Contacts of the helix formed by residues 217 - 234 (chain D) in PDB entry 3E8C
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 LYS 217 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D HIS* 3.3 46.7 + - + +
161D ASP* 3.4 39.1 + - - +
162D LEU 3.7 7.4 - - - +
163D ILE* 3.9 16.6 - - + +
191D VAL* 2.6 32.1 + - - +
192D LYS* 4.8 0.6 - - - +
193D GLY 5.3 3.0 + - - +
216D ASN* 1.3 83.2 - - + +
218D ALA* 1.3 61.2 + - - +
219D VAL* 3.1 0.4 - - - -
220D ASP* 3.0 24.1 + - - +
221D TRP* 3.9 4.9 + - + +
283D ASN* 5.8 1.1 - - - +
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Residues in contact with ALA 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ASN* 2.8 23.1 + - - +
217D LYS* 1.3 73.4 - - - +
219D VAL* 1.3 60.0 + - - +
220D ASP 3.2 0.2 - - - -
221D TRP* 3.1 17.0 + - - +
222D TRP 3.1 13.9 + - - -
277D LEU* 3.3 27.8 - - + -
280D ARG* 3.1 16.8 + - - +
283D ASN* 3.7 25.5 + - + -
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Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ILE* 4.1 13.9 - - + -
165D ARG* 4.5 9.4 - - + -
204D TYR 4.9 1.4 - - - +
206D ALA* 3.8 23.9 + - + +
208D GLU* 3.1 22.0 - - - +
209D ILE* 4.1 14.1 - - + -
215D TYR* 3.6 38.1 - - + -
216D ASN 3.2 15.3 - - - +
217D LYS 3.1 0.8 + - - -
218D ALA* 1.3 76.9 - - - +
220D ASP* 1.3 64.2 + - - +
222D TRP* 3.7 3.7 + - - +
223D ALA* 3.2 22.0 + - - +
280D ARG* 4.0 0.2 - - - +
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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
----------------------------------------------------------
154D PHE* 3.3 32.8 - - + -
158D HIS* 3.0 29.2 - - - +
163D ILE* 3.4 8.4 - - - +
164D TYR* 2.9 28.9 + - - +
165D ARG* 2.9 27.6 + - - -
166D ASP 4.7 0.2 + - - -
167D LEU* 5.4 0.9 + - - +
217D LYS 3.0 11.3 + - - +
219D VAL* 1.3 82.5 - - - +
221D TRP* 1.3 56.3 + - - +
223D ALA* 3.4 8.1 + - - +
224D LEU* 3.0 22.3 + - - +
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Residues in contact with TRP 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D VAL* 3.8 15.0 - - + -
154D PHE* 3.5 27.1 - + + -
155D GLU* 4.3 3.8 - - - -
158D HIS* 3.5 30.9 - + - -
217D LYS* 4.0 14.4 - - + +
218D ALA* 3.1 14.9 + - - +
220D ASP* 1.3 74.5 - - - +
222D TRP* 1.3 64.1 + - - +
224D LEU* 3.4 25.9 + - + +
225D GLY 3.3 14.7 + - - -
272D LEU* 3.5 17.3 - - + +
280D ARG* 4.5 2.7 - - - -
281D PHE 3.6 18.6 - - - +
282D GLY* 3.6 28.9 + - - -
283D ASN* 5.3 0.2 - - + -
288D VAL* 3.6 32.5 - - + -
291D ILE* 3.3 24.7 - - + -
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Residues in contact with TRP 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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203D GLU 5.2 0.4 + - - -
204D TYR 3.8 12.2 + - - -
205D LEU 3.5 12.1 + - - -
206D ALA* 3.6 16.6 - - + -
207D PRO* 3.7 21.3 - - + -
218D ALA 3.1 6.5 + - - -
219D VAL 3.7 7.0 - - - +
221D TRP* 1.3 75.8 - - - +
223D ALA* 1.3 59.7 + - - +
225D GLY 3.0 15.6 + - - -
226D VAL* 3.2 23.2 + - + +
238D PHE* 3.7 27.0 - + - -
250D ILE* 3.8 24.5 - - + -
255D VAL* 6.0 0.2 - - + -
272D LEU 3.6 13.0 - - - -
