Contacts of the helix formed by residues 207 - 223 (chain B) in PDB entry 4EMX
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 GLY 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU 5.2 3.1 - - - -
96A PRO* 5.1 13.0 - - - -
202B SER 3.0 9.0 + - - +
203B LEU* 3.0 19.4 + - - -
204B GLN 4.8 0.2 - - - -
205B LYS 3.8 0.6 - - - -
206B PHE* 1.3 77.5 - - - +
208B GLU* 1.3 69.0 + - - +
209B ARG* 3.1 3.9 + - - -
210B ALA* 3.1 10.7 + - - +
211B PHE* 3.3 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU 5.5 0.4 + - - -
97A GLU* 3.2 45.2 + - - +
203B LEU* 4.1 15.3 + - + +
207B GLY* 1.3 71.6 - - - -
209B ARG* 1.3 61.2 + - - +
211B PHE* 3.1 4.5 + - - +
212B LYS* 2.8 50.3 + - + +
239B THR* 4.0 20.1 - - + +
243B THR* 5.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 4.4 3.9 + - - +
206B PHE 5.4 1.8 - - - +
207B GLY* 3.1 2.3 - - - -
208B GLU* 1.3 86.0 - - - +
210B ALA* 1.3 56.8 + - - +
212B LYS* 3.9 7.0 - - + +
213B ALA* 3.0 28.5 + - + +
323B LYS* 5.3 4.4 - - - +
324B ASP* 2.8 35.1 + - - +
327B LEU* 4.3 7.7 - - - +
351B LYS* 5.5 4.2 - - - +
354B GLU* 3.5 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER* 4.5 5.3 - - - +
206B PHE* 3.7 36.0 + - + +
207B GLY 3.1 4.4 + - - +
209B ARG* 1.3 75.2 - - - +
211B PHE* 1.3 65.5 + - - +
213B ALA* 3.6 6.2 + - - +
214B TRP* 3.1 22.0 + - - +
347B LEU* 5.1 2.8 - - - +
481B LEU* 4.8 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 3.7 37.0 - - + -
202B SER* 4.6 11.8 - - - -
203B LEU* 3.4 36.3 - - + -
207B GLY 3.3 3.4 + - - +
208B GLU 3.1 3.8 + - - +
210B ALA* 1.3 76.9 - - - +
212B LYS* 1.3 65.8 + - - +
214B TRP* 3.0 31.5 + + + +
215B ALA* 3.0 27.2 + - + +
238B LEU* 4.2 6.1 - - + -
239B THR* 3.6 39.9 - - + -
242B HIS* 3.8 27.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 2.8 49.9 + - + +
209B ARG* 3.9 7.0 - - + +
211B PHE* 1.3 71.2 - - - +
213B ALA* 1.3 56.5 + - - +
215B ALA* 3.1 2.8 + - - +
216B VAL* 2.9 36.8 + - + +
235B VAL* 3.8 16.4 - - + +
236B THR* 4.0 20.2 + - - +
239B THR* 3.4 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ARG* 3.0 18.2 + - + +
210B ALA* 3.7 7.4 - - - +
211B PHE 3.2 0.2 - - - -
212B LYS* 1.3 71.7 - - - +
214B TRP* 1.3 67.2 + - - +
216B VAL* 3.3 3.1 + - - +
217B ALA 3.0 18.0 + - - -
331B LEU* 3.6 14.3 - - + +
347B LEU* 3.5 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 5.2 14.1 - - + +
199B LYS* 3.6 24.7 - - + -
202B SER* 6.2 1.8 - - - +
210B ALA 3.1 11.1 + - - +
211B PHE* 3.0 31.9 + + + +
213B ALA* 1.3 78.6 - - - +
215B ALA* 1.3 75.7 + - + +
217B ALA* 3.3 2.9 + - - +
218B ARG* 3.0 51.0 + - + +
219B LEU* 6.0 1.8 - - + -
222B ARG* 6.1 0.4 - - - -
238B LEU* 4.5 9.6 - - + -
343B VAL* 3.4 29.1 - - + +
344B VAL* 6.1 3.1 - - + -
347B LEU* 4.0 15.1 - - + +
451B ASP* 5.4 3.8 + - - -
481B LEU* 6.5 1.1 - - + -
602B CL 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.0 26.8 + - + +
212B LYS 3.7 3.4 - - - +
214B TRP* 1.3 91.3 - - + +
216B VAL* 1.4 62.0 - - - +
218B ARG 4.5 0.4 - - - +
219B LEU* 2.9 37.6 + - - +
235B VAL* 3.5 21.3 - - + -
