Contacts of the helix formed by residues 226 - 240 (chain C) in PDB entry 6N1G
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 226 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C MET* 3.2 24.7 - - - +
74C PHE* 5.4 1.2 - - - -
93C MET 3.0 25.2 + - - +
94C ASN* 2.5 38.2 + - - +
224C ALA 3.1 5.4 - - - +
225C ILE* 1.4 86.7 - - - +
227C PRO* 1.3 68.1 - - - +
228C SER* 3.9 3.8 - - - +
229C ARG* 3.0 31.5 + - + +
230C ASP* 3.5 13.3 + - - +
257C PRO 4.4 0.2 - - - -
403C GOL 4.1 12.3 + - - -
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Residues in contact with PRO 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASN* 3.1 15.3 - - - +
95C ALA* 3.9 18.6 - - + -
96C ALA* 4.0 10.1 - - + +
120C PHE* 5.6 0.5 - - - -
226C ASN* 1.3 82.7 - - - +
228C SER* 1.3 56.7 + - - +
230C ASP* 4.6 0.6 - - + +
231C LEU* 3.3 33.1 + - - +
257C PRO 3.5 19.8 - - - +
258C VAL* 3.7 33.2 - - + +
261C PRO* 3.8 17.3 - - + -
262C LEU* 4.7 5.4 - - + +
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 4.2 4.8 - - - +
93C MET 5.4 1.6 - - - -
95C ALA* 4.7 6.9 - - - +
116C VAL* 5.3 1.8 - - - -
119C GLN* 2.3 56.0 + - - -
120C PHE* 3.3 10.4 + - - -
123C SER* 3.1 12.5 + - - -
226C ASN* 3.0 4.4 - - - +
227C PRO* 1.3 77.3 - - - +
229C ARG* 1.3 60.2 + - - +
230C ASP 3.3 1.8 - - - -
232C PRO* 3.0 24.0 - - - +
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Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 5.4 0.2 - - - +
47C MET* 4.6 7.6 - - + -
48C MET* 3.5 33.2 - - - +
51C GLY 5.3 6.5 + - - -
55C VAL* 5.5 3.2 - - - +
74C PHE* 4.0 38.0 - - + -
123C SER* 4.9 1.6 - - - -
157C ILE 4.6 7.3 + - - -
158C PHE 3.1 21.2 + - - -
159C ALA* 3.4 17.4 - - - +
160C THR* 3.9 16.6 - - - +
222C GLY 4.9 3.6 + - - -
223C TYR* 4.7 11.5 + - - -
224C ALA* 4.4 20.4 - - - +
225C ILE* 5.1 1.3 - - + +
226C ASN* 3.0 34.4 + - + +
228C SER* 1.3 77.8 - - - +
230C ASP* 1.3 55.4 + - - +
233C PRO* 3.6 4.8 - - - +
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Residues in contact with ASP 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ALA* 3.2 10.3 - - - +
160C THR* 2.7 44.0 + - - +
224C ALA* 4.2 7.4 - - + -
226C ASN 3.5 9.1 + - - +
227C PRO 4.6 1.1 - - - +
228C SER 3.3 0.2 - - - -
229C ARG* 1.3 81.0 - - - +
231C LEU* 1.3 62.4 + - - +
232C PRO 3.7 0.2 - - - -
233C PRO* 3.9 2.5 - - - -
234C ARG* 2.9 37.0 + - - +
254C TRP 5.0 0.5 - - - +
257C PRO* 3.2 37.9 - - + +
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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
----------------------------------------------------------
120C PHE* 3.4 25.4 - - + -
227C PRO 3.3 15.2 + - - +
230C ASP* 1.3 78.7 + - - +
232C PRO* 1.3 67.3 - - + +
234C ARG* 3.0 20.7 + - - +
235C ILE* 3.1 33.8 + - + +
247C PHE* 4.5 13.5 - - + -
254C TRP* 4.9 20.2 - - + +
257C PRO* 6.3 0.7 - - + -
258C VAL* 4.1 26.9 - - + -
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Residues in contact with PRO 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C PHE* 3.1 48.7 - - + +
123C SER* 3.6 1.1 - - - -
124C PHE* 3.5 20.0 - - - +
228C SER* 3.0 39.5 - - - +
231C LEU* 1.3 95.4 - - + +
233C PRO* 1.3 64.7 - - + +
235C ILE* 3.0 27.9 - - + +
236C PHE* 3.3 4.2 + - - +
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Residues in contact with PRO 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C MET* 3.4 36.3 - - + -
123C SER* 4.3 4.5 - - - +
127C ALA* 4.2 16.2 - - + -
158C PHE* 3.5 29.1 - - + +
