Contacts of the helix formed by residues 217 - 229 (chain B) in PDB entry 5FJH
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 HIS 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B CYS* 5.7 2.1 - - - -
213B ILE* 4.0 15.8 - - + +
214B PRO* 2.8 27.2 + - + +
216B GLU* 1.3 106.2 + - + +
218B GLY* 1.3 65.7 + - - +
219B LYS 3.3 2.9 - - - -
220B ARG* 3.0 50.5 + - - +
221B LEU 3.4 7.8 + - - -
257B ILE* 5.0 0.9 - - + +
258B PRO* 3.7 31.0 - - + +
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Residues in contact with GLY 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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213B ILE* 4.4 4.0 - - - -
214B PRO 3.4 5.1 + - - -
215B PRO 3.2 9.4 + - - -
216B GLU 3.6 0.2 - - - -
217B HIS* 1.3 77.8 - - - +
219B LYS* 1.3 62.4 + - - +
221B LEU* 3.1 7.6 + - - +
222B GLU* 3.1 22.7 + - - +
275B TYR* 3.4 23.3 - - - -
277B TYR* 3.8 17.6 - - - -
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Residues in contact with LYS 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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216B GLU 5.3 1.5 + - - +
217B HIS 3.3 1.2 - - - -
218B GLY* 1.3 75.5 - - - +
220B ARG* 1.3 59.3 + - + +
222B GLU* 3.0 28.3 + - - +
223B ARG* 3.1 46.2 + - - +
275B TYR* 3.3 26.4 + - + +
306B LYS* 3.4 24.0 - - - +
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Residues in contact with ARG 220 (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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216B GLU 5.6 0.9 - - - +
217B HIS* 3.0 48.9 + - + +
219B LYS* 1.3 76.8 - - + +
221B LEU* 1.3 65.0 + - - +
223B ARG* 3.3 28.1 + - - +
224B LEU* 3.0 24.1 + - - +
255B TYR 4.4 4.0 + - - -
256B GLY* 2.3 35.8 + - - -
257B ILE* 3.9 16.0 - - + +
258B PRO* 3.8 12.2 - - - +
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Residues in contact with LEU 221 (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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189B TRP* 4.2 16.4 - - + -
213B ILE* 3.6 32.1 - - + -
217B HIS 3.4 4.8 + - - +
218B GLY* 3.1 11.4 + - - +
220B ARG* 1.3 79.6 - - - +
222B GLU* 1.3 56.9 + - - +
224B LEU* 3.3 6.4 + - + +
225B ALA* 2.8 28.1 + - + +
240B LEU* 4.5 8.3 - - + -
247B ILE* 4.4 17.3 - - + -
252B LEU* 3.8 22.2 - - + -
257B ILE* 4.4 5.9 - - + +
277B TYR* 3.4 42.6 - - + -
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Residues in contact with GLU 222 (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 GLY 3.1 9.6 + - - +
219B LYS* 3.0 25.7 + - + +
220B ARG 3.3 0.2 - - - -
221B LEU* 1.3 75.9 - - - +
223B ARG* 1.3 57.6 + - + +
225B ALA* 3.4 6.4 + - - +
226B GLN* 2.8 46.1 + - - +
239B PHE* 5.3 0.4 - - - -
240B LEU* 4.5 7.4 - - + -
275B TYR* 2.8 28.1 + - - -
277B TYR* 2.6 32.2 + - + +
306B LYS* 2.8 30.8 + - - +
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Residues in contact with ARG 223 (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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219B LYS* 3.1 36.7 + - - +
220B ARG* 3.3 33.2 - - - +
221B LEU 3.3 0.2 - - - -
222B GLU* 1.3 75.3 - - + +
224B LEU* 1.3 64.2 + - - +
226B GLN* 3.4 16.3 + - - +
227B GLY* 3.1 19.4 + - - -
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Residues in contact with LEU 224 (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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220B ARG 3.0 17.2 + - - +
221B LEU* 3.7 4.5 - - + +
223B ARG* 1.3 76.1 - - - +
225B ALA* 1.3 63.0 + - - +
227B GLY* 3.1 3.2 + - - -
228B PHE* 3.0 54.1 + - + -
247B ILE* 4.6 8.1 - - + -
251B VAL* 4.3 10.8 - - + +
252B LEU* 4.2 15.9 - - + -
255B TYR* 3.6 32.8 - - + -
257B ILE* 4.1 23.1 - - + -
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Residues in contact with ALA 225 (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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221B LEU* 2.8 21.4 + - + +
222B GLU 3.7 3.4 - - - +
224B LEU* 1.3 72.4 - - - +
226B GLN* 1.3 58.3 + - - +
228B PHE* 3.1 0.8 + - - -
229B PHE* 2.8 43.4 + - + +
239B PHE* 3.8 18.8 - - + -
240B LEU* 4.1 20.0 - - + -
247B ILE* 4.1 20.6 - - + +
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Residues in contact with GLN 226 (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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222B GLU* 2.8 46.7 + - - +
223B ARG* 3.7 15.1 - - - +
224B LEU 3.3 0.2 - - - -
225B ALA* 1.3 71.4 - - - +
227B GLY* 1.3 61.8 + - - +
230B PRO* 3.4 26.0 - - - +
233B SER* 3.4 30.3 - - - +
237B ASP 5.0 4.9 + - - -
239B PHE* 4.1 11.2 - - + -
306B LYS* 4.0 15.4 - - - +
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Residues in contact with GLY 227 (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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223B ARG 3.1 13.9 + - - -
224B LEU* 3.1 4.0 + - - -
226B GLN* 1.3 78.4 - - - +
228B PHE* 1.3 65.5 + - - +
230B PRO* 3.8 12.2 - - - +
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Residues in contact with PHE 228 (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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83B LEU* 3.6 33.7 - - + +
224B LEU* 3.0 48.6 + - + +
225B ALA* 5.1 0.9 - - - -
227B GLY* 1.3 80.8 - - - +
229B PHE* 1.3 82.8 + + + +
230B PRO* 3.3 8.7 - - - +
247B ILE* 5.3 0.7 - - + -
251B VAL* 3.7 18.8 - - + -
255B TYR* 3.5 33.9 - + - -
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Residues in contact with PHE 229 (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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83B LEU* 3.9 25.1 - - + -
84B PHE 3.9 11.9 - - - -
85B THR* 3.8 23.8 - - - -
225B ALA* 2.8 25.7 + - + +
226B GLN 3.6 3.3 - - - +
228B PHE* 1.3 90.5 - - + +
230B PRO* 1.3 66.2 - - - +
231B SER* 3.3 2.7 - - - -
232B SER* 3.5 21.2 + - - +
233B SER* 3.0 22.5 + - - -
239B PHE* 4.1 5.9 - + + -
245B THR* 3.5 33.4 - - + -
246B LEU 3.9 14.6 - - - -
247B ILE* 4.1 8.5 - - + -
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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