Contacts of the helix formed by residues 223 - 239 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D GLN* 5.6 2.1 + - - -
221D ASN 4.5 3.7 - - - +
222D ILE* 1.3 76.6 - - - +
224D LEU* 1.4 64.3 + - + +
225D GLN* 3.1 32.6 + - - +
226D HIS* 3.0 35.1 + - - +
227D THR* 3.0 29.1 + - - -
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLN* 3.9 24.2 - - + +
13D CYS* 4.5 18.8 - - - -
206D ASN* 5.1 15.3 - - - +
223D ASP* 1.4 76.9 - - + +
225D GLN* 1.4 52.7 + - - +
226D HIS 3.2 0.2 - - - -
227D THR* 3.1 11.1 + - + +
228D ASN* 2.8 50.4 + - - +
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Residues in contact with GLN 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLN* 5.6 0.6 - - - +
16D HIS* 4.5 16.5 - - + +
19D LYS* 6.2 0.2 - - - +
20D PHE* 3.5 36.1 - - + -
223D ASP* 3.1 18.9 + - - +
224D LEU* 1.4 73.2 - - - +
226D HIS* 1.3 94.4 + - - +
228D ASN* 3.6 13.8 - - - +
229D GLN* 3.5 17.0 - - - +
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Residues in contact with HIS 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D PHE* 3.2 18.9 - - + -
221D ASN* 4.1 7.0 + - - +
222D ILE* 3.8 17.0 - - + -
223D ASP* 3.0 38.7 + - - +
224D LEU 3.2 0.2 - - - -
225D GLN* 1.3 109.5 + - - +
227D THR* 1.3 56.5 + - - +
229D GLN* 3.2 25.9 + - - +
279D TYR* 3.5 56.0 + + + -
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Residues in contact with THR 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ASN* 5.9 1.3 - - - +
209D LEU* 3.6 38.8 - - + -
210D LEU* 5.3 5.9 - - - +
213D SER* 3.3 27.7 + - - +
217D PHE* 4.9 0.7 - - - -
222D ILE* 4.4 2.3 - - - +
223D ASP 3.0 15.2 + - - -
224D LEU* 3.1 18.0 + - + +
226D HIS* 1.3 74.6 - - - +
228D ASN* 1.4 58.6 + - - +
229D GLN 3.2 0.2 - - - -
230D LEU* 3.0 23.8 + - - +
231D ILE* 3.3 10.4 + - + +
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Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLN* 3.8 9.5 + - - -
13D CYS* 4.5 9.5 + - - +
16D HIS* 3.2 27.9 - - - +
17D VAL* 3.5 28.1 - - + +
20D PHE* 4.0 14.1 - - + -
224D LEU* 2.8 37.1 + - - +
225D GLN* 3.6 12.9 - - - +
226D HIS 3.4 0.2 - - - -
227D THR* 1.4 74.1 - - - +
229D GLN* 1.3 50.5 + - - +
231D ILE* 3.2 15.7 + - - +
232D SER* 2.9 34.7 + - - -
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Residues in contact with GLN 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 4.1 16.9 - - + -
24D GLN* 4.3 0.9 + - - +
217D PHE* 3.5 3.0 - - + -
225D GLN* 3.5 30.5 - - - +
226D HIS* 3.2 29.6 + - - +
228D ASN* 1.3 74.9 - - - +
230D LEU* 1.4 59.4 + - - +
232D SER* 3.0 21.1 + - - -
233D THR* 3.2 18.8 + - - -
278D ASP* 3.4 43.1 + - + +
279D TYR* 3.4 17.7 - - - +
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LEU* 4.4 13.7 - - + +
212D ILE* 4.1 15.7 - - + +
213D SER* 3.5 42.6 - - - +
216D VAL* 5.7 2.7 - - + -
217D PHE* 3.6 33.4 - - + -
227D THR* 3.0 10.7 + - - +
229D GLN* 1.4 74.7 - - - +
231D ILE* 1.4 63.8 + - - +
233D THR* 3.5 7.1 + - - +
234D ILE* 3.2 31.5 + - + +
275D PHE* 4.2 27.1 - - + -
276D THR 5.6 2.0 - - - +
278D ASP* 5.2 3.1 - - - +
303D ASN* 5.7 2.0 - - - +
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Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D CYS* 6.2 1.6 - - + -
17D VAL* 4.1 14.8 - - + -
172D VAL* 4.1 20.9 - - + -
204D PHE* 4.4 21.3 - - + -
209D LEU* 3.6 38.8 - - + -
227D THR* 3.3 8.2 + - + +
228D ASN* 3.2 24.2 + - - +
230D LEU* 1.4 74.6 - - - +
232D SER* 1.4 55.7 + - - +
234D ILE* 3.1 9.0 + - - +
235D ILE* 2.9 51.1 + - + +