273D LEU* 3.3 53.7 - - + +
274D GLN 3.6 11.0 - - - -
275D VAL* 3.7 6.1 - - + -
280D ARG* 3.5 35.0 - - - +
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Residues in contact with ALA 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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165D ARG 6.6 0.2 - - - -
167D LEU* 3.7 25.8 - - + +
204D TYR* 3.7 22.6 - - + +
219D VAL 3.2 12.7 + - - +
220D ASP* 3.5 12.8 - - - +
221D TRP 3.3 0.2 - - - -
222D TRP* 1.3 81.4 - - - +
224D LEU* 1.3 59.4 + - - +
226D VAL* 3.2 6.9 + - - +
227D LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 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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147D ALA* 4.3 6.3 - - - +
150D ILE* 3.5 34.1 - - + -
151D VAL* 3.7 24.9 - - + -
154D PHE* 4.4 2.7 - - + -
167D LEU* 3.5 10.4 - - + +
220D ASP 3.0 14.0 + - - +
221D TRP* 3.5 31.0 - - + +
222D TRP 3.2 0.2 - - - -
223D ALA* 1.3 77.0 - - - +
225D GLY* 1.3 56.6 + - - +
227D LEU* 3.3 6.8 + - + +
228D ILE* 2.8 54.8 + - + +
272D LEU* 4.2 13.9 - - + -
291D ILE* 4.7 4.9 - - + -
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Residues in contact with GLY 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 TRP 3.3 4.6 + - - -
222D TRP 3.0 9.3 + - - -
224D LEU* 1.3 79.5 - - - +
226D VAL* 1.3 55.4 + - - +
229D TYR* 3.0 28.1 + - - +
269D LEU* 3.2 17.7 - - - +
272D LEU* 3.9 25.3 - - - +
273D LEU* 3.9 9.1 - - - +
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Residues in contact with VAL 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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203D GLU 3.4 24.9 - - - +
204D TYR* 3.6 24.0 - - + -
222D TRP* 3.5 26.0 - - + +
223D ALA* 3.2 8.4 + - - +
225D GLY* 1.3 74.2 - - - +
227D LEU* 1.3 58.1 + - - +
229D TYR* 3.5 2.1 + - - +
230D GLU* 3.0 28.6 + - - +
236D PRO* 4.5 3.1 - - + -
237D PRO* 3.5 29.7 - - + +
238D PHE* 4.5 2.2 - - + -
273D LEU* 3.4 21.1 - - + -
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Residues in contact with LEU 227 (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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128D MET* 4.7 1.1 - - + -
150D ILE* 4.0 15.9 - - + -
167D LEU* 3.8 22.0 - - + -
168D LYS* 4.1 4.9 - - - -
169D PRO* 3.8 36.1 - - + -
172D LEU* 3.8 27.8 - - + -
204D TYR* 3.4 9.5 - - + +
223D ALA 2.9 13.6 + - - +
224D LEU* 3.5 12.6 - - + +
226D VAL* 1.3 74.1 - - - +
228D ILE* 1.3 59.9 + - - +
230D GLU* 3.3 2.1 + - - +
231D MET* 2.9 57.2 + - + +
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Residues in contact with ILE 228 (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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143D ALA* 4.8 2.0 - - + +
147D ALA* 3.6 32.5 - - + -
224D LEU* 2.8 42.6 + - + +
227D LEU* 1.3 73.6 - - - +
229D TYR* 1.3 61.9 + - - +
231D MET* 3.6 12.5 + - + +
232D ALA* 3.2 23.1 + - + +
265D LEU* 3.5 29.8 - - + -
268D LEU* 4.4 7.6 - - + -
269D LEU* 3.6 12.6 - - + -
272D LEU* 4.4 13.0 - - + -
296D TRP* 4.2 17.3 - - + -
297D PHE* 4.5 2.9 - - + -
