Contacts of the helix formed by residues 209 - 228 (chain C) in PDB entry 4BPU
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 HIS 209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C TYR* 3.9 28.0 - + - -
207C LYS 3.8 4.4 + - - -
208C ILE* 1.3 72.1 - - - +
210C PRO* 1.3 82.3 - - + +
211C PHE* 3.3 14.1 + - - +
212C ILE* 2.9 32.7 + - + +
213C ARG 3.2 8.0 + - - -
168D ALA 3.7 6.4 + - - +
169D SER* 3.5 23.9 - - - +
198D ARG* 3.3 49.4 - - + +
200D VAL 2.8 26.5 + - - -
201D TYR* 4.8 4.9 - + - -
202D LEU 5.1 1.3 - - - -
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Residues in contact with PRO 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE 3.5 4.7 - - - +
209C HIS* 1.3 93.7 - - + +
211C PHE* 1.3 56.8 + - - +
213C ARG* 3.2 20.6 + - + +
214C LYS* 2.8 45.6 + - - +
165D GLU* 3.9 29.8 - - - +
168D ALA* 3.9 7.4 - - + -
169D SER* 3.5 21.8 - - - +
201D TYR* 4.0 17.0 - - + -
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Residues in contact with PHE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 4.5 8.1 - - + -
142C ILE* 6.0 0.4 - - + -
144C ARG* 3.3 24.9 + - - +
145C ALA* 3.5 22.7 - - + -
149C ASP* 3.7 7.6 + - - +
188C TYR* 3.5 46.4 + + + +
189C LEU* 3.6 29.8 - - + -
191C LEU* 4.5 6.1 - - + -
209C HIS* 3.1 12.5 + - + +
210C PRO* 1.3 77.7 - - - +
212C ILE* 1.3 65.3 + - + +
214C LYS* 3.6 2.0 + - - +
215C SER* 2.8 49.7 + - - -
302C PHE* 3.8 26.2 - + - -
198D ARG* 4.2 3.6 - - - -
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LEU* 3.5 44.6 - - + -
204C LEU* 4.0 18.6 - - + -
207C LYS 6.1 0.2 - - - +
208C ILE* 3.9 7.6 - - + -
209C HIS* 2.9 21.9 + - + +
211C PHE* 1.3 83.4 - - + +
213C ARG* 1.3 61.1 + - - +
215C SER* 3.2 4.8 + - - -
216C ILE* 2.8 51.9 + - + +
298C LEU* 3.9 11.7 - - + -
198D ARG* 3.9 18.4 - - - +
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Residues in contact with ARG 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 3.7 22.2 + - + +
209C HIS 3.2 4.1 + - - +
210C PRO* 3.2 28.5 + - - +
212C ILE* 1.3 78.7 - - - +
214C LYS* 1.3 79.8 + - - +
216C ILE* 3.1 10.8 + - + +
217C ASN* 2.9 46.5 + - - +
294C TRP* 6.1 5.6 - - + -
164D GLN 6.1 0.4 - - - -
165D GLU* 3.2 33.1 + - - +
168D ALA* 4.7 9.9 - - - +
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Residues in contact with LYS 214 (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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144C ARG* 3.4 45.3 - - - +
148C GLU* 4.5 9.4 + - - +
149C ASP* 4.5 7.5 + - - +
210C PRO* 2.8 31.1 + - - +
211C PHE* 4.1 0.9 - - - +
213C ARG* 1.3 96.5 - - - +
215C SER* 1.3 60.8 + - - +
217C ASN* 3.7 11.2 + - - +
218C ILE* 3.3 26.9 + - - +
165D GLU* 4.6 3.4 + - - -
201D TYR* 4.2 21.4 + - - -
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Residues in contact with SER 215 (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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141C ILE* 3.4 29.9 + - - +
144C ARG* 4.9 1.8 + - - +
211C PHE* 2.8 34.6 + - - -
212C ILE* 3.6 5.2 - - - -
213C ARG 3.2 0.2 - - - -
214C LYS* 1.3 74.7 - - - +
216C ILE* 1.3 65.3 + - - +
218C ILE* 3.1 7.2 + - - +
219C ILE* 2.9 28.0 + - - +
298C LEU* 5.0 1.6 - - - -
302C PHE* 3.8 27.5 - - - -
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Residues in contact with ILE 216 (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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204C LEU* 4.8 1.6 - - + -
208C ILE* 4.6 4.0 - - + -
212C ILE* 2.8 41.6 + - + +
213C ARG* 3.1 11.9 + - + +
215C SER* 1.3 76.7 - - - +
217C ASN* 1.3 63.8 + - - +
219C ILE* 2.9 10.5 + - - +
220C LYS* 2.8 36.1 + - + +
294C TRP* 3.7 62.6 - - + +
297C MET* 4.7 6.1 - - + -
298C LEU* 4.0 22.6 - - + +
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Residues in contact with ASN 217 (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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213C ARG* 2.9 39.5 + - - +
214C LYS* 4.0 10.4 - - - +
216C ILE* 1.3 80.4 - - - +
218C ILE* 1.3 63.3 + - + +
220C LYS* 3.6 32.1 + - - +
221C LYS* 3.7 7.1 + - - +
294C TRP* 6.1 0.9 - - - -
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Residues in contact with ILE 218 (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 MET* 4.8 4.5 - - - +
140C ARG* 3.8 64.6 - - + +
141C ILE* 4.1 18.2 - - + -
144C ARG* 3.9 20.9 - - + +
214C LYS 3.3 16.1 + - - +
215C SER* 3.1 7.5 + - - +
217C ASN* 1.3 77.0 - - + +
219C ILE* 1.3 65.9 + - - +
221C LYS* 3.3 10.7 + - + +
222C TYR* 3.1 24.1 - - + -
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Residues in contact with ILE 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C MET* 4.4 11.9 - - + -
