Contacts of the helix formed by residues 198 - 220 (chain H) in PDB entry 1XFB
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 198 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H ASP 3.8 1.2 + - - -
197H HIS* 1.3 78.6 - - - +
199H LEU* 1.3 65.8 + - - +
200H LYS* 3.1 37.2 + - - +
201H ARG* 3.2 26.9 + - - +
202H CYS 3.3 8.0 + - - -
236H PRO* 4.1 2.9 - - - -
240H CYS* 4.0 15.5 - - - -
242H ILE* 4.3 8.6 - - + +
244H TYR* 3.4 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198H ASP* 1.3 73.5 - - - +
200H LYS* 1.3 64.4 + - - +
202H CYS* 3.1 4.3 + - - +
203H GLN* 3.0 21.4 + - - +
234H VAL* 3.3 19.7 - - + +
235H THR* 3.2 33.4 - - - -
236H PRO* 3.8 12.8 - - + +
244H TYR* 3.3 44.1 + - + -
248H GLU* 3.7 28.3 - - + +
249H ILE* 4.4 5.2 - - + -
252H ALA* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E SER* 6.0 0.2 - - - -
6E PRO* 4.6 18.2 - - - +
198H ASP* 3.1 19.3 + - - +
199H LEU* 1.3 79.2 - - - +
201H ARG* 1.3 62.6 + - - +
203H GLN* 3.1 10.6 + - - +
204H TYR* 3.0 21.3 + - - +
244H TYR* 4.8 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E HIS* 3.0 47.2 + - - +
4E SER* 4.3 12.7 + - - +
157F ARG* 3.6 17.9 - - - +
154H ILE* 3.4 21.2 - - + +
155H SER 3.3 24.2 + - - -
156H GLU* 4.6 1.2 + - - +
157H ARG* 5.6 0.2 - - - +
158H THR 5.5 0.4 - - - +
159H PRO* 4.8 3.2 - - - +
197H HIS* 3.7 22.4 - - + -
198H ASP* 3.2 20.7 + - - +
200H LYS* 1.3 79.8 - - - +
202H CYS* 1.3 63.0 + - - +
204H TYR* 3.1 7.8 + - - +
205H VAL* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H ILE* 4.1 18.1 - - - +
191H ILE* 5.2 4.0 - - - -
192H LEU 6.1 0.2 - - - -
197H HIS* 4.0 12.4 - - + +
198H ASP 3.3 3.5 + - - +
199H LEU 3.1 7.4 + - - +
201H ARG* 1.3 78.9 - - - +
203H GLN* 1.3 58.1 + - - +
205H VAL* 4.0 0.3 - - - +
206H THR* 2.8 42.1 + - - -
232H ASN* 4.2 7.2 - - - -
233H MET 4.4 0.9 - - - -
234H VAL* 3.5 10.3 - - - -
235H THR* 3.2 45.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H LEU* 3.0 11.8 + - - +
200H LYS* 3.4 13.0 - - - +
202H CYS* 1.3 77.8 - - - +
204H TYR* 1.3 56.9 + - - +
206H THR* 3.2 2.8 + - - -
207H GLU* 2.6 58.9 + - - +
234H VAL* 3.8 16.3 - - + +
252H ALA* 3.4 38.0 + - + +
255H THR* 3.7 15.1 - - - +
256H ALA* 3.9 6.0 - - + +
259H ARG* 3.2 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E HIS* 2.6 62.7 + + + +
4E SER* 3.1 30.3 - - - +
5E TYR 5.1 0.2 - - - -
221E HIS* 3.5 17.3 - + - -
118F GLY 4.9 0.3 + - - -
200H LYS 3.0 12.3 + - - +
201H ARG* 3.3 11.9 - - - +
203H GLN* 1.3 76.8 - - - +
205H VAL* 1.3 66.8 + - + +
207H GLU* 3.1 13.3 + - + +
208H LYS* 3.0 62.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E HIS* 3.9 26.0 - - + +
154H ILE* 3.9 26.0 - - + -
159H PRO* 3.6 31.0 - - + -
