Contacts of the helix formed by residues 207 - 226 (chain D) in PDB entry 1FM6
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 GLU 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D PRO* 1.3 78.0 - - - +
208D SER* 1.3 62.4 + - - +
209D ALA* 3.4 9.2 - - + +
210D ASP* 2.7 47.4 + - - +
211D LEU* 2.9 7.4 + - - -
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Residues in contact with SER 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D PRO 4.1 0.8 + - - -
207D GLU* 1.3 74.5 - - - +
209D ALA* 1.3 64.4 + - - +
211D LEU* 2.9 8.6 + - - +
212D ARG* 2.8 30.4 + - - +
419D LEU* 4.0 25.2 - - - +
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Residues in contact with ALA 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GLU* 3.4 8.2 - - + +
208D SER* 1.3 77.2 - - - +
210D ASP* 1.3 60.7 + - - +
212D ARG* 3.6 7.3 + - - +
213D ALA* 3.1 27.2 + - - +
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Residues in contact with ASP 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D PRO* 4.2 11.6 - - + +
207D GLU* 2.7 44.6 + - - +
209D ALA* 1.3 73.1 - - - +
211D LEU* 1.3 57.7 + - - +
213D ALA* 3.1 7.2 + - - +
214D LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D PRO* 4.1 29.8 - - + +
207D GLU 2.9 13.6 + - - +
208D SER* 2.9 8.6 + - - +
210D ASP* 1.3 76.0 - - - +
212D ARG* 1.3 58.4 + - - +
214D LEU* 3.5 9.8 + - + +
215D ALA* 3.0 27.2 + - - +
412D ASN* 4.0 8.7 - - + +
415D GLN* 3.8 31.2 - - + +
416D ALA* 3.8 29.2 - - + +
419D LEU* 3.5 30.1 - - + -
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Residues in contact with ARG 212 (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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208D SER* 2.8 22.4 + - - +
209D ALA* 3.9 6.7 - - - +
211D LEU* 1.3 76.7 + - - +
213D ALA* 1.3 60.1 + - - +
215D ALA* 3.3 16.2 + - - +
216D LYS* 2.9 27.4 + - - +
416D ALA 4.6 1.0 + - - -
419D LEU* 3.4 22.6 - - + +
420D GLN* 3.2 53.5 + - - +
423D LEU* 3.5 27.6 - - + +
424D ASN* 6.3 0.2 - - - +
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Residues in contact with ALA 213 (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 ALA 3.1 17.6 + - - +
210D ASP* 3.1 8.6 + - - +
212D ARG* 1.3 73.1 - - - +
214D LEU* 1.3 55.3 + - - +
216D LYS* 3.0 8.2 + - - +
217D HIS* 2.7 36.8 + - - +
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Residues in contact with LEU 214 (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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210D ASP 2.9 17.0 + - - +
211D LEU* 3.6 9.2 - - + +
213D ALA* 1.3 75.9 - - - +
215D ALA* 1.3 63.5 + - - +
217D HIS* 3.3 7.5 + - + +
218D LEU* 2.9 40.5 + - + +
304D PRO* 4.3 26.5 - - + -
412D ASN* 4.0 19.7 - - + +
413D LEU* 3.9 30.5 - - + -
416D ALA* 3.9 17.9 - - + -
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Residues in contact with ALA 215 (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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211D LEU 3.0 15.2 + - - +
212D ARG* 3.4 29.2 - - - +
213D ALA 3.2 0.2 - - - -
214D LEU* 1.3 79.4 - - - +
216D LYS* 1.3 61.8 + - - +
218D LEU* 3.7 3.8 - - - +
219D TYR* 3.0 23.4 + - - +
382D SER* 5.3 2.8 - - - +
386D ILE* 3.9 32.7 - - + +
416D ALA* 5.0 1.1 - - + +
420D GLN* 4.4 5.6 - - - +
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Residues in contact with LYS 216 (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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212D ARG 2.9 13.8 + - - +
213D ALA* 3.5 9.2 - - - +
215D ALA* 1.3 73.2 - - - +
217D HIS* 1.3 67.3 + - - +
219D TYR* 3.3 7.3 + - + +
220D ASP* 3.0 49.4 + - - +
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Residues in contact with HIS 217 (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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213D ALA 2.7 20.5 + - - +
214D LEU* 3.5 10.1 - - + +
216D LYS* 1.3 76.6 - - - +
218D LEU* 1.3 69.1 + - + +
220D ASP* 3.3 7.4 + - - +
221D SER* 3.2 23.7 + - - -
302D SER* 3.1 31.2 + - - -
304D PRO* 4.1 20.2 - - + +