141C ILE* 3.7 26.7 - - + -
215C SER 2.9 15.4 + - - +
216C ILE* 2.9 8.0 + - - +
218C ILE* 1.3 78.5 - - - +
220C LYS* 1.3 57.6 + - - +
222C TYR* 3.0 4.2 + - - +
223C PHE* 2.8 29.1 + - + +
297C MET* 4.1 25.8 - - + +
298C LEU* 3.8 28.9 - - + -
301C CYS* 3.6 41.1 - - + -
302C PHE* 4.0 7.4 - - - +
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Residues in contact with LYS 220 (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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216C ILE* 2.8 17.8 + - + +
217C ASN* 3.6 29.7 + - - +
219C ILE* 1.3 74.0 - - - +
221C LYS* 1.3 62.3 + - - +
222C TYR 3.1 1.0 + - - -
223C PHE* 3.5 9.2 + - - +
224C GLU* 4.6 4.7 + - - +
293C GLU* 4.6 9.9 - - - -
294C TRP* 3.9 32.6 - - - +
297C MET* 3.6 21.7 - - + +
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Residues in contact with LYS 221 (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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140C ARG* 4.6 15.6 - - - +
217C ASN 3.7 6.8 + - - +
218C ILE* 3.3 14.2 + - - +
219C ILE 3.1 1.4 - - - -
220C LYS* 1.3 77.7 - - - +
222C TYR* 1.3 88.7 + - + +
224C GLU 5.6 0.2 - - - -
340C ASP* 3.9 10.1 + - - -
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Residues in contact with TYR 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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133C THR* 3.9 22.2 - - + -
136C THR* 3.9 13.0 - - + -
137C MET* 3.7 30.3 - - + -
140C ARG* 2.9 41.8 + - - -
218C ILE* 3.1 28.9 - - + -
219C ILE 3.0 2.5 + - - +
221C LYS* 1.3 100.8 + - + +
223C PHE* 1.3 66.6 + - - +
224C GLU 3.3 2.5 + - - -
225C GLU* 3.4 7.1 + - - +
226C TYR* 3.0 23.6 + - - +
340C ASP* 2.4 31.3 + - - -
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Residues in contact with PHE 223 (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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219C ILE* 2.8 17.5 + - + +
220C LYS* 3.5 5.8 + - - +
222C TYR* 1.3 77.4 - - - +
224C GLU* 1.3 63.1 + - - +
226C TYR* 4.6 3.1 - - - -
227C ALA* 2.8 59.3 + - + +
228C LEU* 3.7 8.9 + - + -
233C ILE* 3.9 16.8 - - + -
269C TRP* 3.5 44.9 - + - -
296C ILE* 5.1 1.6 - - + -
297C MET* 3.8 48.9 - - + -
300C TYR* 4.6 4.5 - - + -
301C CYS* 3.6 24.0 - - - -
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Residues in contact with GLU 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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220C LYS 4.6 4.2 + - - +
222C TYR 3.4 0.6 - - - -
223C PHE* 1.3 79.3 - - + +
225C GLU* 1.3 62.0 + - - +
228C LEU* 3.1 43.6 + - + +
229C VAL* 3.3 7.1 + - + +
266C LEU* 3.8 28.9 - - + +
269C TRP* 6.2 0.2 - - + -
270C GLU* 5.7 1.2 - - - +
273C LYS* 5.8 1.9 + - - -
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Residues in contact with GLU 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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222C TYR* 3.4 6.1 + - - +
223C PHE 3.4 0.2 - - - -
224C GLU* 1.3 79.7 - - - +
226C TYR* 1.3 58.7 + - - +
229C VAL* 3.3 17.5 - - + +
230C ASN* 3.1 47.7 + - - +
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Residues in contact with TYR 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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118C VAL 4.0 12.6 + - - -
119C ARG* 4.6 0.5 - - - +
130C LYS 3.5 25.8 - - - -
131C CYS* 4.3 3.4 - - - -
133C THR* 3.7 28.3 - - + -
134C LEU* 3.2 42.8 - - + +
137C MET* 4.1 6.5 - - + -
222C TYR 3.0 19.6 + - - +
223C PHE* 4.7 0.9 - - - -
225C GLU* 1.3 79.2 - - - +
227C ALA* 1.3 71.1 + - + +
230C ASN* 3.6 7.7 - - - +
231C GLN* 3.0 53.7 + - + +
233C ILE* 5.9 0.4 - - + -
300C TYR* 4.1 7.9 + + + -
301C CYS* 3.8 27.4 - - - -
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Residues in contact with ALA 227 (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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223C PHE* 2.8 56.3 + - + +
226C TYR* 1.3 87.7 - - + +
228C LEU* 1.3 57.9 + - - +
229C VAL 3.6 0.2 - - - -
231C GLN* 4.0 4.9 - - - -
232C ASP 2.9 20.4 + - - -
233C ILE* 3.0 27.2 + - + +
300C TYR* 5.7 1.1 - - + -
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Residues in contact with LEU 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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223C PHE* 4.1 15.7 - - + -
224C GLU* 3.1 37.7 + - + +
227C ALA* 1.3 79.1 - - - +
229C VAL* 1.3 60.5 + - - +
232C ASP* 3.5 10.5 - - - +
233C ILE* 4.1 17.3 - - + -
234C LEU* 4.2 6.1 - - + -
265C SER* 3.4 29.9 - - - +
266C LEU* 4.0 28.2 - - + +
269C TRP* 3.6 48.0 - - + -
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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