Contacts of the helix formed by residues 197 - 219 (chain W) in PDB entry 1XDM
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 197 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196W HIS* 1.3 74.0 - - - +
198W LEU* 1.3 59.0 + - - +
199W GLU* 3.1 31.0 - - + +
200W HIS* 2.7 61.9 + - - +
201W CYS* 3.4 3.1 + - - +
234W THR 5.8 0.9 - - - -
243W TYR* 3.3 8.7 - - - +
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Residues in contact with LEU 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197W ASP* 1.3 71.5 - - - +
199W GLU* 1.3 64.3 + - + +
201W CYS* 3.2 6.5 + - - +
202W GLN* 3.1 20.1 + - - +
233W VAL* 3.7 12.1 - - + +
234W THR* 3.3 40.6 - - - +
243W TYR* 2.5 57.8 + - + -
247W GLN* 3.9 27.8 - - + +
248W VAL* 4.8 3.1 - - + -
251W ALA* 4.2 13.7 - - + -
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Residues in contact with GLU 199 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197W ASP* 3.2 33.5 - - + +
198W LEU* 1.3 76.0 + - - +
200W HIS* 1.3 61.8 + - - +
202W GLN* 3.6 15.2 - - - +
203W TYR* 3.0 26.3 + - - +
243W TYR* 5.4 3.5 + - - -
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Residues in contact with HIS 200 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196W HIS* 3.3 41.2 + + + +
197W ASP* 2.7 44.7 + - - +
199W GLU* 1.3 75.9 - - - +
201W CYS* 1.3 51.8 + - - +
203W TYR* 3.6 6.8 + - - +
204W VAL* 2.7 38.0 + - + +
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Residues in contact with CYS 201 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196W HIS* 6.3 0.9 - - + -
197W ASP 3.4 2.2 + - - +
198W LEU 3.2 9.1 + - - +
200W HIS* 1.3 77.9 + - - +
202W GLN* 1.3 56.5 + - - +
204W VAL* 2.9 12.0 + - - +
205W THR* 2.7 47.9 + - - -
231W ASN* 5.0 2.5 - - - -
232W MET 4.7 3.4 - - - -
233W VAL* 4.0 25.4 - - + -
234W THR 4.3 17.7 - - - +
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Residues in contact with GLN 202 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198W LEU* 3.1 12.2 + - - +
199W GLU* 3.3 18.6 + - - +
201W CYS* 1.3 75.6 - - - +
203W TYR* 1.3 63.7 + - - +
205W THR* 3.7 7.4 - - - -
206W GLU* 3.1 39.6 + - - +
233W VAL* 4.3 6.5 - - + -
251W ALA* 3.2 38.8 - - + +
254W THR* 3.0 19.4 - - - +
255W ALA* 4.2 3.1 - - + -
258W ARG* 3.1 6.2 + - - -
364W SO4 2.9 32.5 + - - -
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Residues in contact with TYR 203 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199W GLU 3.0 15.8 + - - +
200W HIS* 3.9 6.3 - - - +
202W GLN* 1.3 73.8 - - - +
204W VAL* 1.3 75.8 + - + +
206W GLU* 3.3 12.2 + - + +
207W LYS* 3.2 44.5 + - + +
217X ASN* 5.6 7.4 - - - -
218X ASP 5.6 1.6 + - - -
220X HIS* 4.2 31.4 - + + -
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Residues in contact with VAL 204 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158W PRO* 5.2 17.9 - - + -
163W ILE* 6.0 2.5 - - + -
190W VAL 5.0 13.5 - - - +
200W HIS* 2.7 39.0 - - + +
201W CYS* 2.9 10.0 + - - +
203W TYR* 1.3 83.8 - - + +
205W THR* 1.3 64.3 + - - +
207W LYS* 3.0 20.8 + - - +
208W VAL* 3.0 28.7 + - + +
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Residues in contact with THR 205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201W CYS* 2.7 38.2 + - - -
202W GLN* 3.7 7.2 - - - -
204W VAL* 1.3 72.3 - - - +
206W GLU* 1.3 58.0 + - - +
208W VAL* 3.6 6.3 - - - +
