Contacts of the helix formed by residues 209 - 224 (chain C) in PDB entry 3ER8
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 ASN 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLY* 6.5 0.9 - - - -
111C ILE* 3.3 32.3 - - - +
175C TYR* 4.5 3.5 + - - -
182C SER* 3.6 29.0 - - - +
207C GLN* 3.0 9.0 + - - +
208C THR* 1.3 85.4 + - - +
210C SER* 1.3 56.4 + - - +
211C ARG* 2.5 20.3 + - - -
212C THR* 2.8 23.6 + - - +
213C PHE* 3.0 13.0 + - - +
256C ASN* 4.0 5.0 - - - +
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLN* 3.6 13.7 + - - +
209C ASN* 1.3 76.0 + - - +
211C ARG* 1.3 56.0 + - - +
212C THR 3.5 0.2 - - - -
213C PHE* 3.6 13.7 - - - -
214C LEU* 3.2 28.8 + - - +
241C MET* 5.2 3.3 - - - +
254C SER* 3.0 32.1 + - - -
255C PHE 3.8 0.7 + - - -
256C ASN* 3.2 32.5 + - - +
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 3.0 41.1 + - - -
86B GLY* 5.1 12.2 + - - +
88B ILE* 3.4 33.3 - - + +
99C GLU* 3.7 16.1 + - - -
103C VAL* 5.1 5.1 - - - +
209C ASN 2.5 8.8 + - - -
210C SER* 1.3 75.0 + - - +
212C THR* 1.3 72.5 + - - +
213C PHE 3.2 0.2 - - - -
214C LEU* 4.5 1.4 - - - +
215C ILE* 3.0 54.8 + - + +
231C LEU* 5.2 0.4 - - + +
241C MET* 4.1 23.1 - - + -
256C ASN* 4.6 5.2 + - - +
470C ILE* 5.4 1.3 - - + -
479C PHE* 5.9 2.0 - - - -
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Residues in contact with THR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 4.7 10.4 - - + +
107C THR* 3.3 44.2 - - + +
111C ILE* 3.7 13.5 - - + -
209C ASN* 2.8 15.9 + - - +
211C ARG* 1.3 89.8 + - - +
213C PHE* 1.3 68.2 + - - +
215C ILE* 3.4 3.0 + - - +
216C ASP* 3.2 27.1 + - - +
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Residues in contact with PHE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 4.3 11.2 - - + -
112C LEU* 4.7 9.9 - - + -
172C MET* 3.5 26.2 - - - -
175C TYR* 3.6 37.2 - + - +
205C ILE* 4.2 5.4 - - + -
207C GLN* 2.7 43.5 - - - +
209C ASN* 3.0 13.0 + - - +
210C SER* 3.6 11.4 - - - +
212C THR* 1.3 81.9 - - - +
214C LEU* 1.3 97.2 + - + +
215C ILE 3.0 0.5 + - - -
216C ASP* 3.2 10.4 + - - +
217C LEU* 3.3 27.3 + - + -
252C ILE* 5.2 4.3 - - + -
253C ASP 5.2 1.1 - - - -
254C SER* 5.0 0.9 - - - -
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Residues in contact with LEU 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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210C SER 3.2 17.4 + - - +
211C ARG* 4.5 1.8 - - - +
213C PHE* 1.3 106.0 - - + +
215C ILE* 1.3 63.8 + - - +
217C LEU* 3.5 1.8 + - - +
218C ALA* 3.1 21.1 + - - +
231C LEU* 3.7 23.3 - - + -
241C MET* 3.0 51.1 - - + +
242C VAL* 3.8 4.0 - - - +
243C ILE* 3.6 27.5 - - + +
252C ILE* 4.3 10.3 - - + +
253C ASP 4.6 0.9 - - - +
254C SER* 4.3 12.1 - - - -
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Residues in contact with ILE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLU* 6.2 0.4 - - - -
100C LEU* 3.7 20.6 - - + -
103C VAL* 3.5 39.5 - - + -
211C ARG* 3.0 42.0 + - + +
212C THR* 3.7 4.3 - - - +
213C PHE 3.0 1.0 + - - -
214C LEU* 1.3 76.0 - - - +
216C ASP* 1.3 67.3 + - - +
218C ALA* 2.7 19.9 + - - +
219C PHE* 2.9 36.2 + - + +
231C LEU* 4.3 14.4 - - + -
470C ILE* 4.6 9.6 - - + -
472C ILE* 5.9 0.7 - - + -
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 3.2 26.4 - - - +
104C LEU* 3.3 13.0 - - - +
107C THR* 2.9 20.1 + - - -
108C TYR* 4.2 15.4 + - + -
111C ILE* 3.5 18.4 - - + +
112C LEU* 3.6 22.9 - - + +
212C THR 3.2 13.0 + - - +
213C PHE 3.2 6.8 + - - +
215C ILE* 1.3 78.2 - - - +
217C LEU* 1.3 57.3 + - - +
219C PHE* 3.1 10.4 + - - +
220C LEU* 2.9 25.8 + - - +
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Residues in contact with LEU 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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112C LEU* 3.7 13.3 - - + +
