Contacts of the helix formed by residues 227 - 236 (chain C) in PDB entry 1ML3
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 GLY 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C THR* 1.3 74.5 + - - +
228C ALA* 1.3 67.1 + - - +
229C ALA 3.2 2.9 - - - -
230C LYS* 2.8 27.2 + - - +
231C ALA* 2.8 14.7 + - - -
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Residues in contact with ALA 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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165C SER* 4.3 4.2 + - - +
167C THR* 3.4 40.2 - - + -
168C THR* 3.4 20.0 + - - +
171C LEU* 4.9 1.1 - - + -
190C MET* 4.8 3.4 - - - -
226C THR* 3.2 16.4 + - + +
227C GLY* 1.3 76.2 - - - +
229C ALA* 1.3 62.6 + - - +
231C ALA* 3.2 5.1 + - - +
232C VAL* 3.1 24.5 + - - +
2166C CYX 4.7 0.2 - - - +
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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
----------------------------------------------------------
171C LEU* 4.1 12.7 - - + +
190C MET* 3.8 16.5 - - + +
226C THR* 4.9 2.7 + - - +
227C GLY 2.9 4.8 + - - -
228C ALA* 1.3 76.8 - - - +
230C LYS* 1.3 62.5 + - - +
232C VAL* 3.1 19.1 + - - +
233C GLY 3.7 1.9 + - - -
243C LEU* 3.9 15.7 - - + +
244C THR* 3.3 40.6 - - - +
245C GLY* 3.6 4.9 - - - +
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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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226C THR 5.6 2.5 - - - +
227C GLY* 2.8 17.2 + - - +
229C ALA* 1.3 73.4 - - - +
231C ALA* 1.3 55.4 + - - +
233C GLY* 2.8 27.3 + - - +
234C MET* 3.6 5.6 + - - +
240C GLN* 5.2 8.3 - - - +
243C LEU 3.8 16.8 - - - +
244C THR* 4.1 15.9 - - - +
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Residues in contact with ALA 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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136C PRO* 5.9 7.4 - - + -
143C THR* 5.6 3.2 - - + +
164C ALA* 5.9 1.8 - - + -
168C THR* 3.5 20.9 - - + +
227C GLY 2.8 11.3 + - - +
228C ALA* 3.2 12.6 - - - +
230C LYS* 1.3 74.0 - - - +
232C VAL* 1.3 66.4 + - - +
234C MET* 2.9 35.0 + - - +
235C VAL* 3.3 8.9 + - + +
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Residues in contact with VAL 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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168C THR* 4.3 11.4 - - + -
171C LEU* 3.7 31.4 - - + -
172C ALA* 4.2 10.8 - - + +
175C VAL* 4.2 10.8 - - + -
228C ALA 3.1 15.5 + - - +
229C ALA 3.2 10.3 - - - +
230C LYS 3.1 0.4 - - - -
231C ALA* 1.3 75.2 - - - +
233C GLY* 1.3 51.4 + - - +
235C VAL* 2.8 9.7 + - - +
236C ILE* 2.7 56.4 + - + -
239C THR* 4.0 10.3 - - - +
243C LEU* 4.0 11.7 - - + -
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Residues in contact with GLY 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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229C ALA 3.7 2.2 + - - -
230C LYS* 2.8 14.2 + - - -
232C VAL* 1.3 79.7 - - - +
234C MET* 1.3 55.8 + - - +
236C ILE 4.0 0.7 - - - -
237C PRO* 3.1 28.2 - - - +
239C THR* 3.4 18.9 + - - -
240C GLN* 4.0 27.1 - - - +
241C GLY 5.5 0.2 - - - -
243C LEU* 5.2 0.4 - - - +
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Residues in contact with MET 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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137C ALA 5.4 7.2 - - - +
141C ALA 5.0 5.4 - - - +
142C LYS* 5.6 3.5 + - - -
143C THR* 3.5 31.0 - - + +
149C ASN* 5.1 1.6 + - - -
152C GLU* 5.7 0.9 - - - +
230C LYS 3.6 5.3 + - - +
231C ALA* 2.9 23.1 + - - +
233C GLY* 1.3 78.5 - - - +
235C VAL* 1.3 64.5 + - + +
237C PRO* 3.9 11.5 - - - +
240C GLN* 5.6 4.3 - - - +
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Residues in contact with VAL 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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143C THR* 3.9 22.4 - - + +
145C VAL* 3.9 23.3 - - + -
148C VAL* 3.4 24.5 - - + +
149C ASN* 3.1 46.2 + - - +
152C GLU* 4.5 4.0 - - - +
168C THR* 4.9 4.7 - - + -
172C ALA* 5.1 4.3 - - + -
231C ALA 3.3 11.0 + - - +
232C VAL* 2.8 9.9 + - - +
234C MET* 1.3 80.4 - - - +
236C ILE* 1.3 59.8 + - + +
237C PRO* 3.4 6.9 - - - +
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Residues in contact with ILE 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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148C VAL* 4.0 18.2 - - + -
172C ALA* 3.9 11.0 - - + +
175C VAL* 3.9 3.8 - - + -
176C HIS* 3.8 35.9 - - + +
179C VAL* 4.5 13.9 - - + -
180C LYS* 6.2 0.7 - - - +
232C VAL* 2.7 30.5 + - + +
233C GLY 3.5 3.4 - - - +
235C VAL* 1.3 81.6 - - + +
237C PRO* 1.3 51.8 - - - +
238C SER* 2.6 38.4 + - - +
239C THR* 2.7 35.0 + - + +
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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