Contacts of the helix formed by residues 199 - 208 (chain A) in PDB entry 1MA3
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 ALA 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.4 19.7 - - + -
100A GLN* 4.2 12.8 - - + -
117A LEU* 3.7 31.2 - - + -
118A HIS* 4.4 13.0 - - + +
169A LEU* 4.7 2.0 - - + +
174A LEU* 6.5 0.9 - - - -
196A VAL 3.7 8.1 - - - +
197A TYR 3.3 2.2 - - - -
198A PRO* 1.3 78.8 - - - +
200A ALA* 1.3 57.1 + - - +
201A GLU 2.9 6.2 + - - -
202A LEU* 3.0 25.7 + - - +
203A PRO* 3.7 0.3 - - - +
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Residues in contact with ALA 200 (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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21A PHE* 4.5 0.6 - - - -
100A GLN* 5.8 0.2 - - - -
194A LEU* 3.7 40.4 - - + +
196A VAL 2.8 21.5 + - - +
197A TYR* 3.7 29.3 - - + +
198A PRO 3.0 0.6 + - - -
199A ALA* 1.3 71.4 - - - +
201A GLU* 1.3 59.0 + - - +
202A LEU 3.4 0.4 - - - -
203A PRO* 3.2 14.9 - - - +
204A TYR* 3.8 15.9 - - - -
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Residues in contact with GLU 201 (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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197A TYR* 3.7 25.6 - - - -
198A PRO* 2.8 20.1 + - + +
200A ALA* 1.3 77.5 - - - +
202A LEU* 1.3 64.7 + - + +
203A PRO* 3.4 0.4 - - - -
204A TYR* 3.1 36.6 + - + +
205A ILE* 3.1 23.8 + - + +
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Residues in contact with LEU 202 (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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21A PHE* 3.7 13.7 - - + -
98A ILE* 3.9 12.1 - - + -
117A LEU* 3.7 31.6 - - + -
174A LEU* 5.4 6.1 - - + -
177A ALA* 3.9 15.3 - - + +
178A ILE* 3.9 34.3 - - + +
181A ALA* 3.8 7.5 - - + +
187A PHE* 4.1 11.6 - - + -
198A PRO 4.8 2.0 - - - +
199A ALA* 3.0 13.7 + - - +
201A GLU* 1.3 77.1 - - - +
203A PRO* 1.3 65.6 - - + +
205A ILE* 3.1 19.0 + - + +
206A ALA* 3.1 21.1 + - - +
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Residues in contact with PRO 203 (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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21A PHE* 4.8 3.1 - - + -
187A PHE* 3.4 28.9 - - + -
189A VAL* 4.1 4.7 - - + -
194A LEU* 3.9 26.9 - - + -
199A ALA 3.7 3.4 - - - +
200A ALA* 3.2 19.3 - - - +
201A GLU 3.4 0.2 - - - -
202A LEU* 1.3 94.1 - - + +
204A TYR* 1.3 57.4 + - + +
206A ALA 3.2 1.4 + - - -
207A LYS* 2.8 24.1 + - - +
213A MET* 3.2 21.5 - - + +
226A ILE* 4.4 4.3 - - + -
227A PHE* 4.3 12.6 - - + -
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Residues in contact with TYR 204 (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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194A LEU* 5.7 0.4 - - + -
197A TYR* 5.9 3.4 - + - -
200A ALA 3.8 19.5 - - - -
201A GLU* 3.1 25.2 + - + +
203A PRO* 1.3 76.1 - - + +
205A ILE* 1.3 61.5 + - + +
207A LYS* 3.2 7.3 + - + +
208A LYS* 2.8 30.1 + - - +
222A MET 4.0 4.9 + - - -
223A ALA* 3.3 40.1 + - + +
226A ILE* 3.9 30.9 - - + +
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Residues in contact with ILE 205 (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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178A ILE* 4.3 20.0 - - + +
181A ALA* 4.0 10.3 - - + -
182A LYS* 3.6 31.4 - - + +
201A GLU* 3.1 21.9 + - + +
202A LEU* 3.1 29.8 + - + +
204A TYR* 1.3 76.0 - - + +
206A ALA* 1.3 59.0 + - - +
208A LYS* 3.3 14.2 + - + +
209A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 206 (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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181A ALA* 3.4 21.3 - - + +
184A CYS* 4.1 4.0 - - - -
187A PHE* 3.7 39.0 - - + -
202A LEU 3.1 10.1 + - - +
203A PRO 3.5 8.5 - - - +
205A ILE* 1.3 76.5 - - - +
207A LYS* 1.3 62.7 + - - +
209A ALA* 3.0 11.3 + - - +
210A GLY 3.2 0.2 + - - -
211A ALA* 3.2 20.6 + - + +
213A MET* 4.1 3.6 - - - -
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Residues in contact with LYS 207 (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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203A PRO 2.8 14.5 + - - +
204A TYR* 3.5 12.1 - - + +
206A ALA* 1.3 75.5 - - - +
208A LYS* 1.3 63.1 + - - +
210A GLY* 3.1 14.4 + - - -
211A ALA 4.8 4.0 - - - +
213A MET* 3.7 17.7 - - + -
226A ILE* 3.2 57.2 - - + +
228A ASP* 5.5 4.3 - - - +
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Residues in contact with LYS 208 (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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204A TYR 2.8 16.3 + - - +
205A ILE* 3.4 13.7 - - + +
207A LYS* 1.3 79.9 - - - +
209A ALA* 1.3 58.8 + - - +
210A GLY* 3.2 1.5 + - - -
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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