Contacts of the helix formed by residues 196 - 204 (chain A) in PDB entry 4U0J
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 THR 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 3.5 29.8 - - - +
20A SER* 4.6 0.4 - - - -
21A ILE* 4.6 1.1 - - + +
194A ILE* 2.9 13.8 + - + +
195A ARG* 1.3 78.4 - - - +
197A LEU* 1.3 66.1 + - - +
198A ALA* 3.8 6.7 + - - +
199A MET* 3.2 24.0 + - - +
200A SER* 3.1 17.8 + - - -
400A NAD 3.2 48.7 + - - +
401A 566 5.3 1.6 - - - +
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Residues in contact with LEU 197 (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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17A THR* 4.0 27.4 - - + -
19A SER* 3.0 16.2 + - - +
196A THR* 1.3 72.8 - - - +
198A ALA* 1.3 60.6 - - - +
200A SER* 3.1 11.1 + - - -
201A ALA* 2.9 28.4 + - + +
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Residues in contact with ALA 198 (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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196A THR* 3.3 6.7 - - - +
197A LEU* 1.3 80.6 - - - +
199A MET* 1.3 53.1 + - + +
201A ALA* 3.0 10.4 + - - +
202A ILE* 2.7 44.8 + - + +
400A NAD 5.4 8.1 - - - +
401A 566 5.7 12.1 - - + -
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Residues in contact with MET 199 (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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193A PRO* 5.8 5.4 - - + -
194A ILE 3.4 20.9 - - - +
195A ARG* 4.1 8.7 - - - -
196A THR* 3.2 23.6 + - - +
198A ALA* 1.3 73.7 - - + +
200A SER* 1.3 61.5 + - - +
202A ILE* 3.2 14.4 + - - +
203A VAL* 2.8 35.1 + - - +
215A ILE* 3.8 32.8 - - + -
219A GLU* 4.9 4.7 - - - +
400A NAD 4.1 3.6 - - - +
401A 566 3.2 56.3 - - + +
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Residues in contact with SER 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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195A ARG* 3.5 35.9 + - - +
196A THR 3.1 13.6 + - - -
197A LEU* 3.5 11.2 - - - -
199A MET* 1.3 76.1 - - - +
201A ALA* 1.3 56.6 + - - +
203A VAL* 3.5 2.5 + - - +
204A GLY* 2.9 25.8 + - - -
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Residues in contact with ALA 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 LEU* 2.9 16.3 + - + +
198A ALA* 3.1 16.2 - - - +
200A SER* 1.3 76.1 - - - +
202A ILE* 1.3 61.1 - - + +
204A GLY* 3.2 4.3 + - - -
205A GLY 3.2 6.1 + - - -
206A ALA* 2.9 34.9 + - + +
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Residues in contact with ILE 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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103A MET* 4.9 6.7 - - + -
104A GLY* 6.1 0.2 - - - -
198A ALA* 2.7 27.7 + - + +
199A MET* 3.7 24.2 - - + +
201A ALA* 1.3 70.9 - - + +
203A VAL* 1.3 60.8 + - - +
205A GLY* 2.8 21.0 + - - -
206A ALA* 3.7 9.8 + - + +
207A LEU* 4.0 40.8 - - + +
208A GLY 4.7 0.5 - - - +
211A ALA* 4.9 7.9 - - + -
212A GLY* 3.4 8.4 + - - -
215A ILE* 3.2 29.2 - - + -
401A 566 4.4 11.0 - - + +
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Residues in contact with VAL 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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195A ARG* 3.8 31.6 - - - +
199A MET* 2.8 25.4 + - + +
200A SER 3.8 3.6 - - - +
202A ILE* 1.3 72.5 - - - +
204A GLY* 1.3 58.5 + - - +
205A GLY 3.1 1.3 + - - -
209A GLU* 5.5 1.9 - - - +
212A GLY* 3.9 17.7 - - - +
215A ILE* 3.8 30.1 - - + -
216A GLN* 3.5 33.4 - - + +
219A GLU* 4.0 4.3 - - - +
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Residues in contact with GLY 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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200A SER 2.9 16.1 + - - -
201A ALA* 3.5 7.9 - - - -
202A ILE 3.1 0.6 - - - -
203A VAL* 1.3 75.8 - - - +
205A GLY* 1.3 56.9 + - - +
206A ALA 3.7 0.4 - - - -
209A GLU* 5.4 1.9 - - - +
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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