Contacts of the helix formed by residues 204 - 214 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ARG* 2.7 32.3 + - - -
20I GLN* 5.0 6.0 - - - +
36I LEU* 3.8 12.0 - - + +
37I ALA 5.0 0.9 - - - +
172I LYS* 4.5 3.4 - - - +
175I GLU* 4.6 13.9 - - - +
203I GLY* 1.3 75.4 - - - +
205I LYS* 1.3 69.4 + - - +
206I GLU* 3.0 25.3 + - - +
207I ALA* 3.2 10.2 + - - +
208I VAL* 3.3 17.2 + - - +
501I NAD 5.1 3.4 - - - -
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Residues in contact with LYS 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204I ASP* 1.3 79.3 + - + +
206I GLU* 1.3 56.0 + - - +
208I VAL* 3.3 1.9 + - - +
209I ASP* 2.9 57.1 + - - +
231I TYR* 3.4 32.9 - - - -
501I NAD 3.3 46.2 + - + +
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Residues in contact with GLU 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 2.5 34.9 + - - +
37I ALA 4.6 0.7 - - - +
38I SER* 3.3 20.5 - - - -
39I THR* 3.2 37.3 + - + +
204I ASP* 3.0 12.4 + - - +
205I LYS* 1.3 78.7 - - - +
207I ALA* 1.3 59.0 + - - +
209I ASP* 3.5 7.6 + - + +
210I ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ALA* 3.8 17.3 + - + +
38I SER 5.5 0.2 - - - -
42I VAL* 3.8 21.6 - - + +
172I LYS* 3.8 21.1 - - + -
201I VAL* 4.8 1.1 - - + -
202I ASN 4.6 3.6 - - - +
203I GLY* 4.1 13.0 - - - -
204I ASP* 3.2 8.7 + - - +
206I GLU* 1.3 75.9 - - - +
208I VAL* 1.3 65.4 + - - +
210I ALA* 3.4 3.3 - - - +
211I LEU* 3.2 26.2 + - - +
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Residues in contact with VAL 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I ILE* 3.8 20.9 - - + -
172I LYS* 3.5 26.5 - - + +
204I ASP 3.3 7.7 + - - +
205I LYS 3.5 7.2 - - - +
207I ALA* 1.3 74.3 - - - +
209I ASP* 1.3 60.1 + - - +
211I LEU* 3.2 10.9 + - - +
212I LEU* 3.0 33.2 + - + +
232I ILE* 3.5 31.9 - - + -
501I NAD 3.5 26.9 - - + +
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Residues in contact with ASP 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I THR* 5.8 1.8 - - + -
205I LYS* 2.9 43.3 + - - +
206I GLU* 3.9 7.2 - - + +
207I ALA 3.5 0.2 - - - -
208I VAL* 1.3 76.4 - - - +
210I ALA* 1.3 62.7 + - - +
212I LEU* 3.4 4.5 + - - +
213I HIS* 2.7 46.2 + - + +
231I TYR* 2.6 31.3 + - - -
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Residues in contact with ALA 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I THR* 4.0 24.0 - - - +
42I VAL* 3.5 29.6 - - + -
43I GLU* 6.0 1.7 - - + +
46I ILE* 4.5 0.5 - - - +
206I GLU 3.0 18.1 + - - +
207I ALA 3.4 7.2 - - - +
208I VAL 3.2 0.2 - - - -
209I ASP* 1.3 76.0 - - - +
211I LEU* 1.3 61.9 + - - +
213I HIS* 4.0 2.1 - - - +
214I ASP* 3.2 27.7 + - - +
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Residues in contact with LEU 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL* 3.9 14.4 - - + -
46I ILE* 4.2 9.6 - - + -
143I ALA* 4.0 29.2 - - + -
145I ILE* 4.5 13.2 - - + -
170I VAL* 3.6 34.5 - - + +
172I LYS* 3.8 27.8 - - + -
201I VAL* 5.0 1.6 - - + -
207I ALA 3.2 14.5 + - - +
208I VAL* 3.2 8.6 + - - +
210I ALA* 1.3 79.2 - - - +
212I LEU* 1.3 65.3 + - + +
213I HIS 3.4 0.3 + - - -
214I ASP 3.9 1.0 + - - -
217I VAL* 3.5 33.5 - - + +
220I VAL* 5.5 0.4 - - - -
241I LYS* 3.7 2.1 + - - -
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Residues in contact with LEU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I ILE* 4.8 3.6 - - + -
208I VAL* 3.0 33.7 + - + +
209I ASP* 3.4 5.8 + - - +
211I LEU* 1.3 77.0 - - - +
213I HIS* 1.3 63.8 + - - +
220I VAL* 4.0 30.1 - - + -
231I TYR* 4.2 12.3 - - + +
232I ILE* 4.0 19.3 - - + +
235I THR* 3.9 28.0 - - + -
236I ALA* 4.0 21.3 - - + +
239I ASN* 3.4 13.7 - - - +
241I LYS* 3.1 24.6 + - - +
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Residues in contact with HIS 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I ASP* 2.7 45.8 + - + +
210I ALA* 4.4 2.2 - - - +
211I LEU 3.3 0.2 - - - -
212I LEU* 1.3 77.9 - - + +
214I ASP* 1.3 63.3 + - - +
215I ASP* 3.6 9.1 + - - +
231I TYR* 4.9 1.6 - - - -
235I THR* 4.0 24.4 - - + +
239I ASN* 3.5 29.4 + - - +
241I LYS* 4.5 0.7 - - - -
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Residues in contact with ASP 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I GLU* 3.8 17.9 - - + +
46I ILE* 3.7 18.1 - - + +
210I ALA 3.2 16.8 + - - +
211I LEU 3.9 2.0 + - - +
212I LEU 3.6 0.4 - - - -
213I HIS* 1.3 78.3 - - - +
215I ASP* 1.3 59.4 + - - +
216I ARG* 2.8 57.7 + - - +
217I VAL* 3.2 8.5 + - + +
241I LYS* 2.7 26.3 + - - -
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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