Contacts of the helix formed by residues 163 - 179 (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 SER 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ASP* 5.7 1.2 + - - -
162C SER* 1.3 72.7 - - - +
164C LEU* 1.3 68.4 + - - +
165C VAL 3.1 0.6 + - - -
166C LYS* 3.3 19.6 + - - +
167C ASN* 3.4 12.0 + - - +
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.3 7.2 - - + -
67C VAL* 5.8 2.9 - - + -
162C SER* 3.4 10.1 + - - +
163C SER* 1.3 75.0 - - - +
165C VAL* 1.3 59.6 + - - +
166C LYS 3.0 2.9 - - - -
167C ASN* 2.9 36.1 - - + +
168C VAL* 2.6 46.7 + - + +
221C ILE* 3.7 25.1 - - + -
225C THR* 3.6 32.8 - - + +
227C ASN* 4.6 11.4 - - - +
245C ASP* 5.9 1.1 - - + -
251C ILE* 4.7 10.3 - - + -
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C VAL* 3.3 11.0 - - + -
162C SER* 2.8 46.3 + - - +
163C SER 3.1 0.4 - - - -
164C LEU* 1.3 79.0 - - - +
166C LYS* 1.3 71.8 + - + +
168C VAL* 4.0 3.0 - - - +
169C ASN* 3.2 27.7 + - - +
201C GLY 4.0 20.2 - - - +
202C ASP* 5.7 1.6 - - + -
250C HIS 3.1 21.5 - - - +
251C ILE* 4.2 18.8 - - - +
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C VAL* 4.5 6.5 + - - +
162C SER 3.2 24.2 + - - -
163C SER* 3.3 9.4 + - - +
164C LEU 3.0 0.2 - - - -
165C VAL* 1.3 88.6 - - + +
167C ASN* 1.3 58.8 + - - +
168C VAL 2.8 10.9 + - - -
169C ASN* 3.4 19.2 + - - +
170C LYS* 3.9 13.2 + - - +
201C GLY* 6.3 2.7 - - - -
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Residues in contact with ASN 167 (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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63C PHE 3.2 25.2 - - - +
64C PHE* 3.0 33.3 - - - -
66C ASP* 3.4 30.3 - - - +
67C VAL* 5.0 2.7 - - - +
163C SER* 3.4 7.3 + - - +
164C LEU* 2.9 43.1 + - + +
166C LYS* 1.3 77.7 - - - +
168C VAL* 1.3 57.5 + - - +
170C LYS* 4.3 10.1 - - - +
171C LEU* 4.5 1.7 + - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.6 12.3 - - + -
164C LEU* 2.6 27.6 + - + +
165C VAL* 4.0 4.3 - - - +
166C LYS 2.8 1.6 + - - -
167C ASN* 1.3 74.7 - - - +
169C ASN* 1.3 55.2 + - - +
170C LYS 2.6 6.4 + - - -
171C LEU* 2.4 43.3 + - + +
172C MET* 3.2 16.7 + - + -
217C LEU* 4.7 15.3 - - + -
221C ILE* 4.0 29.8 - - + -
251C ILE* 4.1 7.0 - - + +
252C ILE* 4.7 13.9 - - + -
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Residues in contact with ASN 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C VAL* 3.2 22.1 + - - +
166C LYS* 3.4 13.2 + - - +
168C VAL* 1.3 78.9 - - - +
170C LYS* 1.3 61.3 + - + +
172C MET* 3.4 4.7 + - - +
173C GLU* 3.1 30.1 + - - +
200C TYR* 4.5 16.1 - - + -
201C GLY* 3.6 9.9 + - - -
202C ASP* 3.4 22.6 - - - +
203C ILE* 3.1 46.0 + - + +
252C ILE* 5.7 1.4 - - - +
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Residues in contact with LYS 170 (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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63C PHE* 3.8 21.2 - - + +
166C LYS 3.9 11.0 + - - +
167C ASN* 4.3 10.8 - - - +
168C VAL 2.6 5.2 + - - +
169C ASN* 1.3 72.9 - - + +
171C LEU* 1.3 66.0 + - - +
172C MET 3.4 0.3 + - - -
173C GLU* 3.2 35.3 + - - +
174C GLU* 3.9 1.4 + - - +
200C TYR* 4.8 7.4 - - - -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN* 4.6 2.7 - - - +
63C PHE* 3.4 25.0 - - + -
64C PHE* 3.3 39.3 - - + -
112C LEU* 4.7 4.9 - - + -
115C LEU* 3.0 38.9 - - + +
167C ASN 4.5 0.6 + - - +
168C VAL* 2.4 27.4 + - + +
170C LYS* 1.3 74.8 - - - +
172C MET* 1.3 58.0 + - + +
174C GLU* 3.4 18.9 - - - +
175C TYR* 3.6 4.3 + - + +
217C LEU* 3.6 18.8 - - + -
220C LEU* 3.5 17.5 - - + -
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Residues in contact with MET 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C VAL* 3.2 19.1 + - + +
169C ASN* 3.7 9.9 - - - +
170C LYS 3.3 0.4 - - - -
