Contacts of the helix formed by residues 228 - 243 (chain C) in PDB entry 3E6G
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 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C THR* 4.9 1.2 + - - -
202C ASP* 5.1 7.3 + - - +
225C VAL* 4.2 9.6 - - + -
226C GLY* 3.6 1.8 + - - -
227C ASP* 1.3 80.0 + - - +
229C ALA* 1.3 67.8 + - - +
230C GLU* 2.7 17.9 + - - +
231C LEU* 2.9 46.8 + - + +
232C ALA* 3.2 9.4 + - - +
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Residues in contact with ALA 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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228C ASN* 1.3 73.3 - - - +
230C GLU* 1.3 62.2 + - - +
232C ALA* 3.2 8.0 + - - +
233C GLU* 2.8 48.3 + - - +
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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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228C ASN* 2.7 21.6 + - - +
229C ALA* 1.3 91.9 + - - +
231C LEU* 1.3 54.4 + - - +
233C GLU* 3.9 5.5 - - - +
234C GLN* 3.0 42.6 + - - +
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.1 23.8 - - + -
181C LEU* 4.4 18.2 - - + -
202C ASP* 3.9 34.5 - - + +
203C LEU* 4.0 18.8 - - + -
225C VAL* 4.1 6.3 - - + -
228C ASN* 2.9 36.4 + - - +
230C GLU* 1.3 73.5 - - - +
232C ALA* 1.3 60.5 + - - +
234C GLN* 3.3 24.2 + - - +
235C MET* 2.9 32.6 + - + +
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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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80C THR* 4.9 5.6 - - - +
81C ARG* 4.5 19.3 - - + -
83C PHE* 3.5 6.2 - - - -
225C VAL* 4.0 25.5 - - + +
228C ASN 3.2 9.0 + - - +
229C ALA* 3.2 13.7 + - - +
231C LEU* 1.3 77.0 - - - +
233C GLU* 1.3 66.0 + - - +
236C ALA* 2.9 30.2 + - - +
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Residues in contact with GLU 233 (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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81C ARG* 3.3 23.8 + - - -
229C ALA* 2.8 37.2 + - - +
230C GLU* 3.9 6.1 - - - +
232C ALA* 1.3 76.9 - - - +
234C GLN* 1.3 57.2 + - - +
236C ALA* 3.4 6.0 + - - +
237C PHE* 2.9 31.4 + - - +
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Residues in contact with GLN 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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98C LEU* 3.5 35.1 + - + +
181C LEU* 5.7 2.6 - - - +
230C GLU* 3.0 33.3 + - - +
231C LEU* 3.4 15.7 + - - +
232C ALA 3.2 0.2 - - - -
233C GLU* 1.3 74.7 - - - +
235C MET* 1.3 57.5 + - - +
237C PHE* 3.1 9.9 + - - +
238C LEU* 2.9 34.2 + - + +
125D ARG* 5.9 3.7 - - - +
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Residues in contact with MET 235 (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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83C PHE* 3.6 26.5 - - + -
85C PHE* 4.1 20.9 - - + -
94C THR* 4.6 3.1 - - + -
95C VAL* 3.9 36.1 - - + +
98C LEU* 4.0 19.1 - - + -
203C LEU* 4.4 17.0 - - + -
223C ALA* 3.8 27.8 - - + -
225C VAL* 5.4 0.2 - - + -
231C LEU* 2.9 19.6 + - + +
234C GLN* 1.3 72.8 - - - +
236C ALA* 1.3 66.0 + - - +
238C LEU* 4.2 7.2 - - - -
239C GLN* 2.9 28.1 + - - +
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Residues in contact with ALA 236 (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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81C ARG* 3.6 31.2 - - - +
83C PHE* 3.3 12.4 - - + -
232C ALA 2.9 21.9 + - - +
233C GLU* 3.6 9.0 - - - +
235C MET* 1.3 71.7 - - - +
237C PHE* 1.3 61.9 + - - +
239C GLN* 4.0 4.9 - - - +
240C ASN* 3.2 24.1 + - - +
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Residues in contact with PHE 237 (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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233C GLU 2.9 14.8 + - - +
