Contacts of the helix formed by residues 212 - 219 (chain B) in PDB entry 1FRP
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 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLY* 4.5 6.1 - - - -
242A ALA* 3.0 33.3 + - - +
243A ARG* 3.5 11.3 - - - +
211B ILE* 1.3 75.3 - - - +
213B GLU* 1.3 59.5 + - - +
214B GLY* 3.2 9.8 + - - -
215B TYR* 3.4 36.1 + - + -
219B PHE* 3.5 15.8 - - - -
244B TYR* 3.6 25.8 + - + +
263B MET 4.7 0.6 + - - -
264B TYR* 5.3 1.8 - - + -
336B FDP 2.9 25.0 + - - +
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Residues in contact with GLU 213 (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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209A TYR* 3.8 15.3 - - - +
213A GLU* 3.8 16.0 - - - +
231A LYS* 3.4 16.9 + - - +
242A ALA* 4.0 5.7 - - + +
209B TYR* 2.8 31.3 + - - -
211B ILE* 3.3 22.3 + - + +
212B ASN* 1.3 66.8 + - - +
214B GLY* 1.3 59.7 + - - +
215B TYR 3.0 5.2 - - - -
216B ALA* 3.1 23.0 + - + +
219B PHE* 4.2 12.5 - - + -
227B ILE* 3.8 14.1 - - + +
231B LYS* 3.0 24.6 + - - -
242B ALA* 5.2 1.6 - - - +
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Residues in contact with GLY 214 (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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209A TYR* 3.9 13.4 + - - -
231A LYS* 4.5 7.7 - - - +
239A PRO* 3.3 28.8 - - - +
240A TYR 3.3 22.6 - - - +
241A GLY* 4.8 0.9 - - - -
242A ALA* 3.9 1.8 - - - +
212B ASN* 3.2 12.1 + - - -
213B GLU* 1.3 75.5 - - - +
215B TYR* 1.3 64.3 + - - +
216B ALA 3.4 1.2 + - - -
217B LYS 5.2 0.2 + - - -
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Residues in contact with TYR 215 (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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239A PRO* 5.9 1.6 - - + -
212B ASN* 3.4 41.9 + - + -
213B GLU 3.0 1.2 - - - -
214B GLY* 1.3 81.2 - - - +
216B ALA* 1.3 53.1 + - - +
217B LYS* 3.1 4.5 - - - -
218B GLU* 2.8 42.0 + - + -
219B PHE* 3.4 26.8 + + + -
264B TYR* 3.5 22.9 + + - -
267B ASN* 3.9 26.2 - - + -
269B LYS* 5.0 17.9 - - + +
336B FDP 2.8 19.4 + - - -
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Residues in contact with ALA 216 (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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231A LYS* 3.8 26.7 - - + +
232A PHE* 4.4 11.5 - - + -
213B GLU* 3.1 19.3 + - + +
214B GLY 3.4 1.8 - - - -
215B TYR* 1.3 75.4 - - - +
217B LYS* 1.3 60.2 + - - +
218B GLU 3.3 0.9 + - - -
219B PHE* 3.4 34.5 + - + +
224B THR* 4.8 2.9 + - - +
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Residues in contact with LYS 217 (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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231A LYS 4.0 11.4 + - - +
232A PHE* 3.7 42.2 - - + -
233A PRO* 4.4 9.1 - - - +
236A ASN* 6.1 3.4 - - - +
237A SER 4.7 4.6 + - - -
239A PRO* 4.0 29.4 - - + +
215B TYR* 2.9 1.5 + - - -
216B ALA* 1.3 79.8 - - - +
218B GLU* 1.3 74.7 + - + +
219B PHE 3.7 2.3 + - - +
268B LYS* 4.8 4.9 + - - -
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Residues in contact with GLU 218 (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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239A PRO* 6.1 2.2 - - + +
215B TYR* 2.8 28.7 + - + +
217B LYS* 1.3 91.8 - - + +
219B PHE* 1.3 65.9 + - - +
220B ASP* 3.6 1.4 + - - -
266B ALA 4.4 0.7 - - - +
267B ASN* 3.7 25.6 - - + +
268B LYS* 3.6 56.4 + - + +
269B LYS* 4.4 11.3 + - - +
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Residues in contact with PHE 219 (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 ILE* 3.7 20.6 - - + -
212B ASN 3.5 22.9 - - - -
213B GLU* 4.2 7.0 - - + -
215B TYR* 3.4 28.5 - + + -
216B ALA* 3.4 31.2 + - + +
217B LYS 3.4 2.1 - - - +
218B GLU* 1.3 81.9 - - - +
220B ASP* 1.3 66.0 + - - +
221B PRO* 4.5 0.3 - - - +
223B ILE* 3.9 18.4 - - + -
224B THR* 3.4 22.6 + - - +
227B ILE* 3.7 24.5 - - + -
265B PRO* 4.5 14.1 - - + -
266B ALA 5.1 1.8 - - - -
267B ASN* 5.0 6.3 - - + -
268B LYS* 5.8 0.2 + - - -
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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