164H ILE* 6.0 0.4 - - + -
191H ILE* 3.7 15.9 - - + -
201H ARG* 2.9 30.7 + - + +
202H CYS 4.0 0.4 - - - +
204H TYR* 1.3 74.4 - - + +
206H THR* 1.3 64.2 + - - +
208H LYS* 3.2 5.9 + - + +
209H VAL* 2.9 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H ILE* 3.4 16.0 - - + +
202H CYS* 2.8 28.0 + - - -
203H GLN* 3.5 6.1 - - - -
205H VAL* 1.3 75.9 - - - +
207H GLU* 1.3 64.2 + - - +
209H VAL* 3.8 0.3 - - - +
210H LEU* 2.9 46.1 + - + +
231H PRO* 5.8 2.0 - - + -
232H ASN* 3.3 29.5 + - - +
234H VAL* 4.4 9.3 - - + +
256H ALA* 4.1 15.7 - - + -
257H LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E SER* 5.7 0.2 - - - -
203H GLN* 2.6 51.6 + - - +
204H TYR* 3.4 11.6 + - + +
206H THR* 1.3 77.4 - - - +
208H LYS* 1.3 63.0 + - + +
210H LEU* 4.8 0.4 - - - -
211H ALA* 2.9 30.9 + - - +
256H ALA* 3.7 23.3 - - - +
259H ARG* 3.0 31.7 + - - +
260H THR* 3.4 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E HIS* 6.1 2.0 - - + -
218E SER* 3.0 37.2 + - - +
219E ASP* 4.9 2.1 + - - +
221E HIS* 3.0 23.5 + - - +
164H ILE* 4.7 12.9 - - + +
204H TYR* 3.0 61.0 + - + +
205H VAL* 3.2 7.2 + - + +
207H GLU* 1.3 75.1 - - - +
209H VAL* 1.3 66.7 + - + +
211H ALA* 3.4 6.0 + - - +
212H ALA* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 3.3 36.3 - - + -
159H PRO* 4.8 0.4 - - + -
164H ILE* 4.4 22.4 - - + +
189H PRO* 4.2 14.8 - - + +
191H ILE* 3.6 19.5 - - + -
205H VAL* 2.9 29.0 + - + +
206H THR 3.8 2.9 - - - +
208H LYS* 1.3 75.4 - - + +
210H LEU* 1.3 66.6 + - + +
212H ALA* 3.0 5.5 + - - +
213H VAL* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H PRO* 4.0 17.3 - - + -
206H THR* 2.9 38.3 + - + +
207H GLU 4.0 0.2 - - - +
209H VAL* 1.3 77.5 - - + +
211H ALA* 1.3 65.1 + - - +
213H VAL* 2.9 16.1 + - + +
214H TYR* 2.9 24.0 + - + -
229H LEU* 3.9 33.0 - - + -
231H PRO* 4.7 7.9 - - + -
256H ALA 5.0 0.9 - - - +
257H LEU* 3.8 26.2 - - + -
260H THR* 3.5 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E LYS* 3.7 11.3 - - + +
218E SER* 3.4 31.4 - - - +
207H GLU 2.9 18.5 + - - +
208H LYS 3.6 6.5 - - - +
210H LEU* 1.3 76.3 - - - +
212H ALA* 1.3 60.8 + - - +
214H TYR* 3.8 3.8 + - - +
215H LYS* 3.3 21.0 + - - +
260H THR* 4.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E LYS* 3.9 17.9 - - - +
164H ILE* 3.5 28.9 - - + -
165H LEU* 6.1 0.7 - - - -
168H ALA* 4.1 9.9 - - + +
208H LYS 3.1 8.1 + - - +
209H VAL 3.0 9.2 + - - +
211H ALA* 1.3 74.7 - - - +
213H VAL* 1.3 68.5 + - - +
215H LYS* 3.2 3.3 + - - +
216H ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ALA* 4.0 17.0 - - + +
171H LEU* 4.2 12.8 - - + -
187H VAL* 3.9 27.6 - - + -
189H PRO* 4.1 17.3 - - + -
209H VAL* 2.9 36.1 + - + +
210H LEU* 2.9 11.9 + - + +
