Contacts of the helix formed by residues 225 - 243 (chain D) in PDB entry 1F5Q
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 THR 225 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D CYS* 5.2 2.0 - - - -
223D TYR 5.3 0.9 - - - +
224D ILE* 1.3 82.4 - - - +
226D LYS* 1.3 63.4 + - - +
227D GLU* 3.1 14.1 + - - +
228D GLU* 2.7 51.1 + - + +
229D LEU* 3.2 18.9 + - - +
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Residues in contact with LYS 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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216D ASP* 4.6 14.8 - - - +
219D CYS* 6.0 2.0 - - - -
225D THR* 1.3 72.9 - - - +
227D GLU* 1.3 63.5 + - - +
229D LEU* 3.6 10.0 + - + +
230D HIS* 3.1 57.6 + - + +
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D THR* 3.2 11.9 + - - +
226D LYS* 1.3 78.3 - - - +
228D GLU* 1.3 65.1 + - - +
230D HIS* 2.9 18.8 + - - +
231D GLN* 3.0 39.0 + - + +
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Residues in contact with GLU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 4.3 17.6 - - + +
223D TYR 3.5 15.3 - - - +
224D ILE* 4.0 13.3 - - + +
225D THR* 2.7 52.5 + - + +
227D GLU* 1.3 72.7 - - + +
229D LEU* 1.3 62.6 + - - +
231D GLN* 3.3 17.2 + - - +
232D CYS* 3.1 24.8 + - - +
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 4.1 11.2 - - + +
197D LEU* 3.7 13.2 - - + +
198D ALA* 3.5 33.7 - - + +
201D HIS* 4.2 27.1 - - + +
211D TYR* 4.4 0.9 - - - +
215D ILE* 4.2 12.1 - - + -
219D CYS* 3.9 24.2 - - - -
224D ILE* 4.4 6.7 - - + -
225D THR 3.2 14.5 + - - +
226D LYS* 3.8 9.0 - - + +
228D GLU* 1.3 79.0 - - - +
230D HIS* 1.3 67.3 + - + +
232D CYS* 3.5 1.4 + - - +
233D CYS* 3.1 28.1 + - - -
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Residues in contact with HIS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D HIS* 4.2 30.1 + + - -
226D LYS* 3.1 49.2 + - + +
227D GLU* 2.9 12.9 + - - +
229D LEU* 1.3 82.1 - - + +
231D GLN* 1.3 65.4 + - + +
233D CYS* 3.3 15.6 + - + +
234D ASP* 3.3 19.4 + - - +
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Residues in contact with GLN 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D LYS* 6.2 2.0 - - - +
227D GLU* 3.0 37.4 + - + +
228D GLU* 3.6 27.8 - - - +
230D HIS* 1.3 76.8 - - + +
232D CYS* 1.3 58.6 + - - +
234D ASP* 3.1 13.2 + - - +
235D LEU* 2.9 33.8 + - + +
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Residues in contact with CYS 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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187D SER* 5.6 1.3 - - - -
190D LYS* 4.5 10.3 - - + -
194D LEU* 3.7 33.9 - - + -
195D ILE* 4.0 18.4 - - - -
198D ALA* 3.6 20.0 - - + -
228D GLU 3.1 16.4 + - - +
229D LEU 3.8 4.7 - - - +
231D GLN* 1.3 74.3 - - - +
233D CYS* 1.3 62.1 + - - +
235D LEU* 3.5 13.6 - - + +
236D VAL* 2.9 37.0 + - - +
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Residues in contact with CYS 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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198D ALA* 3.6 26.5 - - - -
201D HIS* 3.5 34.8 - - - -
202D LEU* 4.0 17.7 - - + +
229D LEU* 3.1 25.4 + - - -
230D HIS* 3.5 12.1 - - + +
231D GLN 3.2 0.6 - - - -
232D CYS* 1.3 75.7 - - - +
234D ASP* 1.3 59.9 + - - +
236D VAL* 3.6 3.2 + - - +
237D ASP* 3.0 32.4 + - - +
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Residues in contact with ASP 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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230D HIS* 3.3 15.8 + - - +
231D GLN* 3.1 12.6 + - - +
232D CYS 3.1 0.4 - - - -
233D CYS* 1.3 80.8 - - - +
235D LEU* 1.3 62.1 + - + +