209W LEU* 2.9 58.0 + - + +
230W PRO* 6.1 1.8 - - + -
231W ASN* 3.9 23.3 + - - +
233W VAL* 3.9 15.7 - - + +
255W ALA* 4.6 6.1 - - + -
256W LEU* 5.9 1.1 - - + -
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Residues in contact with GLU 206 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202W GLN* 3.1 49.8 + - - +
203W TYR* 3.5 13.3 - - + +
204W VAL 3.2 0.2 - - - -
205W THR* 1.3 80.5 - - - +
207W LYS* 1.3 53.0 + - - +
210W ALA* 2.8 34.7 + - - +
255W ALA* 3.3 20.7 - - + -
258W ARG* 3.3 32.1 + - - +
259W THR* 3.3 21.8 - - + +
217X ASN* 4.1 11.7 + - - +
220X HIS* 5.5 6.4 + - - -
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Residues in contact with LYS 207 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158W PRO* 5.3 8.4 + - - +
160W SER* 4.7 18.0 + - - +
163W ILE* 3.2 31.0 - - + +
203W TYR* 3.2 32.9 + - + +
204W VAL* 3.0 13.6 + - - +
206W GLU* 1.3 76.2 - - - +
208W VAL* 1.3 67.9 + - - +
210W ALA* 3.4 1.2 + - - +
211W ALA* 2.8 30.3 + - + +
214X LYS* 5.7 1.8 - - - -
217X ASN* 4.1 17.0 + - - +
218X ASP* 5.2 12.3 - - - +
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Residues in contact with VAL 208 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163W ILE* 4.1 28.8 - - + +
166W ASN* 4.8 10.3 - - - +
188W PRO* 4.0 25.6 - - + -
189W GLU* 5.0 10.1 - - + +
190W VAL 5.9 4.7 - - - -
204W VAL* 3.0 33.4 + - + +
205W THR* 3.6 6.7 - - - +
207W LYS* 1.3 73.6 - - - +
209W LEU* 1.3 59.2 + - + +
211W ALA* 3.0 6.6 + - - +
212W VAL* 2.9 34.1 + - + +
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Residues in contact with LEU 209 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188W PRO* 4.8 11.4 - - + -
205W THR* 2.9 43.1 + - + +
206W GLU 3.5 3.4 - - - +
208W VAL* 1.3 73.6 - - + +
210W ALA* 1.3 58.7 + - - +
211W ALA 2.9 4.7 - - - -
212W VAL* 2.8 23.4 + - + +
213W TYR* 3.1 28.6 + - + -
228W LEU* 4.4 15.9 - - + -
230W PRO* 5.3 6.5 - - + -
256W LEU* 4.0 18.4 - - + +
259W THR* 3.5 24.0 - - + +
260W VAL* 3.7 22.7 - - + -
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Residues in contact with ALA 210 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206W GLU 2.8 12.5 + - - +
207W LYS 3.7 1.8 - - - +
209W LEU* 1.3 72.1 - - - +
211W ALA* 1.3 57.2 + - - +
213W TYR* 4.3 3.5 - - - +
214W LYS* 3.3 22.2 + - - +
258W ARG 5.2 0.7 - - - +
259W THR* 4.1 19.3 - - + +
213X TYR 5.5 2.7 - - - +
214X LYS* 3.5 13.2 - - + +
217X ASN* 3.0 42.0 - - + +
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Residues in contact with ALA 211 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163W ILE* 3.5 24.7 - - + -
164W GLN* 6.1 0.7 - - - -
167W ALA* 3.6 14.1 - - + +
207W LYS* 2.8 21.2 + - + +
208W VAL 3.0 7.2 - - - +
210W ALA* 1.3 78.3 - - - +
212W VAL* 1.3 61.7 + - - +
214W LYS* 3.7 5.8 - - - +
215W ALA* 3.3 15.1 + - - +
214X LYS* 4.5 14.8 - - - +
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Residues in contact with VAL 212 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166W ASN* 4.6 2.5 - - - +
167W ALA* 4.2 13.2 - - + +
170W LEU* 4.1 21.3 - - + -
186W VAL* 4.0 18.2 - - + -
188W PRO* 4.1 22.7 - - + -
208W VAL* 2.9 25.4 + - + +
209W LEU* 2.8 8.7 + - - +
211W ALA* 1.3 75.7 - - - +
213W TYR* 1.3 64.0 + - + +
214W LYS 2.9 4.3 - - - -
215W ALA* 2.9 5.2 + - - +
216W LEU* 2.7 48.8 + - + +
