Contacts of the helix formed by residues 197 - 206 (chain A) in PDB entry 4DHZ
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ALA* 6.0 1.8 - - - -
192A ILE* 4.0 2.7 - - - -
195A GLY 5.1 2.5 - - - +
196A MET* 1.3 76.2 - - - +
198A VAL* 1.3 59.1 + - - +
199A ALA* 3.5 8.4 + - - +
200A GLN* 3.0 45.3 + - - +
201A TYR* 2.8 28.8 + - - +
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Residues in contact with VAL 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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181A LEU* 3.9 37.9 - - + +
182A LYS* 4.1 14.4 - - + +
185A SER* 3.8 23.8 - - - +
188A TYR* 4.6 2.5 - - + -
189A ALA* 3.6 35.0 - - + +
192A ILE* 3.4 19.7 - - + +
197A THR* 1.3 72.8 - - - +
199A ALA* 1.3 57.4 + - - +
201A TYR* 3.4 1.9 + - - +
202A CYS* 3.0 28.7 + - - -
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Residues in contact with ALA 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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182A LYS* 4.7 13.2 - - + +
197A THR* 3.2 7.2 + - - +
198A VAL* 1.3 80.1 - - - +
200A GLN* 1.3 62.1 + - + +
202A CYS* 3.5 5.8 + - - +
203A GLU* 3.1 44.5 + - - +
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Residues in contact with GLN 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 GLY 4.2 2.8 - - - +
196A MET* 3.4 23.5 - - + +
197A THR* 3.0 50.2 + - - +
199A ALA* 1.3 75.9 - - + +
201A TYR* 1.3 65.6 + - - +
203A GLU* 4.1 7.4 - - - +
204A GLN* 3.2 26.7 + - - +
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Residues in contact with TYR 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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181A LEU* 4.5 4.7 - - + -
192A ILE* 3.6 34.1 - - + -
193A ASP* 5.2 7.2 - - - -
196A MET* 3.9 18.0 - - - +
197A THR 2.8 15.2 + - - +
198A VAL 3.7 3.4 - - - +
200A GLN* 1.3 77.9 - - - +
202A CYS* 1.3 55.3 + - - +
205A GLU* 2.7 64.4 + - + +
206A ILE* 3.6 29.3 - - + +
214A ASP* 4.0 24.4 + - - +
216A LEU* 4.1 28.3 - - + +
217A ALA* 4.8 3.7 + - + +
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Residues in contact with CYS 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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178A SER* 3.2 39.7 - - - +
181A LEU* 3.8 31.0 - - - -
182A LYS* 4.0 16.2 - - - -
198A VAL* 3.0 20.8 + - - +
199A ALA 3.7 4.5 - - - +
201A TYR* 1.3 76.3 - - - +
203A GLU* 1.3 58.0 + - - +
206A ILE* 2.8 31.6 + - - -
207A GLU* 2.8 15.3 + - - +
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Residues in contact with GLU 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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182A LYS* 5.2 5.2 + - - +
199A ALA* 3.1 32.7 + - - +
200A GLN* 4.1 6.2 - - - +
202A CYS* 1.3 79.8 - - + +
204A GLN* 1.3 58.0 + - - +
207A GLU* 4.1 26.5 - - - +
208A PRO* 3.3 20.8 - - - +
94F LYS* 5.6 5.7 - - + +
96F SER* 5.1 5.1 - - - -
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A MET* 3.4 28.9 - - + +
200A GLN 3.2 16.5 + - - +
201A TYR 3.9 0.2 - - - +
203A GLU* 1.3 79.3 - - - +
205A GLU* 1.3 73.5 + - + +
208A PRO* 3.1 14.0 - - - +
211A LYS* 3.1 29.3 + - - +
94F LYS* 4.5 27.7 - - + +
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Residues in contact with GLU 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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90A TYR* 5.1 0.5 + - - -
174A ARG* 4.1 2.8 + - - -
196A MET* 5.0 5.4 - - - -
201A TYR* 2.7 58.2 + - + +
204A GLN* 1.3 105.2 + - + +
206A ILE* 1.3 59.3 + - + +
207A GLU 3.9 0.2 - - - -
208A PRO* 3.9 2.2 - - - -
211A LYS* 3.3 41.8 + - - +
212A ASP 4.2 11.9 - - - +
574B ARG* 4.3 16.3 + - - -
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Residues in contact with ILE 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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90A TYR* 4.0 14.6 - - - +
174A ARG* 3.1 53.6 + - - +
177A THR* 3.9 13.7 - - + +
178A SER* 3.9 15.3 - - - +
181A LEU* 3.4 32.8 - - + -
201A TYR* 3.6 23.6 - - + +
202A CYS* 2.8 20.6 + - - +
205A GLU* 1.3 77.7 - - + +
207A GLU* 1.3 61.0 + - - +
208A PRO* 3.4 0.9 - - - -
217A ALA* 3.9 18.4 - - + -
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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