Contacts of the helix formed by residues 208 - 225 (chain C) in PDB entry 7CE1
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 PHE 208 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LYS* 3.6 60.8 - - + -
144C ILE 4.0 3.1 - - - +
145C GLU* 4.2 7.6 - - + -
146C PRO* 4.1 2.4 - - - +
205C PRO* 3.1 30.1 + - + +
206C SER 3.1 7.8 - - - +
207C ARG* 1.3 117.2 - - - +
209C ALA* 1.3 65.1 + - - +
210C PHE* 3.5 27.1 - + + -
211C HIS* 3.3 18.4 - - - +
212C ASP* 4.3 2.3 + - - +
238C GLU* 3.6 25.1 - - + -
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 3.0 21.5 + - + +
146C PRO* 3.8 27.0 - - + +
166C ARG 3.3 23.8 - - - +
167C SER* 5.2 0.2 - - - -
208C PHE* 1.3 68.2 - - - +
210C PHE* 1.3 53.8 + - - +
211C HIS 3.1 5.4 - - - -
212C ASP* 3.0 20.8 + - - +
213C HIS* 2.6 31.5 + - + -
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Residues in contact with PHE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LYS* 5.8 6.7 - - + -
144C ILE 5.3 2.9 - - - -
177C ASP* 5.2 7.6 - - - +
180C ASN* 3.1 32.2 + - - +
204C PRO* 3.3 30.2 - - + +
208C PHE* 3.6 30.7 - + + -
209C ALA* 1.3 75.2 - - - +
211C HIS* 1.3 65.9 + - - +
212C ASP 3.2 0.2 - - - -
213C HIS* 3.2 16.0 + - + +
214C ALA* 2.9 25.9 + - + +
237C ILE* 4.0 12.3 - - + -
264C ILE* 3.8 18.2 - - + -
292C LYS* 4.7 5.8 - - - -
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Residues in contact with HIS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.2 20.2 - - + +
204C PRO* 2.8 35.8 + - + +
205C PRO 3.3 12.6 - - - +
206C SER* 3.3 28.7 - - - -
208C PHE 3.3 16.5 + - - +
209C ALA 3.1 0.2 - - - -
210C PHE* 1.3 83.1 - - - +
212C ASP* 1.3 83.8 + - - +
214C ALA* 3.9 1.9 - - - +
215C ARG* 3.3 35.2 + - + +
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Residues in contact with ASP 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C PRO* 4.5 14.2 - - - +
206C SER* 4.4 5.4 - - - +
208C PHE 4.4 4.8 - - - +
209C ALA 3.0 11.9 + - - +
211C HIS* 1.3 96.3 - - - +
213C HIS* 1.3 65.5 + - + +
215C ARG* 4.9 1.6 - - - +
216C LYS* 3.3 26.0 + - - +
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Residues in contact with HIS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 3.0 53.5 + - + +
177C ASP* 4.5 2.9 + - - -
180C ASN* 4.0 13.5 - - + -
181C GLU* 3.2 36.0 - - + +
209C ALA* 2.6 47.7 + - + -
210C PHE* 3.2 13.0 - - + +
211C HIS 3.3 0.4 - - - -
212C ASP* 1.3 81.0 - - + +
214C ALA* 1.3 61.8 + - - +
216C LYS* 4.0 2.4 - - - +
217C GLY 3.3 8.0 + - - -
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Residues in contact with ALA 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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180C ASN* 3.7 16.2 - - + +
184C ALA* 3.1 11.6 - - + +
201C ILE* 4.7 4.9 - - + -
203C VAL* 5.2 2.0 - - + -
204C PRO* 5.0 3.6 - - + -
210C PHE 2.9 16.6 + - - +
211C HIS* 3.9 4.7 - - - +
213C HIS* 1.3 76.7 - - - +
215C ARG* 1.3 51.5 + - - +
217C GLY 3.1 3.1 + - - -
218C PHE* 2.6 32.4 + - - +
264C ILE* 3.9 32.3 - - + -
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 3.3 28.3 + - - +
203C VAL* 4.4 15.7 - - + +
211C HIS* 3.3 28.7 + - + +
212C ASP* 4.9 1.8 - - - +
214C ALA* 1.3 76.5 - - - +
216C LYS* 1.3 61.2 + - - +
218C PHE* 3.5 11.2 - - + -
219C THR* 2.9 49.4 + - + +
229C GLU* 2.3 41.3 + - - -
231C PRO* 5.8 3.0 - - - +
232C LEU 5.6 4.2 + - - -
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Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLU* 3.2 36.8 + - - +
212C ASP 3.3 20.3 + - - +
213C HIS* 4.0 2.0 - - - +
214C ALA 3.3 0.2 - - - -
