Contacts of the helix formed by residues 223 - 239 (chain C) in PDB entry 5FLZ
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 ASP 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C LEU* 5.2 1.6 - - - -
222C ILE* 1.4 78.6 - - - +
224C LEU* 1.4 78.1 + - - +
225C GLN* 3.3 28.0 + - - +
226C HIS* 3.3 23.3 + - + +
227C THR* 3.2 28.4 + - - +
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C CYS* 3.7 25.8 - - - -
16C HIS* 5.9 1.1 - - + -
143C ALA* 5.5 9.2 - - + -
175C ALA* 4.4 19.7 - - + +
206C ASN* 4.0 22.9 - - + +
210C LEU* 5.3 2.9 - - + -
223C ASP* 1.4 80.8 - - - +
225C GLN* 1.3 63.1 - - + +
227C THR* 2.9 25.9 + - + +
228C ASN* 3.0 29.7 + - - +
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Residues in contact with GLN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C HIS* 3.4 46.1 + - + +
20C PHE* 3.5 24.1 - - + -
223C ASP* 3.3 17.9 + - - +
224C LEU* 1.3 78.1 - - + +
226C HIS* 1.4 67.7 + - + +
228C ASN* 3.3 21.3 + - - +
229C GLN* 3.6 5.0 + - - +
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Residues in contact with HIS 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C SER* 4.6 4.3 + - - -
219C ASN* 3.7 31.3 + - - +
221C ASN 3.4 22.9 + - - -
222C ILE* 3.9 5.4 - - + -
223C ASP* 3.3 32.5 + - + +
224C LEU 3.3 0.2 - - - -
225C GLN* 1.4 79.1 - - + +
227C THR* 1.4 63.1 + - + +
229C GLN* 3.3 25.2 + - - +
230C LEU* 4.1 1.9 + - - +
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Residues in contact with THR 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ASN* 4.6 11.8 + - + +
209C LEU* 4.7 15.5 - - - +
210C LEU* 3.4 35.0 - - + +
213C SER* 3.4 27.6 - - - +
222C ILE* 4.0 1.6 - - + -
223C ASP 3.2 14.2 + - - +
224C LEU* 2.9 27.9 + - + +
226C HIS* 1.4 75.3 - - - +
228C ASN* 1.3 58.0 + - - +
230C LEU* 2.9 23.9 + - - +
231C ILE* 3.2 9.2 + - - +
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Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C CYS* 3.8 39.4 + - - +
16C HIS* 3.9 12.3 - - - +
17C VAL* 3.5 11.9 - - + +
20C PHE* 3.8 14.8 - - + -
172C VAL* 5.0 6.1 - - - +
206C ASN* 5.6 0.9 - - - +
224C LEU* 3.0 26.6 + - - +
225C GLN* 3.5 9.3 - - - +
226C HIS 3.2 0.4 - - - -
227C THR* 1.3 78.7 + - - +
229C GLN* 1.4 56.2 + - - +
230C LEU 3.2 0.2 - - - -
231C ILE* 3.2 23.4 + - - +
232C SER* 2.9 31.1 + - - -
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Residues in contact with GLN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.2 43.1 - - - +
24C GLN* 3.5 14.4 + - - +
217C PHE* 6.2 4.5 - - + -
225C GLN 3.6 6.9 + - - +
226C HIS* 3.3 18.6 - - - +
228C ASN* 1.4 78.5 - - - +
230C LEU* 1.4 59.3 + - - +
232C SER* 2.9 15.7 + - - -
233C THR* 3.0 18.0 + - - -
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C LEU* 4.0 15.3 - - + +
212C ILE* 3.8 42.8 - - + -
213C SER* 4.4 8.3 - - - +
217C PHE* 3.6 35.6 - - + -
226C HIS 4.1 1.0 + - - +
227C THR* 2.9 12.9 + - - +
229C GLN* 1.4 79.5 - - - +
231C ILE* 1.3 61.8 + - - +
233C THR* 3.2 13.1 + - + +
234C ILE* 3.0 26.7 + - + +
272C PHE* 6.2 1.8 - - + -
275C PHE* 4.0 17.3 - - + -
303C ASN* 4.2 11.2 - - - +
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Residues in contact with ILE 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 3.3 26.5 - - + -
172C VAL* 3.6 18.2 - - + -
204C PHE* 2.8 60.8 - - + -
206C ASN* 6.0 0.2 - - - +
209C LEU* 3.6 17.2 - - + +
227C THR 3.2 4.8 + - - +
228C ASN* 3.2 25.7 + - - +