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Residues in contact with SER 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.0 6.7 - - - +
20D PHE* 3.5 28.3 - - - +
21D LEU* 3.5 21.1 - - - +
24D GLN* 2.9 28.4 + - - +
228D ASN 2.9 14.6 + - - -
229D GLN* 3.0 21.7 + - - -
231D ILE* 1.4 67.6 - - - +
233D THR* 1.4 62.9 + - - +
235D ILE* 4.5 1.3 - - - -
236D SER* 3.0 17.8 + - - -
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Residues in contact with THR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 3.3 17.7 + - - +
229D GLN 3.2 17.5 + - - -
230D LEU* 3.9 7.4 - - - -
231D ILE 3.5 0.2 - - - -
232D SER* 1.4 72.5 - - - +
234D ILE* 1.3 64.7 + - + +
236D SER* 2.9 18.2 + - - +
237D SER* 3.0 17.2 + - - +
272D PHE* 4.6 23.1 - - + -
276D THR* 3.8 20.5 + - + +
278D ASP* 3.3 16.6 + - - -
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Residues in contact with ILE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D PHE* 3.8 31.2 - - + -
209D LEU* 5.6 3.4 - - + -
230D LEU* 3.2 17.6 + - + +
231D ILE* 3.1 8.7 + - - +
233D THR* 1.3 80.9 - - + +
235D ILE* 1.4 58.5 + - - +
237D SER* 3.2 10.1 + - - -
238D VAL* 3.0 21.2 - - + +
270D PRO* 4.2 8.1 - - + -
271D SER 6.0 0.2 - - - -
272D PHE* 4.8 23.1 - - + -
275D PHE* 5.9 1.3 - - + -
303D ASN* 3.6 36.6 - - + +
375D MET* 3.4 30.0 - - + +
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.0 11.4 - - + -
21D LEU* 3.7 26.7 - - + -
137D GLN* 4.4 20.0 - - - +
139D LEU* 3.6 27.4 - - + -
170D TYR* 3.8 25.7 - - + -
204D PHE* 4.3 5.2 - - + -
231D ILE* 2.9 43.6 + - + +
232D SER 3.5 0.2 + - - -
234D ILE* 1.4 71.5 - - - +
236D SER* 1.4 60.6 + - - +
238D VAL* 3.5 19.1 + - - +
239D THR* 3.6 15.7 - - + +
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Residues in contact with SER 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.8 10.9 - - - +
24D GLN* 3.3 20.9 + - - -
25D LEU* 5.5 1.8 - - - -
232D SER 3.0 14.7 + - - -
233D THR* 2.9 21.8 + - - +
235D ILE* 1.4 73.9 - - - +
237D SER* 1.4 61.5 + - - +
239D THR* 2.7 23.4 + - - -
243D ARG* 3.1 29.5 + - - -
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Residues in contact with SER 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D THR* 3.0 17.0 + - - +
234D ILE* 3.2 8.1 + - - -
236D SER* 1.4 80.1 + - - +
238D VAL* 1.3 60.1 + - - +
240D ASN* 3.1 21.3 + - - +
243D ARG* 4.8 2.7 - - - +
272D PHE* 3.9 18.9 - - - -
322D ILE* 4.3 9.3 - - - +
358D ARG* 3.5 5.9 + - - -
375D MET* 4.0 20.9 - - - -
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D TYR* 3.8 27.6 - - + +
234D ILE* 3.0 22.9 - - + +
235D ILE* 3.5 13.7 - - - +
237D SER* 1.3 72.4 - - - +
239D THR* 1.4 61.7 + - + +
240D ASN 3.2 1.0 + - - -
241D SER* 4.0 6.1 + - - -
252D MET* 4.2 17.7 - - + +
322D ILE* 3.9 14.5 - - + +
358D ARG* 3.6 10.7 + - - -
375D MET* 3.4 22.7 - - + -
377D LEU* 4.4 21.1 - - + -
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Residues in contact with THR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 6.1 0.2 - - + -
21D LEU* 6.4 0.2 - - + -
25D LEU* 5.0 1.0 - - - +
53D PHE* 3.7 33.9 - - + -
137D GLN* 4.1 14.6 - - - +
170D TYR* 5.8 1.8 - - + +
235D ILE* 3.6 15.9 - - + +
236D SER* 2.7 21.7 + - - -
238D VAL* 1.4 78.6 - - + +
240D ASN* 1.4 66.3 + - - +
241D SER 3.1 3.1 + - - -
242D ILE* 3.2 23.2 + - + +
243D ARG* 3.3 21.3 + - - -
252D MET* 5.4 5.4 - - + -
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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