234C GLN* 3.3 11.9 - - - +
236C ALA* 1.3 74.5 - - - +
238C LEU* 1.3 68.0 + - + +
240C ASN* 3.4 4.7 + - - +
241C SER* 2.9 48.6 + - - -
117D ARG* 4.1 19.3 - - + -
121D ARG* 3.8 61.2 - - + -
122D VAL* 3.9 14.1 - - + -
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Residues in contact with LEU 238 (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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94C THR* 3.7 31.4 - - + +
97C GLU* 3.8 24.5 - - + +
98C LEU* 3.3 33.9 - - + -
234C GLN* 2.9 16.9 + - + +
235C MET* 3.2 9.6 + - - +
237C PHE* 1.3 78.6 - - + +
239C GLN* 1.3 66.4 + - - +
241C SER* 3.1 2.3 + - - -
242C ILE* 2.9 31.5 + - + +
122D VAL* 4.2 28.5 - - + -
125D ARG* 4.3 9.6 - - - +
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Residues in contact with GLN 239 (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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66C ARG* 4.0 17.9 + - - +
70C GLU* 3.3 10.6 + - - +
83C PHE* 3.6 22.4 - - + +
84C ALA 2.8 45.4 + - - +
85C PHE* 3.5 30.2 - - + -
94C THR* 3.8 4.2 - - - +
235C MET 2.9 19.5 + - - +
236C ALA* 4.0 5.4 - - - +
238C LEU* 1.3 71.1 - - - +
240C ASN* 1.3 58.9 + - - +
242C ILE* 5.7 0.2 - - - -
243C GLY* 3.0 30.0 + - - -
244C GLY 4.1 0.7 + - - +
245C VAL* 4.2 11.8 - - + +
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Residues in contact with ASN 240 (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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61C THR* 3.4 28.6 + - - +
236C ALA 3.2 15.8 + - - +
237C PHE* 3.9 4.5 - - - +
238C LEU 3.2 1.2 - - - -
239C GLN* 1.3 80.0 - - - +
241C SER* 1.3 60.6 + - - +
243C GLY* 4.1 5.9 + - - -
89D MET* 4.6 7.4 - - - +
117D ARG* 2.9 33.7 + - - +
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Residues in contact with SER 241 (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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237C PHE* 2.9 30.9 + - - -
238C LEU 3.1 1.8 + - - -
240C ASN* 1.3 77.0 - - - +
242C ILE* 1.3 64.8 + - - +
243C GLY 3.3 0.4 - - - -
89D MET* 3.6 23.2 - - - +
114D GLY 5.3 0.2 - - - +
117D ARG* 2.6 32.6 + - - +
118D LEU* 4.1 16.3 - - - +
122D VAL* 4.1 23.8 - - - -
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Residues in contact with ILE 242 (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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90C ALA* 6.6 0.2 - - + -
93C SER* 6.0 4.9 - - - -
94C THR* 3.6 27.1 - - + +
97C GLU* 4.0 29.6 - - + +
238C LEU* 2.9 28.1 + - + +
239C GLN 5.1 0.4 - - - +
241C SER* 1.3 77.8 - - - +
243C GLY* 1.3 58.3 + - - +
244C GLY* 4.0 12.1 - - - +
89D MET* 4.0 1.1 - - - -
90D ALA* 3.2 23.2 + - + +
93D SER* 3.2 29.6 + - - +
94D THR* 5.6 2.5 - - - +
97D GLU* 5.9 2.2 - - - +
118D LEU* 4.3 4.3 - - + -
122D VAL* 4.6 13.7 - - + -
123D ARG* 5.8 0.2 - - - +
242D ILE* 6.0 4.7 - - + -
244D GLY* 6.5 0.9 - - - -
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Residues in contact with GLY 243 (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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239C GLN 3.0 16.4 + - - -
240C ASN* 4.5 4.3 - - - -
241C SER 3.3 2.0 - - - -
242C ILE* 1.3 77.1 - - - +
244C GLY* 1.3 49.9 + - - +
245C VAL* 2.6 23.0 + - - +
86D ALA* 3.9 2.6 - - - +
87D SER* 2.6 35.0 + - - -
89D MET* 4.0 7.0 - - - -
90D ALA* 3.6 4.4 - - - +
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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
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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