Contacts of the helix formed by residues 204 - 214 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ARG* 3.3 40.3 + - - -
20G GLN* 5.2 2.2 - - - +
36G LEU* 4.5 9.0 - - + +
37G ALA 4.6 1.4 - - - +
172G LYS* 4.1 3.3 - - - +
175G GLU* 3.7 17.3 - - - +
203G GLY* 1.3 75.7 - - - -
205G LYS* 1.3 70.5 + - - +
206G GLU* 3.1 13.6 + - - +
207G ALA* 3.1 13.5 + - - +
208G VAL* 3.3 16.7 + - - +
18J ARG* 4.0 9.3 + - - +
204J ASP* 3.8 9.0 - - - +
205J LYS* 6.1 0.9 - - - +
206J GLU* 5.3 5.7 + - - +
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Residues in contact with LYS 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G ASP* 1.3 79.6 - - - +
206G GLU* 1.3 63.1 + - - +
208G VAL* 3.2 10.1 + - + -
209G ASP* 2.8 45.8 + - - +
228G ILE* 6.3 0.8 - - - +
231G TYR* 3.3 42.3 - - + -
205J LYS* 3.6 32.5 - - + +
206J GLU* 6.6 0.2 - - - -
209J ASP* 4.0 12.9 + - - +
231J TYR* 5.2 2.0 - - - -
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Residues in contact with GLU 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 3.2 22.8 + - - +
37G ALA 4.5 1.3 - - - +
38G SER* 3.2 29.0 - - - -
39G THR* 3.4 22.6 + - + +
204G ASP* 3.1 18.0 + - - +
205G LYS* 1.3 78.0 - - - +
207G ALA* 1.3 56.9 + - - +
209G ASP* 3.6 7.5 + - + +
210G ALA* 3.1 25.6 + - - +
204J ASP* 5.4 4.0 - - - +
205J LYS* 5.5 17.2 + - + +
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Residues in contact with ALA 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ALA* 3.9 17.2 + - + +
38G SER 5.4 0.2 - - - -
42G VAL* 3.8 25.6 - - + +
172G LYS* 3.9 20.0 - - + -
201G VAL* 4.7 0.9 - - + -
203G GLY* 4.3 5.4 - - - -
204G ASP* 3.1 16.6 + - - +
206G GLU* 1.3 76.2 - - - +
208G VAL* 1.3 64.2 + - - +
210G ALA* 3.2 5.4 + - - +
211G LEU* 3.1 26.6 + - - +
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Residues in contact with VAL 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G ILE* 3.7 23.8 - - + -
172G LYS* 3.4 30.3 - - + +
204G ASP 3.3 9.2 + - - +
205G LYS* 3.2 12.1 + - + +
207G ALA* 1.3 72.2 - - - +
209G ASP* 1.3 68.6 + - - +
211G LEU* 3.2 12.0 + - - +
212G LEU* 3.0 28.0 + - + +
231G TYR* 5.2 2.5 - - + -
232G ILE* 3.4 32.8 - - + -
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Residues in contact with ASP 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G LYS* 2.8 44.9 + - - +
206G GLU* 3.8 6.6 - - - +
208G VAL* 1.3 74.2 - - - +
210G ALA* 1.3 62.8 + - - +
212G LEU* 3.3 5.2 + - - +
213G HIS* 2.9 42.4 + - + +
231G TYR* 2.6 33.9 + - - -
205J LYS* 3.8 15.4 + - - +
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Residues in contact with ALA 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G THR* 3.9 26.6 - - + +
42G VAL* 3.6 25.8 - - + -
43G GLU* 5.5 2.9 - - + +
46G ILE* 4.4 0.6 - - + +
206G GLU 3.1 15.3 + - - +
207G ALA 3.3 10.1 - - - +
208G VAL 3.2 0.2 - - - -
209G ASP* 1.3 76.2 - - - +
211G LEU* 1.3 63.6 + - - +
213G HIS* 4.0 1.9 - - - +
214G ASP* 3.1 27.4 + - - +
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Residues in contact with LEU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G VAL* 3.8 14.6 - - + -
46G ILE* 4.0 12.1 - - + -
143G ALA* 4.0 27.4 - - + -
145G ILE* 4.3 16.6 - - + -
170G VAL* 3.7 37.0 - - + +
172G LYS* 4.0 26.5 - - + -
201G VAL* 5.3 0.7 - - + -
207G ALA 3.1 18.0 + - - +
208G VAL* 3.2 7.4 + - - +
210G ALA* 1.3 78.1 - - - +
212G LEU* 1.3 64.9 + - + +
213G HIS 3.3 0.7 + - - -
214G ASP 3.7 1.2 + - - -
217G VAL* 3.4 31.9 - - + +
220G VAL* 5.5 0.2 - - - -
241G LYS* 3.7 1.4 + - - -
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Residues in contact with LEU 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G ILE* 4.9 2.7 - - + -
208G VAL* 3.0 25.8 + - + +
209G ASP* 3.3 8.3 + - - +
211G LEU* 1.3 76.7 - - + +
213G HIS* 1.3 60.9 + - - +
220G VAL* 3.8 35.2 - - + -
231G TYR* 4.2 8.7 - - + -
232G ILE* 3.7 34.8 - - + -
235G THR* 4.0 31.6 - - + -
236G ALA* 4.2 12.9 - - + +
239G ASN* 3.5 11.6 - - - +
241G LYS* 3.1 26.0 + - - +
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Residues in contact with HIS 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209G ASP* 2.9 40.6 + - + +
210G ALA* 4.4 2.2 - - - +
212G LEU* 1.3 77.2 - - + +
214G ASP* 1.3 64.4 + - - +
215G ASP* 3.4 10.1 + - - +
231G TYR* 4.8 2.2 - - - -
235G THR* 3.8 22.6 - - + +
239G ASN* 3.3 35.2 + - - +
241G LYS* 4.4 0.9 - - - -
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Residues in contact with ASP 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G GLU* 3.8 12.5 - - + +
46G ILE* 3.6 24.3 - - + +
210G ALA 3.1 17.2 + - - +
211G LEU 4.2 2.2 - - - +
212G LEU 3.6 0.4 - - - -
213G HIS* 1.3 76.5 - - - +
215G ASP* 1.3 59.7 + - - +
216G ARG* 2.9 66.9 + - - +
217G VAL* 3.2 7.4 + - + +
241G LYS* 2.8 25.0 + - - -
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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