215C ARG* 1.3 76.8 - - - +
217C GLY* 1.3 62.8 + - - +
219C THR* 3.2 6.7 + - - -
220C ARG* 3.1 40.3 + - + +
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Residues in contact with GLY 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLU* 3.5 31.6 - - - -
185C TYR* 3.2 23.5 - - - +
213C HIS 3.3 4.9 + - - -
214C ALA 3.1 8.1 + - - -
216C LYS* 1.3 81.7 - - - +
218C PHE* 1.3 59.2 + - - +
220C ARG* 3.6 5.7 + - - -
221C GLY 3.2 15.8 + - - -
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Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA* 3.6 9.4 - - + +
188C VAL* 3.4 27.6 - - + +
199C ILE* 3.7 34.5 - - + -
201C ILE* 3.4 45.8 - - + -
214C ALA 2.6 20.2 + - - +
215C ARG* 3.5 17.0 - - + +
216C LYS 3.2 0.2 - - - -
217C GLY* 1.3 74.7 - - - +
219C THR* 1.3 66.5 + - + +
221C GLY* 3.2 4.0 + - - -
222C ILE* 2.9 44.2 + - + +
229C GLU* 3.3 29.4 - - + -
262C VAL* 4.5 5.8 - - + -
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Residues in contact with THR 219 (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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215C ARG* 2.9 41.0 + - + +
216C LYS* 3.2 9.2 + - - -
218C PHE* 1.3 78.8 - - + +
220C ARG* 1.3 68.6 + - - +
221C GLY 3.1 1.6 - - - -
222C ILE* 3.8 9.5 - - + +
223C ARG* 3.0 25.5 + - - +
229C GLU* 4.8 8.5 - - - +
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Residues in contact with ARG 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLU* 3.4 32.5 + - - +
182C ALA* 5.3 2.6 - - - +
185C TYR* 3.7 43.6 - - + +
216C LYS* 3.1 35.8 + - + +
217C GLY* 3.8 5.7 - - - +
218C PHE 3.4 0.2 - - - -
219C THR* 1.3 78.5 + - - +
221C GLY* 1.3 57.0 + - - +
223C ARG* 3.3 35.1 - - - +
224C ASP* 2.7 36.2 + - - +
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Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.6 14.8 - - - -
188C VAL* 3.4 20.1 - - - +
217C GLY 3.2 9.5 + - - -
218C PHE 3.4 5.2 - - - -
219C THR 3.1 0.8 - - - -
220C ARG* 1.3 79.3 - - - +
222C ILE* 1.3 60.5 + - - +
225C PHE* 2.9 38.4 + - - +
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Residues in contact with ILE 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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188C VAL* 3.7 20.0 - - + -
199C ILE* 4.1 15.5 - - + -
218C PHE* 2.9 48.4 + - + +
219C THR* 3.2 10.2 + - + +
221C GLY* 1.3 77.1 - - - +
223C ARG* 1.3 60.3 - - - +
226C GLY* 3.8 1.0 + - - -
227C VAL* 3.0 56.8 + - + +
228C SER* 4.1 16.8 - - - +
229C GLU* 4.1 11.7 - - + +
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Residues in contact with ARG 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 THR 3.0 13.3 + - - +
220C ARG* 3.3 39.0 + - - +
222C ILE* 1.3 79.7 - - - +
224C ASP* 1.3 84.8 + - - +
225C PHE 3.4 0.5 + - - -
226C GLY* 3.7 7.6 + - - -
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Residues in contact with ASP 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.3 21.9 + - - +
220C ARG* 2.7 26.4 + - - +
223C ARG* 1.3 106.4 + - - +
225C PHE* 1.3 81.9 + - + +
226C GLY 3.6 0.4 + - - -
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.5 38.4 - + - -
188C VAL* 4.3 2.2 - - + -
189C GLU* 3.4 51.8 - - + -
192C ALA* 4.0 22.1 - - + +
221C GLY* 2.9 31.8 + - - +
224C ASP* 1.3 86.9 - - + +
226C GLY* 1.3 63.2 + - - +
227C VAL* 3.2 14.5 + - + +
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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
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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