Contacts of the helix formed by residues 217 - 234 (chain E) in PDB entry 1L3R
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E HIS* 3.5 60.7 - - + +
161E ASP* 3.6 14.5 + - - +
162E LEU 3.4 20.7 + - - +
163E ILE* 3.7 17.1 - - + +
191E VAL* 3.2 30.9 + - - +
192E LYS* 4.8 4.9 + - - +
193E GLY 5.6 1.0 + - - -
216E ASN* 1.3 78.4 - - + +
218E ALA* 1.3 56.5 + - - +
219E VAL 3.0 0.7 - - - -
220E ASP* 2.9 26.8 + - - +
221E TRP* 3.6 6.4 + - + +
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Residues in contact with ALA 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLU* 4.2 2.0 - - - +
216E ASN* 2.7 23.1 + - - +
217E LYS* 1.3 74.0 - - - +
219E VAL* 1.3 61.0 + - - +
221E TRP* 3.1 16.1 + - - +
222E TRP 3.0 17.3 + - - -
277E LEU* 3.8 17.3 - - + -
280E ARG* 3.1 25.3 + - - +
283E ASN* 3.8 22.5 + - + +
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Residues in contact with VAL 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E ILE* 3.9 18.4 - - + -
165E ARG* 4.5 7.4 - - + -
204E TYR 4.9 1.2 - - - +
206E ALA* 4.0 13.1 - - + +
208E GLU* 3.5 17.5 - - - +
209E ILE* 3.8 24.9 - - + -
215E TYR* 3.4 35.9 - - + -
216E ASN 3.0 12.1 + - - +
218E ALA* 1.3 77.9 - - - +
220E ASP* 1.3 66.6 + - - +
222E TRP* 3.3 3.6 + - - +
223E ALA* 2.9 28.1 + - - +
280E ARG* 4.1 0.2 - - - +
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Residues in contact with ASP 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E PHE* 3.4 28.4 - - + -
158E HIS* 2.9 29.0 + - + +
163E ILE* 3.7 9.3 - - - +
164E TYR* 2.9 31.6 + - - +
165E ARG* 2.9 28.0 + - - -
167E LEU* 5.5 0.9 - - - +
217E LYS 2.9 11.2 + - - +
219E VAL* 1.3 84.0 - - - +
221E TRP* 1.3 56.9 + - - +
223E ALA* 3.2 8.5 + - - +
224E LEU* 2.9 22.3 + - - +
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Residues in contact with TRP 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E VAL* 3.8 19.5 - - + -
154E PHE* 3.6 31.2 - + + -
155E GLU* 4.5 1.8 - - - -
158E HIS* 3.5 28.5 + + - -
217E LYS* 3.6 15.1 + - + +
218E ALA* 3.1 12.9 + - - +
220E ASP* 1.3 73.8 - - - +
222E TRP* 1.3 66.8 + - - +
224E LEU* 3.2 27.2 + - + +
225E GLY 3.1 15.8 + - - -
272E LEU* 3.7 14.7 - - + +
280E ARG* 4.7 3.4 - - - -
281E PHE 3.6 18.8 - - - +
282E GLY* 3.5 31.4 + - - -
283E ASN* 5.2 0.2 - - - -
288E VAL* 3.9 27.6 - - + -
291E ILE* 3.4 23.8 - - + -
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Residues in contact with TRP 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E GLU 5.2 0.8 + - - -
204E TYR 3.6 16.1 + - - -
205E LEU 3.4 11.3 + - - -
206E ALA* 3.6 12.8 - - + -
207E PRO* 3.5 38.8 - - + -
218E ALA 3.0 5.1 + - - -
219E VAL 3.6 7.4 - - - +
220E ASP 3.2 0.2 - - - -
221E TRP* 1.3 76.0 - - - +
223E ALA* 1.3 68.2 + - - +
225E GLY* 2.9 12.5 + - - -
226E VAL* 3.2 22.3 + - + +
238E PHE* 3.7 32.4 - + - -
250E ILE* 3.9 14.8 - - + +
253E GLY* 5.3 1.6 - - - -
272E LEU 3.8 10.3 - - - -
273E LEU* 3.4 45.9 - - + +
274E GLN 3.7 8.3 - - - -
275E VAL* 4.0 5.4 - - + -
280E ARG* 3.6 29.5 - - - +
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Residues in contact with ALA 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ARG 6.5 0.7 - - - -
167E LEU* 3.8 25.1 - - + +
204E TYR* 3.6 25.4 - - + +
219E VAL 2.9 15.1 + - - +
220E ASP* 3.4 13.5 - - - +
222E TRP* 1.3 83.0 - - - +
224E LEU* 1.3 62.2 + - - +
226E VAL* 3.1 7.6 + - - +
227E LEU* 3.0 21.0 + - - +
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Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ALA* 4.6 6.1 - - - +
150E ILE* 4.0 26.9 - - + -
151E VAL* 3.7 26.5 - - + +
154E PHE* 4.6 2.2 - - + -
167E LEU* 3.6 8.9 - - + +
220E ASP 2.9 12.9 + - - +
221E TRP* 3.4 33.2 - - + +
222E TRP 3.1 0.2 - - - -
223E ALA* 1.3 76.2 - - - +
225E GLY* 1.3 64.2 + - - +
227E LEU* 3.3 10.2 + - + +
228E ILE* 2.9 49.9 + - + +
272E LEU* 4.3 9.9 - - + -
291E ILE* 4.8 4.5 - - + -
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Residues in contact with GLY 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E TRP 3.1 6.7 + - - -
222E TRP 2.9 9.4 + - - -
224E LEU* 1.3 77.6 - - - +
226E VAL* 1.3 61.0 + - - +
229E TYR* 3.0 24.3 + - - +
269E LEU* 3.5 10.4 - - - +
272E LEU* 3.9 24.0 - - - +
