Contacts of the helix formed by residues 204 - 214 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ARG* 2.8 40.2 + - - -
20H GLN* 5.2 0.2 - - - +
36H LEU* 4.2 7.3 - - + +
37H ALA 4.4 1.2 - - - +
172H LYS* 4.5 2.2 - - - +
175H GLU* 4.2 16.6 - - - +
203H GLY* 1.3 80.1 - - - +
205H LYS* 1.3 69.1 + - - +
206H GLU* 3.0 10.2 + - - +
207H ALA* 3.1 12.7 + - - +
208H VAL* 3.3 16.5 + - - +
18K ARG* 3.0 28.6 + - - +
204K ASP* 3.6 8.0 - - - +
206K GLU* 5.3 4.2 - - - +
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Residues in contact with LYS 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H ASP* 1.3 78.6 - - - +
206H GLU* 1.3 56.2 + - - +
208H VAL* 3.5 9.5 + - + +
209H ASP* 2.8 38.7 + - - +
231H TYR* 3.5 34.8 - - + -
205K LYS* 3.5 42.0 - - + +
206K GLU* 4.9 26.0 + - + +
209K ASP* 3.6 15.5 + - + +
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Residues in contact with GLU 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ARG* 2.9 29.6 + - - +
37H ALA 4.8 0.4 - - - -
38H SER* 3.4 30.0 - - - -
39H THR* 3.7 20.1 + - + +
204H ASP* 3.0 6.4 + - - +
205H LYS* 1.3 77.3 - - - +
207H ALA* 1.3 65.8 + - - +
209H ASP* 3.9 6.8 - - + +
210H ALA* 3.1 21.7 + - - +
204K ASP* 3.6 16.3 - - - +
205K LYS* 6.0 8.0 - - + +
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Residues in contact with ALA 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ALA* 4.0 11.2 + - + +
38H SER 5.5 0.4 - - - -
42H VAL* 3.9 25.2 - - + +
172H LYS* 3.9 20.2 - - + -
201H VAL* 5.0 1.1 - - + -
202H ASN 4.9 1.8 - - - +
203H GLY* 4.0 16.6 - - - -
204H ASP* 3.1 11.5 + - - +
206H GLU* 1.3 74.4 - - - +
208H VAL* 1.3 65.1 + - - +
210H ALA* 3.1 14.9 + - - +
211H LEU* 3.1 17.4 + - - +
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Residues in contact with VAL 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H ILE* 3.8 25.1 - - + -
172H LYS* 3.5 27.8 - - + +
204H ASP 3.3 8.4 + - - +
205H LYS* 3.5 13.2 - - + +
207H ALA* 1.3 77.7 - - - +
209H ASP* 1.3 60.1 + - - +
211H LEU* 3.1 12.8 + - - +
212H LEU* 3.1 31.9 + - + +
231H TYR* 5.1 1.6 - - + -
232H ILE* 3.4 32.5 - - + -
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Residues in contact with ASP 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H LYS* 2.8 27.1 + - - +
206H GLU* 3.9 7.8 - - + +
208H VAL* 1.3 74.8 - - - +
210H ALA* 1.3 65.7 + - - +
212H LEU* 3.3 5.4 + - - +
213H HIS* 2.8 41.7 + - + +
231H TYR* 2.6 37.3 + - - -
205K LYS* 3.6 30.7 + - - +
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Residues in contact with ALA 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H THR* 3.8 30.9 - - - +
42H VAL* 3.8 21.3 - - + -
43H GLU* 5.9 2.8 - - + +
46H ILE* 4.5 0.9 - - - +
206H GLU 3.1 12.8 + - - +
207H ALA 3.1 10.9 + - - +
209H ASP* 1.3 77.0 - - - +
211H LEU* 1.3 60.3 + - - +
213H HIS* 4.0 3.0 - - - +
214H ASP* 3.2 27.7 + - - +
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Residues in contact with LEU 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H VAL* 3.9 15.3 - - + -
46H ILE* 4.3 10.3 - - + -
143H ALA* 4.2 26.9 - - + -
144H GLY 4.7 0.2 - - - +
145H ILE* 4.4 11.0 - - + -
170H VAL* 3.9 35.4 - - + +
172H LYS* 3.9 29.4 - - + -
201H VAL* 5.1 2.2 - - + -
207H ALA 3.1 16.3 + - - +
208H VAL* 3.1 12.5 + - - +
210H ALA* 1.3 76.5 - - - +
212H LEU* 1.3 66.8 + - + +
213H HIS 3.4 0.7 + - - -
214H ASP 3.9 1.2 + - - -
217H VAL* 3.6 32.6 - - + +
241H LYS* 3.6 2.8 + - - -
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Residues in contact with LEU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H ILE* 4.8 3.8 - - + -
208H VAL* 3.1 21.6 + - + +
209H ASP* 3.3 8.9 + - - +
211H LEU* 1.3 80.7 - - + +
213H HIS* 1.3 57.6 + - - +
220H VAL* 3.9 35.9 - - + -
231H TYR* 4.1 8.1 - - + -
232H ILE* 3.8 33.2 - - + -
235H THR* 3.8 34.3 - - + -
236H ALA* 4.2 11.8 - - + +
239H ASN* 3.6 14.7 - - - +
241H LYS* 3.1 22.7 + - - +
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Residues in contact with HIS 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H ASP* 2.8 39.4 + - + +
210H ALA* 4.0 2.7 - - - +
212H LEU* 1.3 80.1 - - + +
214H ASP* 1.3 61.8 + - - +
215H ASP* 3.6 11.0 + - - +
231H TYR* 4.8 2.0 - - - -
235H THR* 3.8 25.3 - - + +
239H ASN* 3.6 32.1 + - - +
241H LYS* 4.3 1.1 - - - -
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Residues in contact with ASP 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLU* 3.7 18.0 - - + +
46H ILE* 3.7 18.7 - - + +
210H ALA 3.2 16.1 + - - +
211H LEU 3.9 2.4 + - - +
212H LEU 3.7 0.2 - - - -
213H HIS* 1.3 76.1 - - - +
215H ASP* 1.3 59.8 + - - +
216H ARG* 2.6 70.0 + - - +
217H VAL* 3.1 8.7 + - + +
241H LYS* 2.8 22.9 + - - -
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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