168C VAL* 4.7 11.2 - - + -
171C LEU* 3.6 31.0 - - + -
172C MET* 5.7 2.2 - - + -
213C PHE* 3.3 31.2 + - + +
214C LEU 3.9 6.7 - - - +
215C ILE 3.0 1.0 + - - -
216C ASP* 1.3 78.6 - - - +
218C ALA* 1.3 57.7 + - - +
220C LEU* 3.9 9.6 - - + -
221C ILE* 2.9 42.8 + - + +
243C ILE* 4.0 8.1 - - + -
252C ILE* 3.5 31.9 - - + -
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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
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214C LEU 3.1 12.8 + - - +
215C ILE* 2.7 16.5 + - - +
217C LEU* 1.3 70.3 - - - +
219C PHE* 1.3 64.0 + - - +
220C LEU 3.2 0.2 - - - -
221C ILE* 3.9 3.1 + - - +
222C LYS* 3.3 9.5 + - - +
229C ILE* 2.9 48.2 - - + +
231C LEU* 5.4 5.2 - - + -
243C ILE* 4.0 15.2 - - + +
472C ILE* 4.4 10.5 - - + +
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Residues in contact with PHE 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 6.1 0.2 - - + -
81C TYR* 3.2 51.4 - + - -
100C LEU* 3.6 28.3 - - + -
104C LEU* 3.7 27.8 - - + -
215C ILE* 2.9 33.3 + - + -
216C ASP 3.4 9.2 - - - +
218C ALA* 1.3 75.7 - - - +
220C LEU* 1.3 62.1 + - - +
222C LYS* 3.6 4.1 - - + +
223C PHE* 3.2 61.6 + + + -
472C ILE* 3.6 26.9 - - + -
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 4.0 15.5 - - + -
59C ASN* 3.0 37.0 - - - +
64C PHE* 4.2 3.8 - - + -
108C TYR* 4.2 13.0 - - + +
112C LEU* 3.7 21.5 - - + -
171C LEU* 3.5 28.9 - - + -
216C ASP 2.9 12.6 + - - +
217C LEU* 3.3 12.1 - - + +
219C PHE* 1.3 75.9 - - - +
221C ILE* 1.3 55.8 + - - +
222C LYS 2.7 14.3 + - - -
223C PHE* 5.2 1.1 - - - -
224C ILE* 3.2 46.0 + - + +
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Residues in contact with ILE 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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64C PHE* 4.9 12.3 - - + -
164C LEU* 3.7 25.6 - - + -
168C VAL* 4.0 17.3 - - + -
217C LEU* 2.9 39.4 + - + +
218C ALA* 4.1 2.2 - - - +
220C LEU* 1.3 72.9 - - - +
222C LYS* 1.3 56.3 + - - +
225C THR* 3.0 26.9 - - - +
226C GLY 3.7 0.2 + - - -
227C ASN* 3.8 6.0 + - + -
229C ILE* 3.4 27.8 - - + -
243C ILE* 5.4 3.8 - - + -
251C ILE* 3.6 39.0 - - + -
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Residues in contact with LYS 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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77C ARG* 4.1 9.2 - - - +
81C TYR* 4.7 8.0 - - - -
84C LYS* 5.5 1.8 - - - +
218C ALA 3.3 17.3 + - - +
219C PHE* 3.6 7.2 - - + +
220C LEU 2.7 2.6 + - - -
221C ILE* 1.3 74.0 - - - +
223C PHE* 1.3 83.1 + - + +
224C ILE 2.8 2.2 + - - -
225C THR 3.1 0.3 + - - -
226C GLY* 2.6 32.0 + - - +
227C ASN 3.6 17.9 - - - +
228C ASN* 3.3 26.9 + - - +
229C ILE* 4.2 3.1 - - + -
472C ILE* 3.0 45.2 - - + +
473C GLU* 3.8 8.5 - - - +
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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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52C PHE* 3.6 26.7 - + - -
56C VAL* 3.7 29.6 - - + -
74C ILE* 3.1 22.8 - - + +
77C ARG* 3.2 40.2 - - + +
78C ILE* 3.4 32.5 - - + -
81C TYR* 4.3 7.2 - - + -
82C PHE* 4.0 16.2 - + - -
104C LEU* 4.4 1.3 - - + -
219C PHE* 3.2 53.0 + + + +
220C LEU* 4.4 0.4 - - - +
222C LYS* 1.3 89.4 - - + +
224C ILE* 1.3 59.5 + - - +
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Residues in contact with ILE 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.5 32.8 - - + +
59C ASN* 3.6 11.7 - - - +
60C LYS* 3.7 21.1 - - + -
64C PHE* 3.7 29.8 - - + -
67C VAL* 3.7 22.7 - - + +
69C THR* 3.2 23.4 + - - +
74C ILE* 3.3 8.6 - - + +
77C ARG* 4.0 0.2 + - - -
220C LEU* 3.2 35.5 + - + +
221C ILE 5.0 0.2 - - - -
222C LYS 2.8 4.2 + - - -
223C PHE* 1.3 76.1 - - - +
225C THR* 1.3 68.5 + - - +
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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