171C LEU* 1.3 76.9 - - + +
173C GLU* 1.3 65.2 + - - +
174C GLU 3.0 2.5 - - - -
175C TYR* 3.0 30.6 + - + +
176C LEU* 3.0 18.7 + - + +
183C CYS* 4.2 6.3 - - - -
203C ILE* 3.9 19.7 - - + +
205C ILE* 3.4 38.6 - - + -
213C PHE* 3.5 30.3 - - + -
217C LEU* 5.7 2.9 - - + -
252C ILE* 5.0 12.3 - - + -
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASN* 3.1 14.8 + - - +
170C LYS* 3.2 40.5 + - - +
171C LEU 3.5 0.6 - - - -
172C MET* 1.3 77.0 - - - +
174C GLU* 1.3 62.5 + - - +
176C LEU* 3.6 16.6 + - - +
177C ARG* 3.6 28.7 + - - +
189C TYR* 3.5 26.9 + - + +
192C TYR* 5.6 2.3 - - - -
200C TYR* 3.4 23.7 + - - -
203C ILE* 4.1 9.4 - - + -
273C ILE* 4.3 1.7 - - - +
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Residues in contact with GLU 174 (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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62C ARG* 4.3 12.2 + - - +
63C PHE* 3.6 28.3 - - + -
115C LEU* 3.9 21.2 - - + +
170C LYS 3.9 1.4 + - - +
171C LEU 3.4 12.0 + - - +
172C MET 3.0 0.2 - - - -
173C GLU* 1.3 78.1 - - - +
175C TYR* 1.3 67.1 + - - +
177C ARG* 2.8 51.0 + - - +
178C ARG* 2.8 57.6 + - - +
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Residues in contact with TYR 175 (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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111C ILE* 2.9 67.8 - - + +
112C LEU* 4.0 13.5 - - + -
115C LEU* 4.0 16.5 - - + +
171C LEU* 3.6 2.9 + - + +
172C MET* 3.0 30.4 + - + +
174C GLU* 1.3 76.7 - - - +
176C LEU* 1.3 63.6 + - - +
177C ARG 3.1 0.2 + - - -
178C ARG* 4.6 0.2 - - - -
179C HIS* 2.9 55.6 + + + +
182C SER* 4.5 5.4 + - - -
183C CYS* 3.7 23.3 - - + -
207C GLN* 3.8 9.9 - - - -
209C ASN* 4.5 2.9 + - - -
213C PHE* 3.6 25.4 - + - -
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Residues in contact with LEU 176 (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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172C MET* 3.0 19.6 + - + +
173C GLU* 3.7 8.5 - - - +
174C GLU 3.2 0.2 - - - -
175C TYR* 1.3 77.8 - - - +
177C ARG* 1.3 56.4 + - - +
179C HIS 3.5 9.5 - - - +
180C ASN* 3.1 19.6 + - - -
183C CYS* 4.1 33.6 - - - +
185C CYS* 3.7 38.6 - - + +
189C TYR* 4.0 12.1 - - + +
203C ILE* 4.5 8.1 - - + -
205C ILE* 4.3 3.4 - - + -
273C ILE* 3.2 49.1 - - + +
274C TYR 4.8 2.1 + - - +
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Residues in contact with ARG 177 (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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170C LYS 5.8 0.2 + - - -
173C GLU* 3.6 23.5 + - - +
174C GLU* 2.8 58.7 + - - +
176C LEU* 1.3 68.8 - - - +
178C ARG* 1.3 65.0 + - - +
179C HIS 2.9 10.4 + - - -
180C ASN* 3.1 19.1 + - - -
271C ASP* 3.7 16.6 + - - +
272C ASN* 3.7 28.8 - - + +
273C ILE* 3.7 14.9 - - + +
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Residues in contact with ARG 178 (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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114C VAL* 3.3 40.1 + - + +
115C LEU* 3.8 13.5 - - + -
117C ILE* 3.8 31.3 - - - +
174C GLU* 2.8 52.6 + - - +
175C TYR 4.1 1.6 - - - +
177C ARG* 1.3 77.2 + - - +
179C HIS* 1.3 75.3 + - + +
180C ASN 4.0 0.8 + - - -
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Residues in contact with HIS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP 2.7 27.8 - - - -
111C ILE* 2.8 23.5 + - + -
114C VAL* 4.4 10.1 - - + +
115C LEU* 5.1 0.4 - - - +
175C TYR* 2.9 53.3 + + + +
176C LEU 3.5 9.8 - - - +
177C ARG 2.9 0.4 + - - -
178C ARG* 1.3 91.5 + - + +
180C ASN* 1.3 62.8 + - - +
181C LYS 3.5 2.5 - - - +
182C SER* 3.0 24.5 + - - +
183C CYS* 3.5 20.3 + - + +
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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