Contacts of the helix formed by residues 234 - 245 (chain B) in PDB entry 5FHH
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 LYS 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B GLN* 5.1 3.6 + - - -
226B PHE* 3.4 28.0 - - + -
228B GLY 5.0 9.6 - - - +
229B SER 5.4 0.9 - - - +
232B THR* 2.9 17.5 + - - +
233B GLY* 1.3 67.2 - - - +
235B SER* 1.3 63.2 + - - +
236B TYR 3.1 1.9 - - - +
237B LEU* 3.3 17.7 + - - +
238B LEU* 3.8 3.6 + - - +
341B CYS* 3.5 20.5 - - - -
342B GLY 6.0 0.4 - - - +
376B LEU* 3.9 18.3 - - + +
702B ALF 3.2 8.3 - - - -
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Residues in contact with SER 235 (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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233B GLY 2.1 19.2 + - - -
234B LYS 1.3 67.4 - - - -
236B TYR* 1.3 57.8 + - - -
237B LEU 3.2 0.7 + - - -
238B LEU* 4.5 4.1 + - - +
239B LYS* 4.2 13.3 + - - +
262B HIS* 4.3 19.0 + - - -
263B ILE* 5.2 5.3 - - - +
306B ASP* 4.5 16.4 - - - -
341B CYS* 4.9 0.2 - - - -
701B ADP 2.5 25.8 + - - -
702B ALF 1.3 72.1 - - - -
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Residues in contact with TYR 236 (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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205B PRO* 3.5 32.4 - - + +
207B LEU* 5.3 9.4 - - + -
211B GLN* 4.8 12.8 - - - +
233B GLY* 3.1 10.9 + - - -
234B LYS 3.1 0.2 - - - -
235B SER* 1.3 78.9 - - - +
237B LEU* 1.3 62.1 + - - +
239B LYS* 3.7 17.2 - - + +
240B ARG* 3.7 11.9 + - + +
262B HIS* 5.6 2.9 - + - -
701B ADP 3.0 59.9 - + + +
702B ALF 3.1 1.0 - - - -
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Residues in contact with LEU 237 (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 LEU* 5.5 4.0 - - + -
211B GLN* 3.8 36.5 + - + +
214B VAL* 3.6 28.3 - - + -
215B LEU* 4.4 16.8 - - + -
226B PHE* 3.4 26.0 - - + -
234B LYS* 3.5 16.9 - - - +
235B SER 3.2 0.6 - - - -
236B TYR* 1.3 77.3 - - - +
238B LEU* 1.3 56.3 + - - +
239B LYS 3.2 1.1 - - - -
240B ARG* 2.5 34.4 + - + +
241B ILE* 2.6 35.2 + - + +
376B LEU* 5.5 1.8 - - + -
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Residues in contact with LEU 238 (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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226B PHE* 3.3 34.3 - - + -
234B LYS 3.9 5.6 - - - +
235B SER* 4.8 2.5 - - - +
237B LEU* 1.3 72.9 - - - +
239B LYS* 1.3 53.7 + - - +
241B ILE* 2.6 19.3 + - + +
242B LEU* 2.2 45.0 + - + +
263B ILE* 3.9 14.1 - - + -
304B VAL* 3.3 35.2 - - + -
305B ILE 4.3 2.0 - - - +
306B ASP* 2.5 32.5 - - - +
339B ILE* 5.2 2.7 - - + -
340B ILE 5.0 2.0 - - - +
341B CYS* 4.1 8.5 - - - +
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Residues in contact with LYS 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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235B SER 4.2 7.9 + - - +
236B TYR* 3.7 23.1 - - + +
238B LEU* 1.3 75.0 - - - +
240B ARG* 1.3 59.9 + - - +
242B LEU* 3.8 12.9 - - - +
243B GLY* 3.5 13.5 + - - -
262B HIS* 5.7 6.5 - - + +
263B ILE* 5.2 9.2 - - + +
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Residues in contact with ARG 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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207B LEU* 5.5 8.7 - - + -
215B LEU* 4.8 9.6 - - + -
236B TYR* 3.7 12.7 + - + +
237B LEU* 2.5 25.2 + - + +
239B LYS* 1.3 73.1 - - - +
241B ILE* 1.3 57.1 + - - +
242B LEU 3.2 0.2 - - - -
243B GLY* 3.0 4.0 + - - +
244B SER* 2.7 32.6 + - - +
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Residues in contact with ILE 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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214B VAL* 4.2 12.3 - - + -
215B LEU* 3.8 11.2 - - + -
218B VAL* 3.8 29.4 - - + -
226B PHE* 4.9 0.7 - - + -
237B LEU* 2.6 44.2 + - + +
238B LEU* 2.6 34.2 + - + +
240B ARG* 1.3 71.3 - - - +
242B LEU* 1.3 60.4 + - + +
244B SER* 4.0 5.6 - - - -
245B LEU* 3.0 50.5 + - + +
304B VAL* 6.2 3.4 - - + -
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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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238B LEU* 2.2 42.1 + - + +
239B LYS* 3.8 11.4 - - - +
241B ILE* 1.3 69.6 - - + +
243B GLY* 1.3 60.9 + - - +
245B LEU* 3.5 13.0 - - - +
247B PRO* 5.7 1.7 - - - +
250B THR* 5.1 14.0 + - + -
252B ALA* 3.6 13.2 - - + -
263B ILE* 3.3 41.7 - - + +
264B GLY 5.8 0.2 - - - -
304B VAL* 3.4 33.9 - - + -
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Residues in contact with GLY 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 LYS 3.5 7.0 + - - -
240B ARG* 3.0 7.8 + - - -
242B LEU* 1.3 79.5 - - - +
244B SER* 1.3 65.2 + - - +
245B LEU 3.8 3.3 - - - +
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Residues in contact with SER 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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215B LEU* 3.8 19.2 - - - +
219B LEU* 3.6 28.3 - - - +
240B ARG* 2.7 19.6 + - - +
241B ILE 3.2 3.5 + - - -
243B GLY* 1.3 79.2 - - - +
245B LEU* 1.3 63.0 + - - +
246B PRO* 3.7 2.3 - - - +
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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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218B VAL* 4.4 20.0 - - + +
219B LEU* 4.4 31.6 - - + +
221B GLY* 5.9 2.0 - - - +
241B ILE* 3.0 39.3 + - + +
242B LEU 3.5 13.5 - - - +
243B GLY 3.8 3.6 - - - +
244B SER* 1.3 81.0 - - - +
246B PRO* 1.3 82.8 - - + +
247B PRO* 3.5 2.3 - - - +
250B THR* 3.9 22.6 + - + -
302B ARG* 5.4 6.5 - - + -
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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