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Residues in contact with LEU 218 (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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214D LEU* 2.9 35.2 + - + +
215D ALA 3.7 3.8 - - - +
217D HIS* 1.3 88.9 - - + +
219D TYR* 1.3 61.8 + - - +
221D SER* 3.2 7.6 + - - +
222D TYR* 2.9 24.3 + - - +
299D TYR* 3.3 27.3 - - + +
302D SER 4.8 1.1 - - - +
303D ILE* 4.3 26.7 - - + -
304D PRO* 4.7 0.2 - - + -
385D ALA* 3.9 6.3 - - + +
386D ILE* 4.0 31.2 - - + +
389D ALA* 4.3 4.5 - - + -
413D LEU* 3.9 23.1 - - + -
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Residues in contact with TYR 219 (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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215D ALA 3.0 17.4 + - - +
216D LYS* 3.6 9.0 - - + +
218D LEU* 1.3 77.0 - - - +
220D ASP* 1.3 73.4 + - - +
222D TYR* 3.1 5.3 + + - +
223D ILE* 2.9 58.2 + - + +
381D ASP* 3.8 27.0 + - + +
382D SER* 3.7 33.0 - - - -
385D ALA* 3.8 9.8 - - + +
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Residues in contact with ASP 220 (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 LYS* 3.0 42.8 + - - +
217D HIS* 3.3 8.2 + - - +
219D TYR* 1.3 91.6 - - - +
221D SER* 1.3 57.6 + - - +
223D ILE* 3.0 9.2 + - - +
224D LYS* 2.9 27.2 + - - +
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Residues in contact with SER 221 (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 HIS* 3.2 15.1 + - - -
218D LEU* 3.2 14.0 + - - +
220D ASP* 1.3 79.2 - - - +
222D TYR* 1.3 51.7 + - - +
224D LYS* 3.5 19.9 - - - +
225D SER* 2.7 42.4 + - - -
299D TYR* 3.4 5.9 - - - -
302D SER* 3.0 38.8 + - - -
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Residues in contact with TYR 222 (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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218D LEU 2.9 15.0 + - - +
219D TYR* 3.1 13.2 - + - +
220D ASP 3.0 0.2 - - - -
221D SER* 1.3 77.0 + - - +
223D ILE* 1.3 70.9 + - + +
226D PHE* 3.0 48.5 + + + +
229D THR* 4.5 12.5 - - + -
230D LYS 4.4 3.6 + - - -
299D TYR* 3.7 11.7 - + + -
329D MET* 3.9 15.4 - - + +
332D SER* 5.2 1.0 + - - -
381D ASP* 2.8 48.4 + - + -
384D LEU* 3.9 15.2 - - + +
385D ALA* 3.6 31.0 - - + -
388D ILE* 3.9 21.1 - - + -
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Residues in contact with ILE 223 (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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219D TYR* 2.9 57.5 + - + +
220D ASP* 3.0 10.3 + - - +
222D TYR* 1.3 82.1 - - + +
224D LYS* 1.3 63.5 + - - +
225D SER 3.5 0.2 + - - -
226D PHE 3.8 13.6 + - - +
227D PRO* 5.2 0.7 - - - +
229D THR* 3.8 26.4 - - + +
232D LYS* 6.4 0.2 - - - +
381D ASP* 5.2 1.3 - - + +
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Residues in contact with LYS 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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220D ASP 2.9 12.6 + - - +
221D SER* 3.5 21.3 - - - +
223D ILE* 1.3 80.0 - - - +
225D SER* 1.3 63.0 + - - +
226D PHE 5.3 0.3 - - - -
227D PRO* 5.5 1.4 - - - +
302D SER* 6.3 0.4 - - - -
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Residues in contact with SER 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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221D SER* 2.7 30.0 + - - -
224D LYS* 1.3 78.7 - - - +
226D PHE* 1.3 63.2 + - - +
227D PRO* 3.5 4.8 - - - +
295D GLU* 3.4 45.3 - - - +
298D GLU* 4.2 11.9 + - - +
299D TYR* 3.8 24.3 + - - -
302D SER* 5.7 0.2 - - - -
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Residues in contact with PHE 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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222D TYR* 3.0 53.3 + + + +
223D ILE 3.8 10.1 - - - +
224D LYS 3.6 0.8 - - - -
225D SER* 1.3 81.2 - - - +
227D PRO* 1.3 67.1 - - - +
228D LEU 3.5 6.0 + - - +
229D THR* 3.6 18.1 + - - +
288D ARG* 5.8 0.2 - - - -
292D ALA* 6.1 0.2 - - - -
295D GLU* 3.5 38.8 - - + +
296D ILE* 3.9 15.3 - - + -
299D TYR* 3.8 40.2 - + + -
329D MET* 3.5 39.0 - - + -
388D ILE* 4.6 4.9 - - + -
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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