273E LEU* 3.7 16.6 - - - +
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Residues in contact with VAL 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E GLU 3.6 23.8 - - - +
204E TYR* 3.5 25.8 - - + +
222E TRP* 3.4 37.5 - - + +
223E ALA* 3.1 8.0 + - - +
225E GLY* 1.3 76.2 - - - +
227E LEU* 1.3 52.6 + - - +
229E TYR* 3.3 2.1 + - - +
230E GLU* 2.8 34.1 + - - +
236E PRO* 4.6 4.5 - - + -
237E PRO* 3.6 29.3 - - + +
238E PHE* 4.9 1.6 - - + -
273E LEU* 3.8 7.0 - - + -
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Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E MET* 4.3 7.4 - - + -
147E ALA* 5.7 0.2 - - - -
150E ILE* 4.1 17.3 - - + -
167E LEU* 4.0 19.5 - - + -
168E LYS* 4.4 2.9 - - - -
169E PRO* 3.8 36.1 - - + -
172E LEU* 3.8 28.5 - - + -
204E TYR* 3.4 11.3 - - + +
223E ALA 3.0 13.1 + - - +
224E LEU* 3.6 12.1 - - + +
226E VAL* 1.3 76.3 - - - +
228E ILE* 1.3 57.8 + - - +
230E GLU* 3.2 1.4 + - - +
231E MET* 2.8 52.4 + - + +
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Residues in contact with ILE 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ALA* 4.8 1.0 - - + +
147E ALA* 3.9 22.7 - - + -
224E LEU* 2.9 49.5 + - + +
225E GLY 3.9 3.4 - - - +
227E LEU* 1.3 75.2 - - - +
229E TYR* 1.3 64.9 + - - +
231E MET* 3.7 10.6 - - + +
232E ALA* 3.0 24.1 + - + +
265E LEU* 3.6 31.0 - - + -
268E LEU* 4.3 12.6 - - + -
269E LEU* 3.9 6.5 - - + -
272E LEU* 4.0 16.4 - - + -
296E TRP* 4.2 14.8 - - + -
297E PHE* 4.7 3.4 - - + -
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Residues in contact with TYR 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E GLY 3.0 18.6 + - - +
226E VAL* 3.5 4.3 - - - +
228E ILE* 1.3 76.8 - - - +
230E GLU* 1.3 53.4 + - - +
232E ALA 3.7 0.2 - - - -
233E ALA* 2.7 49.1 + - + +
235E TYR* 3.3 37.1 + + - -
236E PRO 3.6 2.2 - - - -
237E PRO* 3.4 44.4 + - + +
255E VAL* 4.0 4.5 - - + -
256E ARG 2.6 29.8 + - - -
257E PHE* 3.8 17.7 - + - -
258E PRO* 3.8 9.5 - - + +
261E PHE* 3.8 8.6 - + - -
269E LEU* 4.0 27.5 - - + +
273E LEU* 4.7 3.8 - - + -
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Residues in contact with GLU 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 4.0 10.1 - - + +
133E ARG* 2.9 33.1 + - - +
169E PRO* 3.9 9.2 - - + +
204E TYR* 2.6 30.9 + - - +
226E VAL 2.8 20.2 + - - +
227E LEU 3.8 2.0 - - - +
229E TYR* 1.3 72.9 - - - +
231E MET* 1.3 58.2 + - - +
234E GLY* 2.8 27.7 + - - -
235E TYR* 3.3 25.4 - - - +
236E PRO* 3.7 13.1 - - + +
19I ARG* 3.1 27.7 + - - -
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Residues in contact with MET 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E MET* 3.6 41.1 - - - +
132E LEU* 3.7 11.9 - - + +
137E ARG* 3.6 4.2 - - - -
138E PHE* 2.8 45.0 + - + -
143E ALA* 3.7 28.3 - - + +
146E TYR* 3.9 15.9 - - + -
147E ALA 4.2 8.5 - - - +
227E LEU* 2.8 43.9 + - + +
228E ILE* 3.7 21.3 - - + +
230E GLU* 1.3 75.7 - - + +
232E ALA* 1.3 56.1 + - - +
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Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ARG* 3.3 22.5 + - - +
138E PHE 3.6 13.7 - - - +
140E GLU* 4.8 8.3 - - + -
143E ALA* 4.4 9.8 - - + +
228E ILE* 3.0 17.3 + - + +
231E MET* 1.3 79.0 - - - +
233E ALA* 1.3 57.2 + - - +
260E HIS* 3.4 9.8 - - + -
261E PHE* 3.6 19.7 - - + -
265E LEU* 3.9 16.6 - - + -
296E TRP* 5.8 0.2 - - + -
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Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ARG* 3.9 12.1 - - - +
229E TYR* 2.7 42.8 + - + +
232E ALA* 1.3 74.4 - - - +
234E GLY* 1.3 57.8 + - - +
235E TYR* 3.3 25.1 - - + +
258E PRO* 3.7 14.4 - - + -
260E HIS* 4.5 4.4 + - - -
261E PHE* 3.6 18.2 - - + -
7I TYR* 5.8 1.6 - - - -
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Residues in contact with GLY 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 4.9 1.3 - - - -
133E ARG* 4.0 16.6 + - - -
136E GLY 3.0 27.7 - - - +
137E ARG* 3.8 4.2 - - - +
230E GLU* 2.8 21.9 + - - -
232E ALA 3.6 1.2 - - - -
233E ALA* 1.3 74.2 - - - +
235E TYR* 1.3 63.0 + - - +
7I TYR* 5.6 6.0 - - - -
10I PHE* 4.0 8.8 - - - -
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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