Contacts of the helix formed by residues 204 - 214 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H ARG* 3.7 5.5 + - - -
204H ASP* 3.6 17.0 - - - +
206H GLU* 3.6 23.5 + - - +
18K ARG* 3.2 30.3 + - - -
20K GLN* 5.0 4.5 - - - +
36K LEU* 4.5 6.6 - - + +
37K ALA 5.4 0.2 - - - +
172K LYS* 4.3 2.9 - - - +
175K GLU* 4.0 16.8 - - - +
203K GLY* 1.3 74.9 - - - +
205K LYS* 1.3 71.4 + - - +
206K GLU* 2.8 11.9 + - - +
207K ALA* 2.9 13.3 + - - +
208K VAL* 3.4 13.0 + - - +
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Residues in contact with LYS 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H LYS* 3.5 23.8 - - + +
206H GLU* 6.0 7.4 - - + +
209H ASP* 3.6 20.8 + - - +
231H TYR* 5.1 2.5 - - - -
204K ASP* 1.3 79.1 - - - +
206K GLU* 1.3 56.2 + - - +
208K VAL* 3.8 10.5 - - + -
209K ASP* 2.8 54.2 + - - +
231K TYR* 3.3 39.1 - - + -
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Residues in contact with GLU 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H ASP* 5.3 4.9 - - - +
205H LYS* 4.9 23.0 - - + +
18K ARG* 3.3 34.0 + - - +
37K ALA 4.8 0.7 - - - +
38K SER* 3.2 13.5 - - - -
39K THR* 3.2 40.4 + - + +
204K ASP* 2.8 8.0 + - - +
205K LYS* 1.3 75.2 - - - +
207K ALA* 1.3 58.1 + - - +
209K ASP* 3.9 4.9 - - - +
210K ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ALA 4.2 12.7 + - - +
38K SER 5.6 0.2 - - - -
42K VAL* 3.8 25.8 - - + +
172K LYS* 3.8 20.6 - - + -
201K VAL* 4.8 1.6 - - + -
202K ASN 4.5 3.4 - - - +
203K GLY* 4.2 11.0 - - - -
204K ASP 2.9 10.4 + - - +
206K GLU* 1.3 74.7 - - - +
208K VAL* 1.3 65.4 + - - +
210K ALA* 3.1 11.8 + - - +
211K LEU* 3.1 19.2 + - - +
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Residues in contact with VAL 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145K ILE* 4.0 21.2 - - + +
172K LYS* 3.6 26.9 - - + +
204K ASP 3.4 8.9 + - - +
205K LYS* 3.3 15.0 + - + +
207K ALA* 1.3 78.1 - - - +
209K ASP* 1.3 67.0 + - - +
211K LEU* 3.3 13.4 + - - +
212K LEU* 3.1 27.7 + - + +
231K TYR* 5.0 2.2 - - + -
232K ILE* 3.4 32.5 - - + -
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Residues in contact with ASP 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H LYS* 3.6 17.4 + - + +
231H TYR* 6.0 0.3 - - - -
205K LYS* 2.8 41.0 + - - +
206K GLU* 4.0 4.7 - - + +
208K VAL* 1.3 71.1 - - - +
210K ALA* 1.3 67.5 + - - +
212K LEU* 3.1 5.8 + - - +
213K HIS* 3.0 42.4 + - + +
231K TYR* 2.7 37.5 + - - -
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Residues in contact with ALA 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K THR* 3.9 26.9 - - - +
42K VAL* 3.8 25.4 - - + -
43K GLU* 6.0 2.2 - - + -
46K ILE* 5.0 0.7 - - - -
206K GLU 3.0 16.7 + - - +
207K ALA 3.1 9.6 + - - +
209K ASP* 1.3 76.9 - - - +
211K LEU* 1.3 56.0 + - - +
213K HIS* 3.3 3.2 + - - +
214K ASP* 3.1 31.5 + - - +
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Residues in contact with LEU 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K VAL* 3.7 15.9 - - + -
46K ILE* 4.2 10.8 - - + -
143K ALA* 4.3 23.8 - - + -
145K ILE* 4.5 11.2 - - + -
170K VAL* 3.6 37.0 - - + +
172K LYS* 3.9 28.7 - - + -
201K VAL* 4.9 1.8 - - + -
207K ALA 3.1 17.9 + - - +
208K VAL* 3.4 10.5 - - - +
209K ASP 3.2 0.2 - - - -
210K ALA* 1.3 76.7 - - - +
212K LEU* 1.3 61.9 - - + +
213K HIS 3.5 0.5 + - - -
214K ASP 3.8 1.2 + - - -
217K VAL* 3.3 36.0 - - + +
220K VAL* 5.5 0.2 - - - -
241K LYS* 3.7 1.4 + - - -
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Residues in contact with LEU 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K ILE* 4.9 2.7 - - + -
208K VAL* 3.1 34.2 + - + +
209K ASP* 3.1 10.3 + - - +
211K LEU* 1.3 76.0 - - + +
213K HIS* 1.3 60.3 + - - +
214K ASP 3.6 0.2 - - - -
220K VAL* 3.9 35.7 - - + -
231K TYR* 4.2 8.3 - - + -
232K ILE* 4.0 22.0 - - + -
235K THR* 3.7 34.8 - - + -
236K ALA* 4.1 13.9 - - + +
239K ASN* 3.5 12.1 - - - +
241K LYS* 3.1 24.6 + - - +
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Residues in contact with HIS 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K ASP* 3.0 41.3 + - + +
210K ALA* 4.3 2.7 - - - +
212K LEU* 1.3 76.7 - - + +
214K ASP* 1.3 63.6 + - - +
215K ASP* 3.5 11.0 + - - +
231K TYR* 4.9 1.6 - - - -
235K THR* 3.9 23.5 - - + +
239K ASN* 3.3 36.8 + - - +
241K LYS* 4.5 0.4 - - - -
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Residues in contact with ASP 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K GLU* 3.8 12.1 - - + +
46K ILE* 3.7 22.3 - - + +
210K ALA 3.1 16.3 + - - +
211K LEU 3.8 3.5 + - - +
212K LEU 3.6 0.2 - - - -
213K HIS* 1.3 76.9 - - - +
215K ASP* 1.3 58.5 + - - +
216K ARG* 2.7 68.0 + - - +
217K VAL* 3.3 8.3 + - + +
241K LYS* 2.7 28.2 + - - -
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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