Contacts of the helix formed by residues 217 - 234 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C HIS* 3.3 71.2 + - + +
161C ASP* 3.5 24.4 + - - -
162C LEU 4.0 9.0 - - - +
163C ILE* 3.7 17.5 - - + +
191C VAL 4.3 16.6 + - - +
192C LYS* 5.9 0.8 - - - +
193C GLY 6.0 1.3 - - - +
216C ASN* 1.3 77.6 - - + +
218C ALA* 1.3 60.6 + - - +
219C VAL 3.1 0.4 - - - -
220C ASP* 3.0 14.1 + - - +
221C TRP* 3.9 2.6 + - - +
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Residues in contact with ALA 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ASN* 3.0 10.5 + - - +
217C LYS* 1.3 76.7 - - - +
219C VAL* 1.3 59.7 + - - +
220C ASP 3.2 0.2 - - - -
221C TRP* 3.2 22.5 + - - +
222C TRP 3.2 5.7 + - - -
277C LEU* 3.1 35.0 - - + -
280C ARG* 3.0 20.6 + - - +
283C ASN* 3.6 25.2 + - + +
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ILE* 4.1 15.5 - - + -
165C ARG* 4.7 6.5 - - + -
204C TYR 5.0 1.4 - - - +
206C ALA* 3.7 26.4 + - + +
208C GLU* 3.3 20.4 - - - +
209C ILE* 4.0 13.2 - - + -
215C TYR* 3.6 39.9 - - + -
216C ASN 3.2 15.5 - - - +
218C ALA* 1.3 76.7 - - - +
220C ASP* 1.3 65.9 + - - +
222C TRP* 3.6 3.2 + - - +
223C ALA* 3.2 22.3 + - - +
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Residues in contact with ASP 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PHE* 3.3 32.2 - - + -
158C HIS* 2.7 30.3 + - + +
163C ILE* 3.7 9.7 - - - +
164C TYR* 3.0 24.3 + - - +
165C ARG* 2.9 29.9 + - - -
167C LEU* 5.8 0.7 + - - +
217C LYS 3.0 10.3 + - - +
219C VAL* 1.3 82.2 - - - +
221C TRP* 1.3 57.8 + - - +
223C ALA* 3.3 7.6 + - - +
224C LEU 3.0 22.2 + - - -
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Residues in contact with TRP 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C VAL* 3.8 14.1 - - + -
154C PHE* 3.7 33.2 - + + -
155C GLU* 4.3 4.5 - - - -
158C HIS* 3.6 23.4 + + - -
217C LYS* 4.1 12.3 - - - +
218C ALA* 3.2 15.2 + - + +
220C ASP* 1.3 73.6 - - - +
222C TRP* 1.3 65.6 + - - +
224C LEU* 3.4 25.6 + - + +
225C GLY 3.3 14.9 + - - -
272C LEU* 3.6 13.6 - - + +
280C ARG* 4.4 4.0 - - - -
281C PHE 3.5 18.6 - - - +
282C GLY* 3.4 32.1 + - - -
288C VAL* 3.5 35.4 - - + -
291C ILE* 3.3 23.8 - - + -
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Residues in contact with TRP 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLU 5.2 0.2 + - - -
204C TYR 3.8 8.9 + - - -
205C LEU 3.4 12.3 + - - -
206C ALA* 3.6 20.0 - - + -
207C PRO* 3.7 25.8 - - + -
218C ALA 3.2 5.3 + - - -
219C VAL 3.7 7.2 - - - +
221C TRP* 1.3 77.4 - - - +
223C ALA* 1.3 58.7 + - - +
225C GLY* 3.0 18.0 + - - -
226C VAL* 3.2 23.3 + - + +
238C PHE* 3.6 30.1 - + - -
250C ILE* 3.7 24.5 - - + -
272C LEU 3.6 11.2 - - - -
273C LEU* 3.5 47.1 - - + +
274C GLN 3.7 12.6 - - - -
275C VAL* 3.8 5.4 - - + -
280C ARG* 3.7 31.9 - - - +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C LEU* 3.7 25.9 - - + +
204C TYR* 3.7 20.5 - - + +
219C VAL 3.2 12.4 + - - +
220C ASP* 3.5 11.7 - - - +
221C TRP 3.3 0.2 - - - -
222C TRP* 1.3 81.9 - - - +
224C LEU* 1.3 60.7 + - - +
226C VAL* 3.2 9.6 + - - +
227C LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ALA* 4.3 9.4 - - - +
150C ILE* 3.5 35.0 - - + -
151C VAL* 3.8 13.9 - - + -
154C PHE* 4.5 3.1 - - + -
167C LEU* 3.5 11.3 - - + +
220C ASP 3.0 12.7 + - - +
221C TRP* 3.5 38.8 - - + +
222C TRP 3.3 0.2 - - - -
223C ALA* 1.3 76.9 - - - +
225C GLY* 1.3 56.4 + - - +
227C LEU* 3.3 4.1 + - + +
228C ILE* 2.8 53.4 + - + +
272C LEU* 4.2 17.0 - - + -
291C ILE* 4.5 4.5 - - + -
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Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C TRP 3.3 4.4 + - - -
222C TRP 3.0 9.7 + - - -
224C LEU* 1.3 79.8 - - - +
226C VAL* 1.3 54.8 + - - +
229C TYR* 3.0 27.0 + - - +
269C LEU* 3.2 24.6 - - - +
272C LEU* 3.8 18.5 - - - +
273C LEU* 4.1 10.2 - - - +
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Residues in contact with VAL 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLU 3.5 22.4 - - - +