230C LEU* 1.3 81.4 - - - +
232C SER* 1.4 52.3 + - - +
234C ILE* 3.1 20.5 + - + +
235C ILE* 3.0 30.1 + - - +
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Residues in contact with SER 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 3.5 30.7 - - - +
20C PHE* 3.4 12.8 - - - +
21C LEU* 3.8 6.6 - - - +
24C GLN* 3.0 22.1 + - - +
228C ASN 2.9 21.7 + - - -
229C GLN* 2.9 17.5 + - - -
231C ILE* 1.4 72.2 - - - +
233C THR* 1.4 53.3 + - - +
235C ILE* 3.1 8.1 - - - +
236C SER* 2.9 31.2 + - - -
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Residues in contact with THR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 3.1 14.3 + - - +
229C GLN 3.0 16.2 + - - -
230C LEU* 3.5 17.0 - - + +
232C SER* 1.4 57.4 - - - +
234C ILE* 1.3 63.2 + - - +
236C SER* 3.1 13.5 + - - +
237C SER* 2.9 32.8 + - - +
272C PHE* 5.1 11.4 - - + -
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Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C PHE* 4.2 18.8 - - + -
209C LEU* 3.8 13.5 - - + -
230C LEU* 3.0 24.1 + - + +
231C ILE* 3.1 17.2 + - + +
233C THR* 1.3 78.0 - - - +
235C ILE* 1.3 63.1 + - - +
237C SER* 3.5 2.6 + - - -
238C VAL* 3.1 36.2 + - + +
270C PRO* 4.8 7.4 - - + -
272C PHE* 4.5 26.6 - - + -
275C PHE* 5.8 0.2 - - + -
303C ASN* 2.7 56.1 - - + +
375C MET* 5.9 0.4 - - + -
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.8 6.3 - - + -
21C LEU* 4.2 23.6 - - + -
137C GLN* 4.3 6.5 - - - +
139C LEU* 4.2 17.7 - - + -
170C TYR* 4.0 44.2 - - + +
204C PHE* 4.7 13.9 - - + -
231C ILE 3.0 11.2 + - - +
232C SER* 3.1 23.8 - - - +
234C ILE* 1.3 79.2 - - - +
236C SER* 1.4 62.1 + - - +
238C VAL* 3.5 9.6 - - + +
239C THR* 3.4 26.0 + - + +
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Residues in contact with SER 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 3.5 21.1 - - - -
24C GLN* 3.1 13.6 + - - +
25C LEU* 4.5 5.4 - - - -
28C GLU* 4.5 15.3 + - - -
232C SER 2.9 20.7 + - - -
233C THR* 3.1 12.3 + - - +
235C ILE* 1.4 76.0 - - - +
237C SER* 1.3 60.4 + - - +
239C THR* 2.8 22.0 + - - -
240C ASN 3.3 0.9 + - - -
243C ARG* 3.0 15.8 + - - -
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C THR* 2.9 25.4 + - - +
234C ILE 3.8 3.1 - - - -
236C SER* 1.3 77.2 + - - +
238C VAL* 1.4 55.2 + - - +
240C ASN* 2.8 33.9 + - - +
241C SER 4.5 0.2 + - - -
243C ARG* 4.9 0.7 - - - +
272C PHE* 4.0 24.2 - - - -
375C MET* 3.6 18.4 - - - +
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C TYR* 5.5 9.4 - - + +
234C ILE* 3.1 28.0 - - + +
235C ILE* 3.5 11.4 - - + +
237C SER* 1.4 73.1 - - - +
239C THR* 1.4 62.8 + - + +
240C ASN 3.7 0.3 + - - -
241C SER* 3.8 5.9 + - - -
242C ILE* 4.5 7.2 - - + +
272C PHE* 5.5 0.2 - - + -
322C ILE* 6.0 0.2 - - + -
358C ARG* 3.6 22.0 + - - +
375C MET* 4.0 31.1 - - + +
377C LEU* 4.9 27.1 - - + -
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 5.7 0.7 - - - +
25C LEU* 5.0 1.9 - - - +
53C PHE* 4.0 28.4 - - + -
137C GLN* 4.3 15.0 - - - +
170C TYR* 5.6 2.2 - - - +
235C ILE* 3.4 14.2 + - + +
236C SER* 2.8 23.4 + - - -
238C VAL* 1.4 78.5 - - + +
240C ASN* 1.4 60.6 + - - +
241C SER 3.3 2.9 - - - -
242C ILE* 3.1 28.9 + - + +
243C ARG* 3.1 27.8 + - - +
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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
------------------------------------------------------------
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