159C ALA 4.5 0.2 - - - +
228C SER 4.0 2.7 - - - +
229C ARG 3.6 7.9 - - - +
230C ASP 3.9 7.6 - - - +
231C LEU 3.6 2.5 - - - -
232C PRO* 1.3 101.5 - - + +
234C ARG* 1.3 55.4 + - - +
236C PHE* 3.2 4.0 + - - +
237C THR* 2.8 32.7 + - - -
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Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 5.5 0.2 - - - -
159C ALA* 3.5 11.3 - - + +
160C THR 3.1 14.1 + - - -
161C TYR* 2.9 32.3 - - - +
230C ASP* 2.9 41.0 + - - +
231C LEU* 3.0 13.4 + - - +
233C PRO* 1.3 77.1 - - - +
235C ILE* 1.3 54.7 + - - +
237C THR* 3.1 1.3 + - - -
238C PHE* 2.6 37.4 + - - +
246C VAL* 2.5 46.6 + - + +
247C PHE* 2.9 33.1 + - + +
249C ASN* 4.2 0.6 - - - +
253C TRP* 3.8 8.5 + - - +
254C TRP* 3.6 27.2 - - - +
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Residues in contact with ILE 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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120C PHE* 3.5 28.7 - - + -
124C PHE* 3.4 26.0 - - + -
231C LEU* 3.1 30.8 + - + +
232C PRO* 3.0 22.7 - - + +
234C ARG* 1.3 75.5 - - - +
236C PHE* 1.3 60.3 + - - +
238C PHE* 3.4 11.6 - - + +
239C ILE* 3.3 27.3 + - + +
247C PHE* 4.0 14.4 - - + -
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Residues in contact with PHE 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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124C PHE* 3.5 33.4 - + + +
127C ALA* 3.7 25.8 - - + -
128C ALA* 3.5 32.8 - - + -
131C TYR* 3.5 43.3 - + + -
158C PHE* 3.9 11.4 - + - -
232C PRO 3.3 6.7 + - - +
233C PRO 3.2 7.5 + - - +
234C ARG 3.0 0.4 - - - -
235C ILE* 1.3 76.7 - - - +
237C THR* 1.3 56.0 + - - +
239C ILE* 2.6 35.4 + - + +
240C ALA* 2.7 29.2 + - + +
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Residues in contact with THR 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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155C ALA* 3.9 12.6 - - + -
158C PHE* 3.0 30.3 - - + +
233C PRO 2.8 17.9 + - - -
234C ARG* 4.3 0.2 - - - -
236C PHE* 1.3 72.8 - - - +
238C PHE* 1.3 60.7 + - - +
240C ALA* 3.3 9.3 + - - -
242C TRP* 3.2 71.9 + - + +
246C VAL* 3.4 22.7 - - + -
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Residues in contact with PHE 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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234C ARG 2.6 21.1 + - - +
235C ILE* 3.4 13.5 - - + +
237C THR* 1.3 74.5 - - - +
239C ILE* 1.3 65.1 - - + +
241C GLY* 3.9 5.0 + - - -
242C TRP 4.1 0.2 + - - -
243C GLY* 3.0 52.7 + - - +
244C LYS* 3.6 6.3 - - + -
246C VAL* 3.7 7.9 - - + +
247C PHE* 3.3 32.1 - + + -
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Residues in contact with ILE 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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124C PHE* 3.9 24.7 - - + -
235C ILE* 3.3 15.2 + - + +
236C PHE* 2.6 27.5 + - + +
238C PHE* 1.3 77.0 - - + +
240C ALA* 1.3 56.5 + - - +
241C GLY* 3.1 11.3 + - - -
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Residues in contact with ALA 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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131C TYR* 4.3 21.2 + - + -
138C ILE* 5.7 0.7 - - - +
236C PHE* 2.7 39.6 + - + +
237C THR* 3.3 1.9 + - - -
239C ILE* 1.3 73.4 - - - +
241C GLY* 1.3 57.1 + - - +
242C TRP* 3.7 31.1 - - + -
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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