238B LEU* 4.4 14.6 - - + -
239B THR* 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LYS* 2.9 25.3 + - + +
213B ALA* 3.8 5.4 - - - +
215B ALA* 1.4 76.1 - - - +
217B ALA* 1.3 56.2 + - - +
220B SER* 2.5 46.9 + - - +
228B PHE* 4.9 7.2 - - + -
231B VAL* 4.4 6.7 - - + +
232B SER* 5.7 4.0 - - - +
235B VAL* 3.4 22.2 - - + +
328B GLY* 4.0 28.3 - - - +
331B LEU* 4.2 11.2 - - + -
332B TYR* 4.0 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ALA 3.0 16.2 + - - +
214B TRP 3.5 4.5 - - - +
216B VAL* 1.3 78.5 - - - +
218B ARG* 1.3 63.3 + - - +
221B GLN* 3.2 29.2 + - - +
331B LEU* 4.2 13.2 - - + +
335B ALA* 3.6 14.8 - - + +
343B VAL* 3.9 17.3 - - + -
346B LEU* 4.6 9.0 - - + -
347B LEU* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 3.0 47.5 + - + +
215B ALA 4.2 1.6 - - - +
217B ALA* 1.3 76.0 - - - +
219B LEU* 1.3 60.6 + - + +
221B GLN* 3.4 17.4 + - - +
222B ARG* 3.1 68.9 + - - +
293B VAL 5.4 1.0 + - - -
295B ASN* 2.6 34.8 + - - +
343B VAL* 3.9 20.8 - - + +
451B ASP* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 6.0 1.3 - - + -
215B ALA* 2.9 20.6 + - - +
218B ARG* 1.3 79.5 - - + +
220B SER* 1.3 57.7 + - - +
221B GLN 3.4 0.2 - - - -
222B ARG* 3.9 23.6 - - - +
223B PHE* 2.9 58.3 + - + +
231B VAL* 4.4 12.0 - - + +
234B LEU* 3.9 30.5 - - + +
235B VAL* 4.0 16.8 - - + +
238B LEU* 4.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 2.5 26.4 + - - +
217B ALA 4.0 2.5 - - - -
219B LEU* 1.3 74.8 - - - +
221B GLN* 1.3 63.8 + - - +
223B PHE 4.6 1.3 - - - +
224B PRO* 3.2 24.8 - - - +
231B VAL* 3.6 15.4 - - - +
332B TYR* 3.4 49.3 - - - -
335B ALA* 4.1 4.9 - - - -
336B ARG* 3.4 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA 3.2 12.5 + - - +
218B ARG* 3.5 30.9 + - - +
220B SER* 1.3 77.5 - - - +
222B ARG* 1.3 60.6 + - - +
224B PRO* 3.6 13.5 - - - +
295B ASN* 3.5 16.3 - - - +
296B ASP 4.6 0.3 - - - +
335B ALA* 3.3 24.9 + - + +
336B ARG* 4.4 3.4 - - - +
338B HIS 2.9 15.8 + - - +
339B PRO* 3.6 21.6 + - + +
341B TYR 2.7 30.5 + - - -
343B VAL* 3.7 15.5 - - - +
346B LEU* 3.6 11.6 - - - +
447B PRO* 5.2 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 6.1 0.4 - - - -
218B ARG* 3.1 56.0 + - - +
219B LEU* 3.9 23.7 - - - +
221B GLN* 1.3 79.9 - - - +
223B PHE* 1.3 90.8 + - + +
224B PRO* 3.2 1.4 - - - +
272B SER* 4.4 0.5 + - - -
290B ILE 4.3 2.5 + - - -
291B ALA* 3.1 33.0 + - - +
292B GLU* 4.2 4.6 - - - +
293B VAL* 3.3 36.8 + - + +
294B GLU 4.3 2.8 - - - +
295B ASN* 3.3 10.7 - - - +
296B ASP* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 2.9 47.3 + - + +
220B SER 3.7 3.6 - - - +
222B ARG* 1.3 108.7 - - + +
224B PRO* 1.3 58.0 - - - +
225B LYS 3.1 4.3 - - - -
226B ALA* 3.0 28.4 + - + +
231B VAL* 4.5 5.9 - - + +
234B LEU* 4.2 18.4 - - + -
264B ILE* 5.1 7.4 - - + -
271B ILE* 3.4 36.3 - - + +
272B SER* 3.6 21.8 - - - -
275B LEU* 4.3 6.7 - - + -
290B ILE* 4.8 17.7 - - + -
293B VAL* 4.3 10.5 - - + -
332B TYR* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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