.9 - - - +
248B PHE* 1.3 62.3 + - - +
250B ARG* 3.3 8.7 + - - +
251B GLN* 3.1 28.8 + - - +
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Residues in contact with PHE 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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197B PHE* 3.8 26.5 - + - -
201B LEU* 4.2 3.6 - - + -
204B MET* 3.5 33.2 - - + -
214B ILE* 4.7 5.4 - - + -
225B VAL* 5.4 0.7 - - + -
231B PHE* 3.8 23.6 - + - -
236B LEU* 4.0 17.0 - - + -
240B PHE* 3.9 17.0 - + - -
243B SER* 4.2 3.7 + - - +
244B ASN 3.1 12.6 + - - +
245B PHE* 3.4 22.2 - + - +
247B SER* 1.3 73.8 - - - +
249B VAL* 1.3 63.0 + - + +
251B GLN* 3.1 9.4 + - - +
252B LEU* 2.9 57.7 + - + +
278B PHE* 5.0 4.9 - + - -
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Residues in contact with VAL 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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245B PHE* 2.9 54.4 + - + +
246B ALA* 3.8 6.5 - - - +
248B PHE* 1.3 77.2 - - + +
250B ARG* 1.3 63.1 + - - +
252B LEU* 3.2 7.0 + - - +
253B ASN* 2.9 42.6 + - - +
259B LYS* 6.3 0.4 - - + -
276B TRP* 4.3 12.1 - - + -
278B PHE* 4.2 21.3 - - + -
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Residues in contact with ARG 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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211A GLU* 2.7 43.0 + - - +
215A HIS* 3.4 33.4 + - - -
216A TRP* 3.4 28.7 + - + +
217A SER 4.3 0.4 - - - -
218A THR* 3.1 31.1 + - - +
246B ALA 2.9 18.1 + - - +
247B SER* 3.5 7.8 + - - +
248B PHE 3.2 0.2 - - - -
249B VAL* 1.3 77.9 - - - +
251B GLN* 1.3 62.2 + - - +
253B ASN* 3.4 9.3 + - - +
254B MET* 3.2 47.7 + - + +
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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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218A THR* 3.2 37.8 - - - +
197B PHE* 3.3 48.3 - - + +
240B PHE* 5.0 4.2 - - - -
247B SER* 3.1 20.4 + - - +
248B PHE* 3.1 3.9 + - - +
250B ARG* 1.3 74.6 - - + +
252B LEU* 1.3 66.1 + - - +
254B MET* 3.0 43.4 + - + +
255B TYR* 3.0 25.5 + - + -
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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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197B PHE* 3.9 13.9 - - + -
201B LEU* 3.9 35.0 - - + -
223B ILE* 5.6 2.7 - - + -
248B PHE* 2.9 43.9 + - + +
249B VAL* 3.5 8.7 - - - +
251B GLN* 1.3 75.5 - - - +
253B ASN* 1.3 64.1 + - - +
255B TYR* 3.0 11.6 + - - +
256B GLY 3.4 0.2 + - - -
257B TRP* 3.0 43.9 + - + +
278B PHE* 3.8 37.9 - - + -
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Residues in contact with ASN 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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208A LYS* 5.4 12.5 - - + +
249B VAL* 2.9 37.7 + - - +
250B ARG* 3.6 9.3 - - - +
252B LEU* 1.3 76.1 - - - +
254B MET* 1.3 63.2 + - - +
255B TYR 3.2 0.7 + - - -
256B GLY* 3.2 8.8 + - - -
257B TRP 2.7 29.2 + - - -
258B HIS* 3.8 31.9 + - + +
259B LYS 5.0 1.6 - - - +
278B PHE* 5.4 1.2 - - - -
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Residues in contact with MET 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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211A GLU* 5.5 3.1 - - - +
218A THR* 4.7 1.3 - - - +
250B ARG* 3.2 55.5 + - + +
251B GLN* 3.0 44.9 + - - +
253B ASN* 1.3 76.9 - - + +
255B TYR* 1.3 76.0 + - + +
256B GLY 3.4 0.9 + - - -
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Residues in contact with TYR 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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195B PRO* 3.2 42.3 - - + +
197B PHE* 3.4 36.1 - + + +
198B VAL* 3.8 16.2 - - + -
201B LEU* 6.2 1.1 - - + -
251B GLN* 3.0 30.9 + - + +
252B LEU* 3.0 8.8 + - - +
254B MET* 1.3 92.4 - - + +
256B GLY* 1.3 58.8 + - - +
257B TRP* 3.4 15.6 + - + +
280B ASN* 3.4 10.2 - - - +
282B ARG* 5.7 1.4 + - - -
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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