Contacts of the helix formed by residues 227 - 236 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A THR* 1.3 74.9 + - - +
228A ALA* 1.3 59.5 + - - +
229A ALA 3.3 2.9 - - - -
230A LYS* 3.1 20.6 + - - +
231A ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 4.1 6.7 + - - +
167A THR* 3.5 36.8 - - + -
168A THR* 2.9 32.1 + - - +
171A LEU* 5.0 1.3 - - + -
190A MET* 4.4 4.7 - - + -
226A THR* 3.3 12.7 + - - +
227A GLY* 1.3 76.8 - - - +
229A ALA* 1.3 61.0 + - - +
231A ALA* 3.5 1.2 + - - -
232A VAL* 3.4 19.3 + - - +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 4.0 14.6 - - + +
190A MET* 3.8 19.2 - - + +
226A THR* 5.2 1.4 + - - +
227A GLY 3.3 0.6 - - - -
228A ALA* 1.3 76.4 - - - +
230A LYS* 1.3 67.4 + - - +
232A VAL* 3.1 18.4 + - - +
233A GLY 4.0 0.9 + - - -
243A LEU* 3.9 15.1 - - + +
244A THR* 3.3 39.7 - - - +
245A GLY* 3.7 3.8 - - - +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR 3.9 17.6 + - - +
227A GLY* 3.1 15.5 + - - +
229A ALA* 1.3 79.1 - - - +
231A ALA* 1.3 56.7 + - - +
233A GLY* 2.8 23.6 + - - -
234A MET* 4.1 3.0 + - - +
240A GLN* 5.8 0.5 - - - +
241A GLY* 6.0 0.6 + - - -
243A LEU 3.8 14.1 - - - +
244A THR* 3.4 25.0 + - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 6.3 3.8 - - + -
143A THR* 5.7 3.9 - - + +
164A ALA* 5.8 3.6 - - + -
168A THR* 3.7 17.5 - - + +
227A GLY 2.9 18.1 + - - +
228A ALA* 3.5 8.1 - - - +
229A ALA 3.2 0.2 - - - -
230A LYS* 1.3 72.4 - - - +
232A VAL* 1.3 61.9 + - - +
233A GLY 2.9 5.6 - - - -
234A MET* 2.9 35.8 + - - +
235A VAL* 3.5 8.8 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 4.1 11.4 - - + -
171A LEU* 3.6 26.0 - - + -
172A ALA* 4.0 18.4 - - + +
175A VAL* 4.2 10.8 - - + -
228A ALA 3.6 14.4 - - - +
229A ALA 3.1 8.7 + - - +
230A LYS 3.1 0.8 - - - -
231A ALA* 1.3 78.2 - - - +
233A GLY* 1.3 56.2 + - - +
235A VAL* 3.3 5.1 + - - +
236A ILE* 2.8 46.4 + - + +
239A THR* 3.9 10.8 - - - +
243A LEU* 4.1 13.5 - - + -
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA 4.0 1.2 + - - -
230A LYS 2.8 13.7 + - - -
232A VAL* 1.3 80.9 - - - +
234A MET* 1.3 57.8 + - - +
236A ILE 3.7 1.1 - - - -
237A PRO* 3.3 14.9 - - - +
239A THR* 3.5 15.6 + - - -
240A GLN* 3.0 43.1 + - - -
243A LEU* 6.2 0.2 - - - +
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Residues in contact with MET 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA 5.5 7.4 - - - +
140A GLY* 5.9 5.8 - - - -
141A ALA 4.8 8.1 - - - +
142A LYS* 5.2 5.7 + - - -
143A THR* 4.2 28.8 - - + +
149A ASN* 4.5 4.5 + - - -
152A GLU* 5.4 0.5 - - - +
230A LYS 4.1 1.5 + - - +
231A ALA* 2.9 23.8 + - - +
233A GLY* 1.3 78.9 - - - +
235A VAL* 1.3 65.5 + - + +
237A PRO* 4.5 7.8 - - - +
240A GLN* 4.6 5.6 - - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 4.2 19.7 - - + +
145A VAL* 3.6 25.6 - - + -
148A VAL* 3.2 33.2 - - + +
149A ASN* 3.3 42.1 + - - +
152A GLU* 5.1 2.4 - - - +
168A THR* 5.1 4.7 - - + -
172A ALA* 5.0 2.9 - - + -
231A ALA 3.5 9.2 + - - +
232A VAL* 3.3 8.4 + - - +
234A MET* 1.3 78.6 - - - +
236A ILE* 1.3 63.4 + - + +
237A PRO* 3.8 5.5 - - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.9 13.9 - - + -
172A ALA* 4.0 5.8 - - - +
175A VAL* 4.2 4.3 - - + -
176A HIS* 3.7 45.8 - - + +
179A VAL* 4.5 13.0 - - + -
232A VAL* 2.8 23.9 + - + +
233A GLY 3.4 4.8 - - - +
235A VAL* 1.3 86.9 - - + +
237A PRO* 1.3 67.3 - - + +
238A SER* 3.2 19.3 - - - +
239A THR* 2.8 33.5 + - + +
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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