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Residues in contact with TYR 213 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186W VAL* 5.0 3.3 - - + +
209W LEU* 3.1 26.0 + - + +
210W ALA* 5.1 2.2 - - - +
212W VAL* 1.3 81.4 - - + +
214W LYS* 1.3 56.2 + - - +
216W LEU* 3.5 23.1 - - + +
217W ASN* 2.8 29.7 + - - +
223W LEU* 4.0 18.3 - - + +
226W THR* 5.1 6.3 - - + -
227W LEU 4.3 2.6 + - - -
228W LEU* 3.2 38.3 - - + +
259W THR 4.1 6.3 - - - +
260W VAL* 3.5 30.5 - - + +
261W PRO* 3.7 28.3 - - + -
264W VAL* 3.8 27.6 - - + +
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Residues in contact with LYS 214 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210W ALA 3.3 20.7 + - - +
211W ALA 3.7 5.8 - - - +
213W TYR* 1.3 76.9 - - - +
215W ALA* 1.3 67.5 + - - +
217W ASN* 3.1 5.5 + - - +
218W ASP* 2.8 62.7 + - - +
207X LYS 4.7 0.8 + - - -
210X ALA* 3.5 11.2 + - + +
211X ALA* 3.2 40.8 - - - +
214X LYS* 3.4 35.0 - - + +
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Residues in contact with ALA 215 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ALA* 3.7 19.5 - - + +
168W ASN* 3.9 16.6 - - - +
171W ALA* 3.8 17.3 - - + -
211W ALA 3.3 11.9 + - - +
212W VAL 2.9 7.8 + - - +
214W LYS* 1.3 79.6 - - - +
216W LEU* 1.3 56.3 + - - +
218W ASP* 2.9 13.2 + - - +
219W HIS* 2.9 33.1 + - + -
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Residues in contact with LEU 216 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170W LEU* 5.8 0.2 - - + -
171W ALA* 3.8 15.5 - - - +
174W ALA* 4.0 13.7 - - + -
186W VAL* 4.3 18.2 - - + -
212W VAL* 2.7 44.2 + - + +
213W TYR* 3.5 32.3 - - + +
215W ALA* 1.3 72.2 - - - +
217W ASN* 1.3 62.7 + - - +
219W HIS 3.0 11.4 + - - -
220W HIS 3.0 9.2 + - - -
221W VAL* 3.1 55.9 + - + -
223W LEU* 4.3 8.7 - - + -
226W THR* 5.7 0.9 - - + +
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Residues in contact with ASN 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213W TYR 2.8 23.0 + - - +
214W LYS* 3.4 7.9 - - - +
216W LEU* 1.3 74.7 - - - +
218W ASP* 1.3 63.7 + - - +
220W HIS* 3.3 15.8 + - - +
221W VAL 5.1 2.7 - - - +
223W LEU* 5.2 4.2 - - + +
203X TYR* 5.9 1.7 - - - -
206X GLU* 3.9 15.2 + - - +
207X LYS* 4.1 19.6 + - - +
210X ALA* 3.7 28.6 - - + +
258X ARG* 4.8 7.9 + - - +
259X THR* 3.9 14.6 - - - +
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Residues in contact with ASP 218 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214W LYS* 2.8 53.4 + - - +
215W ALA* 2.9 11.5 + - - +
217W ASN* 1.3 78.9 - - - +
219W HIS* 1.3 59.7 + - + +
220W HIS* 3.1 9.4 + - - +
207X LYS* 4.6 18.7 + - - +
210X ALA* 5.5 0.2 - - - +
161Z LEU* 3.5 34.9 - - + +
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Residues in contact with HIS 219 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168W ASN* 4.1 11.8 + - - -
171W ALA* 3.0 45.0 + - + +
172W ARG* 3.5 22.1 - - + +
175W SER* 4.1 16.6 + - - -
215W ALA* 2.9 21.2 + - + +
216W LEU 3.0 4.6 + - - +
218W ASP* 1.3 78.5 - - + +
220W HIS* 1.3 69.2 + - - +
221W VAL* 3.2 4.6 + - + -
161Z LEU* 4.2 23.7 - - + +
165Z GLU* 3.2 29.3 + - + -
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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
------------------------------------------------------------
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