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Residues in contact with TYR 229 (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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225D GLY 3.0 17.4 + - - +
226D VAL 3.7 4.5 - - - +
228D ILE* 1.3 77.1 - - - +
230D GLU* 1.3 51.7 + - - +
232D ALA 3.3 0.7 + - - -
233D ALA* 2.7 49.6 + - + +
235D TYR* 3.3 35.2 + + - -
236D PRO 3.8 1.1 - - - -
237D PRO* 3.5 42.7 + - + +
255D VAL* 4.1 2.5 - - + -
256D ARG 2.4 30.8 + - - -
257D PHE* 3.6 27.1 - + - -
258D PRO* 3.5 18.2 - - + +
261D PHE* 3.6 19.7 - + - -
269D LEU* 4.0 6.0 - - + +
273D LEU* 4.8 2.5 - - + -
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Residues in contact with GLU 230 (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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132D LEU* 3.8 9.5 - - + +
133D ARG* 2.8 29.9 + - - +
169D PRO* 3.9 9.8 - - + +
204D TYR* 2.5 29.9 + - - +
226D VAL 3.0 16.9 + - - +
227D LEU 3.8 2.2 - - - +
229D TYR* 1.3 73.5 - - - +
231D MET* 1.3 60.8 + - - +
234D GLY* 2.8 27.9 + - - -
235D TYR* 3.3 22.7 - - - +
236D PRO* 3.5 10.4 - - + +
19J ARG* 2.9 36.2 + - - -
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Residues in contact with MET 231 (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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128D MET* 3.7 41.1 - - - +
132D LEU* 3.7 14.0 - - + +
137D ARG* 3.8 0.9 - - - -
138D PHE* 2.8 42.0 + - + +
143D ALA* 3.3 32.8 - - + +
146D TYR* 3.8 15.7 - - + -
147D ALA* 4.1 10.5 - - + +
227D LEU* 2.9 35.7 + - + +
228D ILE* 3.8 26.7 - - + +
230D GLU* 1.3 77.1 - - - +
232D ALA* 1.3 55.0 + - - +
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Residues in contact with ALA 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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137D ARG* 3.1 29.0 + - - +
138D PHE 3.6 9.6 - - - +
140D GLU* 4.8 7.4 - - + -
143D ALA* 4.5 9.9 - - + -
228D ILE* 3.2 15.9 + - + +
231D MET* 1.3 81.1 - - - +
233D ALA* 1.3 57.6 + - - +
260D HIS* 3.2 8.2 - - + -
261D PHE* 3.6 20.9 - - + -
265D LEU* 3.9 16.2 - - + -
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Residues in contact with ALA 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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137D ARG* 3.8 12.9 - - - +
229D TYR* 2.7 32.1 + - + +
232D ALA* 1.3 73.5 - - - +
234D GLY* 1.3 56.3 + - - +
235D TYR* 3.3 35.7 - - + +
258D PRO* 3.7 25.4 - - + -
260D HIS* 4.4 5.8 + - - -
261D PHE* 3.8 4.9 - - + -
7J TYR* 4.4 5.0 - - - -
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Residues in contact with GLY 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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132D LEU* 4.9 2.0 - - - -
133D ARG* 3.2 21.0 + - - -
136D GLY 3.2 26.0 - - - +
137D ARG* 3.6 6.4 - - - +
230D GLU 2.8 20.7 + - - -
233D ALA* 1.3 72.6 - - - +
235D TYR* 1.3 61.0 + - - +
7J TYR* 3.9 11.4 + - - -
10J PHE* 3.7 7.4 - - - -
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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