204C TYR* 3.3 30.3 - - + +
222C TRP* 3.5 36.1 - - + +
223C ALA* 3.2 8.7 + - - +
225C GLY* 1.3 75.4 - - - +
227C LEU* 1.3 57.5 + - - +
229C TYR* 3.5 2.6 + - - +
230C GLU* 3.0 28.8 + - - +
236C PRO* 4.5 2.7 - - + -
237C PRO* 3.8 27.4 - - + +
238C PHE* 4.8 1.8 - - + -
273C LEU* 3.7 9.2 - - + -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C MET* 4.5 1.1 - - - -
146C TYR 6.1 0.2 - - - -
147C ALA* 5.8 0.4 - - - -
150C ILE* 4.1 13.9 - - + -
167C LEU* 3.7 22.4 - - + -
168C LYS* 4.1 5.6 - - - -
169C PRO* 3.7 40.6 - - + -
172C LEU* 3.6 26.9 - - + -
204C TYR* 3.5 9.4 - - + +
223C ALA 2.9 17.2 + - - +
224C LEU* 3.5 8.3 - - + +
226C VAL* 1.3 73.9 - - - +
228C ILE* 1.3 60.2 + - - +
230C GLU* 3.3 1.2 + - - +
231C MET* 2.9 55.1 + - + +
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Residues in contact with ILE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ALA* 4.8 1.0 - - + +
147C ALA* 3.9 26.5 - - + -
224C LEU* 2.8 44.1 + - + +
227C LEU* 1.3 71.0 - - - +
229C TYR* 1.3 63.4 + - - +
231C MET* 3.6 13.1 + - + +
232C ALA* 3.1 23.5 + - + +
265C LEU* 3.6 31.2 - - + -
268C LEU* 4.1 14.1 - - + -
269C LEU* 3.7 8.7 - - + -
272C LEU* 3.9 17.7 - - + -
296C TRP* 4.0 14.6 - - + -
297C PHE* 4.7 2.5 - - + -
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Residues in contact with TYR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C GLY 3.0 18.6 + - - +
226C VAL 3.6 4.5 - - - +
228C ILE* 1.3 77.3 - - - +
230C GLU* 1.3 51.6 + - - +
232C ALA 3.2 0.9 + - - -
233C ALA* 2.7 49.2 + - + +
235C TYR* 3.3 35.7 + + - -
236C PRO 3.7 2.2 - - - -
237C PRO* 3.5 44.1 + - + +
255C VAL* 4.1 3.4 - - + -
256C ARG 2.5 31.0 + - - -
257C PHE* 3.6 18.1 - + - -
258C PRO* 3.6 12.8 - - + +
261C PHE* 3.6 16.8 - + - -
269C LEU* 3.9 18.4 - - + +
273C LEU* 4.8 2.7 - - + -
5I THR* 5.3 2.3 + - - -
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Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 3.9 9.4 - - + +
133C ARG* 2.8 30.3 + - - +
169C PRO* 3.9 8.3 - - + +
204C TYR* 2.5 32.5 + - - +
226C VAL 3.0 16.4 + - - +
227C LEU 3.3 1.8 + - - +
229C TYR* 1.3 76.0 - - - +
231C MET* 1.3 56.5 + - - +
234C GLY* 2.8 28.8 + - - -
235C TYR* 3.3 23.8 - - - +
236C PRO* 3.6 12.1 - - + +
19I ARG* 3.1 34.9 + - - -
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Residues in contact with MET 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C MET* 3.7 33.2 - - - +
132C LEU* 3.8 13.1 - - + +
137C ARG* 3.7 2.8 - - - -
138C PHE* 2.8 46.8 + - + +
143C ALA* 3.5 29.4 - - + +
146C TYR* 3.9 22.4 - - - -
147C ALA* 4.3 7.2 - - + +
227C LEU* 2.9 42.8 + - + +
228C ILE* 3.7 20.6 - - + +
230C GLU* 1.3 76.2 - - - +
232C ALA* 1.3 55.2 + - - +
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ARG* 3.1 22.8 + - - +
138C PHE 3.6 13.1 - - - +
140C GLU* 4.7 8.5 - - + -
143C ALA* 4.4 10.5 - - + +
228C ILE* 3.1 18.0 + - + +
231C MET* 1.3 75.9 - - - +
233C ALA* 1.3 59.8 + - - +
260C HIS* 3.3 9.2 - - - -
261C PHE* 3.7 20.0 - - + -
265C LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 3.7 13.4 - - - +
229C TYR* 2.7 30.2 + - + +
232C ALA* 1.3 75.2 - - - +
234C GLY* 1.3 55.4 + - - +
235C TYR* 3.3 31.5 + - + +
258C PRO* 3.7 14.6 - - + -
260C HIS* 4.3 6.7 + - - -
261C PHE* 3.6 19.7 - - + -
7I TYR* 4.6 4.3 - - - -
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Residues in contact with GLY 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 4.5 2.2 - - - -
133C ARG* 3.4 19.8 + - - -
136C GLY 3.2 26.4 - - - +
137C ARG* 3.6 5.1 - - - +
230C GLU 2.8 20.8 + - - -
233C ALA* 1.3 73.0 - - - +
235C TYR* 1.3 62.0 + - - +
7I TYR* 3.6 16.9 + - - -
10I PHE* 3.6 3.5 - - - -
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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) + - + + + + + -
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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