Contacts of the helix formed by residues 219 - 232 (chain B) in PDB entry 5FQD
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 CYS 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B SER* 1.3 64.1 + - - +
221B TYR* 4.6 11.7 - - - -
222B LYS* 3.5 34.3 - - + +
223B TRP* 3.5 16.6 + - - +
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Residues in contact with SER 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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219B CYS* 1.3 71.3 + - - +
221B TYR* 1.4 60.1 + - - +
223B TRP* 3.2 8.0 + - - +
224B TRP* 2.9 48.9 + - - -
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Residues in contact with TYR 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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838A PRO* 3.3 46.2 - - + +
839A GLU* 4.1 15.6 + - + -
219B CYS* 3.4 10.2 - - - -
220B SER* 1.4 73.6 - - - +
222B LYS* 1.4 66.9 + - + +
224B TRP* 3.5 6.7 + - + +
225B GLN* 3.1 54.7 + - + +
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Residues in contact with LYS 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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782A PHE* 6.5 0.7 - - - -
784A GLU* 5.3 8.3 - - - +
219B CYS* 3.5 28.0 + - + +
220B SER 3.4 0.4 - - - -
221B TYR* 1.4 87.0 - - + +
223B TRP* 1.4 61.7 + - - +
225B GLN* 3.5 11.5 - - + +
226B LYS* 3.3 60.8 + - - +
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Residues in contact with TRP 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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208B PHE* 5.0 14.9 - + + +
209B PRO 3.9 27.2 + - - -
219B CYS 3.5 9.7 + - - +
220B SER* 3.2 12.9 + - - +
222B LYS* 1.4 77.8 - - - +
224B TRP* 1.3 105.5 + + - +
226B LYS* 3.3 11.5 + - + +
227B TYR* 2.9 54.1 + + + +
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Residues in contact with TRP 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 SER* 2.9 40.8 + - - +
221B TYR* 4.0 7.2 - - - +
222B LYS 3.4 0.2 - - - -
223B TRP* 1.3 98.6 - + - +
225B GLN* 1.3 59.4 + - - +
227B TYR* 3.4 34.1 - + - +
228B GLN* 3.0 30.3 + - - +
251B GLU* 3.7 27.8 - - + -
252B THR* 3.4 34.5 - - + -
255B ASP* 3.5 38.2 + - + -
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Residues in contact with GLN 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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784A GLU* 5.6 7.6 + - - +
838A PRO* 3.8 24.8 - - + +
221B TYR* 3.1 56.8 + - + +
222B LYS* 3.5 13.6 - - + +
224B TRP* 1.3 76.9 - - - +
226B LYS* 1.3 57.6 + - + +
228B GLN* 3.7 10.2 + - - +
229B LYS* 3.1 36.3 + - - +
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Residues in contact with LYS 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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784A GLU* 5.6 4.5 - - - -
208B PHE* 5.5 0.6 - - - -
222B LYS* 3.3 57.4 + - - +
223B TRP* 3.3 12.5 + - + +
225B GLN* 1.3 74.6 - - + +
227B TYR* 1.3 64.5 + - - +
229B LYS* 4.4 5.8 - - - -
230B ARG* 3.1 38.2 + - - +
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Residues in contact with TYR 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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208B PHE* 3.6 34.9 - + - -
223B TRP* 2.9 44.4 + + + +
224B TRP* 3.4 32.5 - + - +
226B LYS* 1.3 76.3 - - - +
228B GLN* 1.3 59.9 + - + +
230B ARG* 3.9 0.7 - - - +
231B LYS* 2.8 68.7 + - + +
232B PHE* 4.4 4.9 - + - -
246B SER* 5.9 0.2 - - - -
249B ASP* 2.7 28.7 + - - -
251B GLU* 3.4 16.5 - - + +
252B THR* 3.4 11.4 - - + -
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Residues in contact with GLN 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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224B TRP 3.0 16.6 + - - +
225B GLN* 3.8 9.6 + - - +
227B TYR* 1.3 80.8 - - + +
229B LYS* 1.3 61.1 + - - +
232B PHE* 3.2 36.2 + - + +
242B ARG* 3.4 39.9 - - + +
243B TRP* 3.7 20.0 - - - +
246B SER* 3.2 28.7 + - - +
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Residues in contact with LYS 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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740A ILE* 5.5 2.0 - - - +
784A GLU* 5.5 6.9 + - - +
785A GLU* 2.9 45.4 + - - +
225B GLN* 3.1 27.7 + - - +
226B LYS* 4.0 7.4 - - - +
227B TYR 3.4 0.2 - - - -
228B GLN* 1.3 75.9 - - - +
230B ARG* 1.3 60.6 + - + +
233B HIS* 3.4 34.2 + - - +
242B ARG* 3.5 46.2 + - - +
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A ARG* 4.6 3.6 - - - +
215A GLU* 3.2 34.2 + - - -
234A GLN* 5.5 8.5 - - - +
198B GLN* 5.2 0.3 + - - -
205B CYS* 3.0 40.1 + - + +
206B GLN* 3.6 17.7 + - - +
207B ILE 3.6 8.9 + - - -
208B PHE* 3.6 27.5 - - + +
209B PRO* 3.6 18.4 - - - +
226B LYS* 3.1 25.4 + - - +
229B LYS* 1.3 78.9 - - + +
231B LYS* 1.3 64.8 + - - +
232B PHE 3.3 0.6 + - - -
233B HIS* 3.6 12.9 + - - +
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Residues in contact with LYS 231 (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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192B SER* 3.9 26.0 - - - +
194B MET* 3.4 18.1 - - + +
198B GLN* 4.1 3.6 + - - -
206B GLN* 3.8 14.3 - - - +
208B PHE* 3.7 18.7 - - + -
227B TYR* 2.8 59.8 + - + +
230B ARG* 1.3 74.1 - - - +
232B PHE* 1.3 73.7 + - + +
233B HIS 3.5 0.9 + - - -
249B ASP* 3.3 19.6 + - - +
251B GLU* 3.2 20.0 + - - -
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Residues in contact with PHE 232 (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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192B SER* 5.0 0.2 - - - -
193B THR* 3.8 15.3 - - + -
194B MET* 3.5 18.6 - - + -
227B TYR* 4.4 9.4 - + - -
228B GLN* 3.2 28.9 + - + +
231B LYS* 1.3 96.1 - - + +
233B HIS* 1.4 62.6 + - - +
234B CYS 3.3 2.7 - - - -
235B ALA* 3.1 14.4 - - + +
242B ARG* 3.1 35.6 - - + +
245B TYR* 3.5 27.4 - - + -
246B SER* 3.6 26.9 - - - -
249B ASP* 3.5 37.7 - - + -
252B THR* 5.0 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