212H ALA* 1.3 76.2 - - - +
214H TYR* 1.3 67.3 + - + +
216H ALA* 3.3 3.8 + - - +
217H LEU* 3.0 35.5 + - + +
229H LEU* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H VAL* 5.7 1.8 - - + +
210H LEU* 2.9 25.7 + - + +
211H ALA* 4.5 3.1 - - - +
213H VAL* 1.3 79.7 - - + +
215H LYS* 1.3 65.6 + - - +
217H LEU* 3.2 16.2 + - + +
218H SER* 2.9 23.0 + - - -
224H LEU* 3.6 35.3 - - + +
227H THR* 5.1 2.5 + - - -
228H LEU 5.2 0.5 - - - -
229H LEU* 3.4 40.2 + - + +
260H THR 3.9 16.8 - - - +
261H VAL* 3.7 21.8 - - + +
262H PRO* 3.7 19.3 - - + -
265H VAL* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E ALA* 3.9 13.2 - - + +
212E ALA* 4.0 25.1 - - - +
215E LYS* 3.7 38.4 - - + -
211H ALA 3.3 16.2 + - - +
212H ALA 3.2 5.5 + - - +
214H TYR* 1.3 77.6 - - - +
216H ALA* 1.3 58.4 + - - +
218H SER* 3.2 8.4 + - - -
219H ASP* 2.9 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ALA* 3.4 34.3 - - + +
169H ASN* 4.3 4.9 - - - +
172H ALA* 3.8 6.7 - - + -
212H ALA 3.0 13.2 + - - +
213H VAL 3.4 8.1 - - - +
215H LYS* 1.3 75.1 - - - +
217H LEU* 1.3 66.8 + - - +
219H ASP* 2.9 10.6 + - - +
220H HIS* 2.9 28.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H LEU 4.8 0.7 - - - -
172H ALA* 3.7 22.4 - - - +
175H ALA* 3.9 8.7 - - + -
187H VAL* 4.4 17.5 - - + -
213H VAL* 3.0 27.6 + - + +
214H TYR* 3.5 40.2 - - + +
216H ALA* 1.3 76.1 - - - +
218H SER* 1.3 64.0 + - - +
220H HIS 3.2 1.2 + - - -
221H HIS 3.1 4.0 + - - -
222H VAL* 3.0 58.7 + - + +
224H LEU* 4.0 15.7 - - + -
227H THR* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E GLU 5.1 0.2 + - - -
208E LYS* 2.7 42.1 + - - +
211E ALA* 3.4 31.0 - - - +
214H TYR 2.9 13.3 + - - -
215H LYS* 3.3 12.0 - - - +
216H ALA 3.1 0.2 - - - -
217H LEU* 1.3 76.1 - - - +
219H ASP* 1.3 60.5 + - - +
221H HIS* 2.9 11.7 + - - +
222H VAL 5.0 2.5 - - - +
224H LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E LYS* 5.0 1.8 - - - +
162G LEU* 3.5 21.8 - - + +
165G LEU* 3.8 25.9 - - + +
215H LYS* 2.9 51.2 + - - +
216H ALA* 2.9 11.1 + - - +
218H SER* 1.3 79.6 + - - +
220H HIS* 1.3 67.2 + - + +
221H HIS* 3.4 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 220 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 5.5 3.1 - - + +
117G ALA* 4.0 3.8 - - - +
162G LEU* 3.7 28.7 - - + +
165G LEU* 4.2 3.2 - - + +
166G GLU* 3.9 11.7 - - + -
169H ASN* 2.8 28.4 + - - -
172H ALA* 3.4 29.7 - - + +
173H ARG* 3.8 36.0 + - + +
176H SER* 3.7 19.0 + - - -
216H ALA* 2.9 22.6 + - - +
217H LEU 3.9 2.5 - - - +
219H ASP* 1.3 82.1 - - + +
221H HIS* 1.3 76.1 + - - +
222H VAL* 3.3 3.3 + - + -
----------------------------------------------------------
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