Contacts of the helix formed by residues 235 - 248 (chain C) in PDB entry 4NY0
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 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C ARG 4.9 3.1 - - - -
233C ASN 3.7 3.2 + - - -
234C LEU* 1.3 70.9 - - - +
236C ARG* 1.3 62.8 + - + +
237C GLU* 4.2 15.9 + - - +
238C GLU* 2.9 34.5 + - - +
239C SER* 2.6 34.0 + - - -
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Residues in contact with ARG 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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177C ARG 5.7 0.2 - - - +
178C ARG* 3.9 38.9 + - + +
181C GLY* 5.4 10.7 - - - -
235C ASN* 1.3 79.8 - - + +
237C GLU* 1.3 61.1 + - - +
239C SER* 3.4 3.5 + - - -
240C ILE* 3.2 30.3 + - + +
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Residues in contact with GLU 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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138C THR* 3.7 29.3 - - - +
141C LYS* 4.7 18.9 + - - +
144C LEU* 4.5 14.1 - - + -
235C ASN* 3.5 13.1 + - - +
236C ARG* 1.3 78.4 - - - +
238C GLU* 1.3 67.7 + - + +
240C ILE* 3.2 11.3 + - - +
241C LEU* 3.0 37.2 + - + +
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Residues in contact with GLU 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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233C ASN 4.8 1.2 - - - +
234C LEU* 3.5 37.6 - - + +
235C ASN* 2.9 26.9 + - - +
236C ARG 3.5 0.6 - - - -
237C GLU* 1.3 81.0 - - + +
239C SER* 1.3 56.6 + - - +
241C LEU* 3.9 9.9 - - + +
242C LYS* 3.1 30.1 + - - +
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Residues in contact with SER 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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148C TYR* 5.8 0.2 - - - -
174C LEU* 3.7 38.5 - - - +
177C ARG* 3.5 21.7 + - - +
178C ARG* 4.0 9.2 - - - -
234C LEU* 3.6 5.5 - - - +
235C ASN 2.6 23.9 + - - -
236C ARG 3.6 4.9 - - - -
237C GLU 3.1 0.8 - - - -
238C GLU* 1.3 75.3 - - - +
240C ILE* 1.3 61.4 + - - +
243C PHE* 2.9 30.5 + - - +
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Residues in contact with ILE 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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144C LEU* 4.1 26.2 - - + -
145C ASN* 3.4 32.1 - - - +
148C TYR* 3.7 36.3 - - + -
178C ARG* 3.7 20.6 - - - -
236C ARG* 3.2 16.4 + - + +
237C GLU* 3.2 9.1 + - - +
239C SER* 1.3 76.2 - - - +
241C LEU* 1.3 64.0 + - - +
243C PHE* 3.0 23.6 + - - +
244C PHE* 3.1 23.0 + - + -
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Residues in contact with LEU 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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134C LEU* 4.4 32.3 - - + +
138C THR* 4.3 20.2 - - + -
144C LEU* 4.7 8.5 - - + -
237C GLU* 3.0 42.5 + - + +
238C GLU* 4.2 9.0 - - + +
240C ILE* 1.3 77.4 - - + +
242C LYS* 1.3 59.4 + - - +
244C PHE* 3.3 7.7 + - + +
245C GLU* 3.0 26.4 + - - +
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Residues in contact with LYS 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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174C LEU* 3.7 10.8 - - + -
231C PHE* 4.1 27.1 - - + -
234C LEU* 4.6 12.8 - - + -
238C GLU 3.1 19.6 + - - +
239C SER 4.1 2.7 - - - +
241C LEU* 1.3 74.1 - - - +
243C PHE* 1.3 64.6 + - - +
245C GLU* 3.4 37.5 + - - +
246C ILE* 3.3 29.5 + - + +
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Residues in contact with PHE 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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148C TYR* 3.5 40.2 - + + -
151C VAL* 4.9 2.0 - - + -
152C LYS* 4.0 32.5 - - + -
155C TYR* 4.2 17.7 - + - -
171C LEU* 3.4 51.6 - - + +
174C LEU* 3.6 13.6 - - + +
175C GLU* 5.5 0.4 - - + -
239C SER 2.9 14.1 + - - +
240C ILE 3.1 12.1 - - - +
242C LYS* 1.3 79.1 - - - +
244C PHE* 1.3 62.7 + + - +
246C ILE 3.4 0.2 + - - -
247C LEU* 3.0 51.0 + - + +
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Residues in contact with PHE 244 (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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134C LEU* 3.7 37.9 - - + -
144C LEU* 4.6 3.1 - - + -
147C PHE* 3.7 15.5 - + - -
148C TYR* 3.5 28.0 - + + -
151C VAL* 3.7 32.3 - - + -
240C ILE* 3.1 41.7 + - + -
241C LEU* 3.3 9.1 + - + +
243C PHE* 1.3 82.9 - + - +
245C GLU* 1.3 66.0 - - - +
247C LEU* 4.4 1.6 - - + -
248C SER* 3.0 27.9 + - - -
253C PHE* 3.5 32.9 - + + -
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Residues in contact with GLU 245 (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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241C LEU 3.0 16.7 + - - +
242C LYS* 3.4 42.7 + - - +
243C PHE 3.3 0.2 - - - -
244C PHE* 1.3 77.6 - - - +
246C ILE* 1.3 66.4 + - - +
248C SER* 4.3 2.2 - - - -
249C PRO* 3.4 17.2 - - - +
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Residues in contact with ILE 246 (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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167C ILE* 3.6 37.9 - - + +
170C LYS* 3.7 36.1 - - + +
171C LEU* 3.9 14.8 - - + -
174C LEU* 4.0 9.2 - - + -
231C PHE* 3.9 20.9 - - + -
242C LYS* 3.3 24.2 + - + +
243C PHE 3.9 3.1 - - - +
244C PHE 3.2 0.2 - - - -
245C GLU* 1.3 81.9 - - + +
247C LEU* 1.3 64.2 + - - +
249C PRO* 3.2 12.9 - - - +
250C VAL* 4.9 1.9 - - - +
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Residues in contact with LEU 247 (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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151C VAL* 3.6 31.0 - - + -
155C TYR* 3.9 27.6 - - + -
159C ILE* 4.4 2.9 - - + -
167C ILE* 5.3 0.4 - - - -
171C LEU* 3.8 24.7 - - + -
243C PHE* 3.0 36.0 + - + +
244C PHE* 4.0 4.0 - - + +
246C ILE* 1.3 80.6 - - - +
248C SER* 1.3 64.5 + - - +
250C VAL* 3.1 20.4 + - + +
251C TYR* 3.3 24.6 + - + -
253C PHE* 4.3 9.9 - - + -
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Residues in contact with SER 248 (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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244C PHE 3.0 17.0 + - - -
245C GLU* 4.3 3.1 - - - -
247C LEU* 1.3 76.6 - - - +
249C PRO* 1.4 69.6 - - - +
250C VAL 3.0 2.1 + - - -
251C TYR 3.3 16.2 + - - +
252C ARG* 3.6 23.4 + - - -
253C PHE* 3.6 22.1 - - - -
254C ASP* 5.3 2.8 + - - -
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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