237D ASP* 3.8 11.4 - - - +
238D ILE* 3.1 35.0 + - + +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASP* 4.9 1.4 - - - +
186D ARG* 3.7 27.4 - - + +
187D SER* 3.8 17.5 - - - -
190D LYS* 3.5 39.3 - - + -
231D GLN* 2.9 22.3 + - + +
232D CYS* 3.2 14.1 + - - +
234D ASP* 1.3 78.0 - - + +
236D VAL* 1.3 60.7 + - - +
238D ILE* 3.3 16.4 + - + +
239D ALA* 3.0 27.4 + - - +
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LYS* 3.9 33.4 - - + +
181D ALA* 4.5 13.2 - - + -
187D SER* 5.0 2.5 - - - -
195D ILE* 4.8 3.8 - - + -
198D ALA* 4.1 12.3 - - + -
199D CYS* 4.1 16.8 - - - +
202D LEU* 4.0 14.8 - - + -
232D CYS* 2.9 26.2 + - - +
233D CYS 3.7 5.2 - - - +
235D LEU* 1.3 76.6 - - + +
237D ASP* 1.3 64.1 + - - +
239D ALA* 3.0 18.0 + - - +
240D ILE* 3.0 21.3 + - + +
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Residues in contact with ASP 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LYS* 4.9 2.1 + - - -
202D LEU* 3.8 25.1 - - - +
233D CYS 3.0 19.6 + - - +
234D ASP* 3.9 14.9 - - - +
235D LEU 3.3 0.4 - - - -
236D VAL* 1.3 75.9 - - - +
238D ILE* 1.3 62.4 + - + +
240D ILE* 3.4 14.1 + - - +
241D VAL* 3.2 27.1 + - + +
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Residues in contact with ILE 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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184D ASP* 4.6 11.9 - - - +
186D ARG* 6.4 2.0 - - + -
234D ASP* 3.1 22.3 + - + +
235D LEU* 3.5 16.2 - - + +
236D VAL 3.2 0.4 - - - -
237D ASP* 1.3 74.6 - - + +
239D ALA* 1.3 67.5 + - - +
241D VAL* 3.2 6.6 + - - +
242D SER* 3.0 31.4 + - - +
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Residues in contact with ALA 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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180D CYS* 3.5 26.4 - - - +
181D ALA* 3.7 16.8 - - - +
184D ASP* 3.7 11.6 - - + +
187D SER* 3.7 8.3 - - - +
235D LEU 3.0 13.6 + - - +
236D VAL 3.0 9.6 + - - +
238D ILE* 1.3 77.0 - - - +
240D ILE* 1.3 56.4 + - - +
242D SER* 3.9 5.7 + - - -
243D PHE* 3.1 30.3 + - - +
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Residues in contact with ILE 240 (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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176D PRO 5.1 0.2 - - - +
177D LYS* 3.7 44.6 - - + +
180D CYS* 4.1 26.5 - - + -
236D VAL* 3.0 26.0 + - + +
237D ASP* 3.7 13.7 - - - +
238D ILE 3.2 0.4 - - - -
239D ALA* 1.3 78.4 - - - +
241D VAL* 1.3 65.8 + - + +
243D PHE* 3.6 13.0 + - - +
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Residues in contact with VAL 241 (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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237D ASP* 3.2 13.2 + - + +
238D ILE* 3.2 10.2 + - - +
240D ILE* 1.3 83.4 - - + +
242D SER* 1.3 62.5 + - - +
243D PHE 3.7 3.1 + - - +
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASP* 3.5 20.6 + - - -
238D ILE* 3.0 22.1 + - - +
239D ALA 3.9 1.7 + - - -
241D VAL* 1.3 78.7 - - - +
243D PHE* 1.3 66.1 + - - +
244D ASP* 3.2 9.4 + - - +
247D TYR* 6.0 0.5 - - - -
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Residues in contact with PHE 243 (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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54D THR* 4.5 8.5 - - + -
57D PHE* 3.7 45.3 - + - -
180D CYS* 3.8 27.8 - - + +
183D CYS* 3.8 38.4 - - + -
239D ALA 3.1 20.1 + - - +
240D ILE 3.8 10.7 - - - +
241D VAL 3.4 4.6 - - - +
242D SER* 1.3 76.9 - - - +
244D ASP* 1.3 64.6 + - - +
245D GLU* 4.2 23.3 - - + -
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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