Contacts of the helix formed by residues 222 - 233 (chain C) in PDB entry 3C6M
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 ASP 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C SER* 2.7 37.2 + - - -
146C PRO* 4.9 0.9 - - - +
147C TYR* 3.9 11.4 - - + -
148C GLN* 2.9 31.9 + - - +
150C ILE* 3.7 0.2 - - - +
220C GLU* 2.7 24.6 + - - +
221C ILE* 1.3 81.9 - - + +
223C GLN* 1.3 60.6 + - - +
224C MET* 3.2 14.0 + - - +
225C VAL* 3.1 24.3 + - + +
226C ILE* 3.3 8.1 + - - +
401C MTA 3.7 0.9 - - - +
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Residues in contact with GLN 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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147C TYR* 5.7 0.2 - - - -
221C ILE 3.8 4.4 + - - -
222C ASP* 1.3 73.0 + - - +
224C MET* 1.3 55.7 + - + +
226C ILE* 3.0 19.5 + - - +
227C ASP* 2.8 62.0 + - - +
230C LYS* 5.0 2.6 + - - -
244C LEU* 5.0 9.5 - - - +
253C ILE* 3.5 39.6 - - + +
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Residues in contact with MET 224 (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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141C TYR* 3.3 29.8 + - - +
143C GLU* 4.2 12.6 - - + +
144C ASP 4.1 7.6 - - - +
145C SER* 3.5 31.9 - - - +
146C PRO* 4.1 9.2 - - + -
150C ILE* 3.8 14.0 - - + +
222C ASP* 3.2 10.3 + - - +
223C GLN* 1.3 77.6 - - + +
225C VAL* 1.3 59.1 + - - +
227C ASP* 3.9 10.3 - - - +
228C GLY* 3.0 23.2 + - - -
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Residues in contact with VAL 225 (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 GLN* 3.8 10.1 - - - +
150C ILE* 3.4 26.0 - - + +
162C LEU* 4.3 18.6 - - + -
164C LEU* 4.0 11.0 - - + -
200C GLY* 3.6 21.1 - - - +
220C GLU* 4.4 0.4 - - - +
222C ASP* 3.1 27.6 + - + +
224C MET* 1.3 75.4 - - - +
226C ILE* 1.3 68.2 + - - +
228C GLY* 3.5 0.7 + - - -
229C CYS* 3.1 23.0 + - - +
401C MTA 3.4 21.8 - - + +
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Residues in contact with ILE 226 (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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200C GLY 3.9 13.5 - - - +
218C MET* 3.8 28.9 - - + -
220C GLU* 3.9 18.4 - - + -
222C ASP 3.3 11.6 + - - +
223C GLN* 3.0 12.2 + - - +
225C VAL* 1.3 76.0 - - - +
227C ASP* 1.3 68.1 + - - +
229C CYS* 3.0 3.6 + - - +
230C LYS* 3.0 41.4 + - + +
241C LEU* 4.0 17.2 - - + +
244C LEU* 4.3 17.5 - - + -
251C VAL* 4.2 9.6 - - + -
253C ILE* 4.1 13.0 - - + -
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Residues in contact with ASP 227 (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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223C GLN* 2.8 50.5 + - - +
224C MET* 4.3 8.1 - - - +
226C ILE* 1.3 71.5 - - - +
228C GLY* 1.3 62.2 + - - +
230C LYS* 3.6 28.4 + - - +
231C LYS* 3.3 26.1 + - - +
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Residues in contact with GLY 228 (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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141C TYR* 5.0 11.6 - - - -
150C ILE* 6.0 0.9 - - - -
152C ILE* 3.4 13.7 - - - +
224C MET 3.0 18.7 + - - -
225C VAL* 3.9 1.1 - - - -
226C ILE 3.3 0.2 - - - -
227C ASP* 1.3 76.7 - - - +
229C CYS* 1.3 56.7 + - - +
231C LYS* 4.6 0.9 - - - -
232C TYR* 2.9 45.4 + - - +
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Residues in contact with CYS 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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162C LEU* 3.9 28.5 - - - -
200C GLY 3.8 10.1 - - - +
201C ASP* 3.8 31.6 - - - +
225C VAL* 3.1 19.0 + - - +
226C ILE 3.0 3.7 + - - +
228C GLY* 1.3 76.6 - - - +
230C LYS* 1.3 62.5 + - - +
231C LYS 3.2 1.1 - - - -
233C MET* 2.9 43.7 + - + -
237C CYS* 3.2 15.6 - - - -
241C LEU* 4.3 1.8 - - + -
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Residues in contact with LYS 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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223C GLN* 5.0 2.0 + - - -
226C ILE* 3.0 28.8 + - + +
227C ASP* 3.6 25.9 + - - +
229C CYS* 1.3 72.0 - - - +
231C LYS* 1.3 57.7 + - + +
234C ARG* 3.2 34.4 + - - +
237C CYS* 4.0 9.6 - - - -
238C GLY 5.6 0.4 - - - -
241C LEU* 2.9 46.5 + - + +
242C ASP* 3.8 22.3 + - - +
244C LEU* 4.9 8.5 - - - +
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Residues in contact with LYS 231 (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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227C ASP 3.3 15.4 + - - +
228C GLY* 5.7 0.2 - - - -
229C CYS 3.2 0.6 - - - -
230C LYS* 1.3 83.5 - - + +
232C TYR* 1.3 111.7 + - + +
233C MET 3.6 0.9 + - - -
234C ARG* 3.9 11.3 - - - +
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Residues in contact with TYR 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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140C VAL* 3.2 35.5 + - + -
141C TYR* 3.8 36.8 - + + -
152C ILE* 3.8 12.3 - - + -
160C ASN* 2.6 32.5 - - - +
172C GLU* 4.1 2.8 - - - +
228C GLY* 2.9 29.1 + - - +
231C LYS* 1.3 119.2 + - + +
233C MET* 1.3 59.2 + - - +
234C ARG 3.8 1.1 - - - -
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Residues in contact with MET 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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152C ILE* 4.2 11.0 - - + -
160C ASN* 3.4 46.4 - - - +
161C ILE 4.3 1.1 - - - -
162C LEU* 4.0 16.2 - - + +
170C LEU* 3.6 23.3 - - + +
172C GLU* 3.7 8.7 - - - +
201C ASP* 5.0 3.1 - - + +
229C CYS* 2.9 43.0 + - + +
232C TYR* 1.3 78.0 - - - +
234C ARG* 1.3 53.6 + - - +
235C LYS 3.0 5.4 - - - -
236C THR* 2.7 57.2 + - + +
237C CYS* 3.1 9.7 + - - -
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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