Contacts of the helix formed by residues 204 - 214 (chain A) in PDB entry 4ZZ7
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 ASP 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.3 37.1 + - - -
20A GLN* 5.1 4.6 - - - +
36A LEU* 4.4 9.5 - - + +
37A ALA 5.2 0.9 - - - +
175A GLU* 3.9 17.7 - - - +
203A GLY* 1.3 75.4 - - - +
205A LYS* 1.3 72.7 + - - +
206A GLU* 2.8 13.9 + - - +
207A ALA* 2.8 13.5 + - - +
208A VAL* 3.3 13.1 + - - +
501A NAD 4.3 4.0 - - - -
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Residues in contact with LYS 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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175A GLU* 5.3 0.2 + - - -
204A ASP* 1.3 78.4 - - - +
206A GLU* 1.3 56.9 + - - +
208A VAL* 3.2 2.3 + - - +
209A ASP* 2.9 48.9 + - - +
231A TYR* 3.5 28.3 - - - -
501A NAD 3.3 55.0 + - + +
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Residues in contact with GLU 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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18A ARG* 2.8 30.5 + - - +
37A ALA 4.8 1.6 - - - +
38A SER* 3.1 16.0 - - - -
39A THR* 2.9 42.5 + - + +
204A ASP* 2.8 17.8 + - - +
205A LYS* 1.3 76.3 - - - +
207A ALA* 1.3 59.1 + - - +
209A ASP* 3.6 6.0 + - - +
210A ALA* 3.1 21.7 + - - +
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Residues in contact with ALA 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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37A ALA 3.9 14.4 + - - +
38A SER 5.6 0.2 - - - -
42A VAL* 3.7 25.9 - - + +
172A LYS* 4.0 19.5 - - + -
201A VAL* 4.8 1.3 - - + -
202A ASN 4.7 2.9 - - - +
203A GLY* 4.3 10.5 - - - -
204A ASP* 2.8 12.2 + - - +
206A GLU* 1.3 73.3 - - - +
208A VAL* 1.3 68.6 + - - +
210A ALA* 3.2 3.3 + - - +
211A LEU* 3.2 26.6 + - - +
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Residues in contact with VAL 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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145A ILE* 3.8 15.9 - - + +
172A LYS* 3.6 24.5 - - + -
204A ASP 3.3 6.2 + - - +
205A LYS 3.2 7.1 + - - +
207A ALA* 1.3 78.5 - - - +
209A ASP* 1.3 63.9 + - - +
211A LEU* 3.2 13.4 + - - +
212A LEU* 3.1 27.7 + - + +
232A ILE* 3.4 32.8 - - + -
501A NAD 3.4 35.7 - - + +
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Residues in contact with ASP 209 (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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205A LYS* 2.9 45.0 + - - +
206A GLU* 4.1 6.0 - - - +
208A VAL* 1.3 76.7 - - - +
210A ALA* 1.3 61.4 + - - +
212A LEU* 3.9 7.5 - - - +
213A HIS* 2.8 44.6 + - + +
231A TYR* 2.4 34.7 + - - -
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Residues in contact with ALA 210 (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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39A THR* 4.1 25.3 - - + +
42A VAL* 3.7 26.0 - - + -
43A GLU* 5.6 3.3 - - + +
46A ILE* 4.9 0.9 - - + -
206A GLU 3.1 15.7 + - - +
207A ALA 3.5 9.0 - - - +
208A VAL 3.2 0.6 - - - -
209A ASP* 1.3 76.2 - - - +
211A LEU* 1.3 61.9 + - - +
213A HIS* 3.4 2.3 + - - +
214A ASP* 3.0 28.2 + - - +
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Residues in contact with LEU 211 (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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42A VAL* 3.7 20.0 - - + -
46A ILE* 4.2 10.8 - - + -
143A ALA* 4.1 26.2 - - + -
145A ILE* 4.4 15.3 - - + -
170A VAL* 3.7 31.9 - - + +
172A LYS* 3.9 27.8 - - + -
201A VAL* 5.1 1.3 - - + -
207A ALA 3.5 13.9 - - - +
208A VAL* 3.2 7.6 + - - +
210A ALA* 1.3 80.6 - - - +
212A LEU* 1.3 66.1 + - + +
213A HIS 3.3 0.7 + - - -
214A ASP 3.5 1.9 + - - -
217A VAL* 3.3 33.2 - - + +
220A VAL* 5.6 0.7 - - + -
241A LYS* 3.5 2.6 + - - -
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Residues in contact with LEU 212 (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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145A ILE* 5.1 2.5 - - + -
208A VAL* 3.1 31.7 + - + +
209A ASP* 3.8 12.6 - - - +
210A ALA 3.4 0.2 - - - -
211A LEU* 1.3 76.9 - - + +
213A HIS* 1.3 70.2 + - - +
220A VAL* 4.1 23.1 - - + -
231A TYR* 4.1 2.9 - - + -
232A ILE* 4.0 32.3 - - + +
235A THR* 3.8 28.0 - - + -
236A ALA* 4.2 15.6 - - + +
239A ASN* 3.7 11.1 - - - +
241A LYS* 2.9 27.6 + - - +
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Residues in contact with HIS 213 (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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209A ASP* 2.8 43.2 + - + +
210A ALA* 4.3 1.6 - - - +
212A LEU* 1.3 78.5 - - + +
214A ASP* 1.3 63.4 + - - +
215A ASP* 3.3 14.3 + - - +
231A TYR* 4.8 1.6 - - - -
235A THR* 3.6 28.6 - - + +
239A ASN* 3.6 25.4 + - - +
241A LYS* 4.4 0.4 - - - -
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Residues in contact with ASP 214 (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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43A GLU* 3.9 12.0 - - + +
46A ILE* 3.6 22.7 - - + +
210A ALA 3.0 17.5 + - - +
211A LEU 3.5 3.5 + - - +
213A HIS* 1.3 75.4 - - - +
215A ASP* 1.3 59.6 + - - +
216A ARG* 2.8 69.1 + - - +
217A VAL* 3.2 9.0 + - + +
241A LYS* 2.7 24.7 + - - -
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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