Contacts of the helix formed by residues 204 - 213 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234D ARG* 5.0 3.3 + - - -
18E ARG* 3.0 41.6 + - - -
20E GLN* 5.1 4.6 - - - +
36E LEU* 4.1 12.6 - - + +
37E ALA 4.8 0.9 - - - +
172E LYS* 4.5 2.0 - - - +
175E GLU* 4.0 19.3 - - + +
203E GLY* 1.3 74.4 - - - +
205E LYS* 1.3 62.6 + - - +
206E GLU* 3.5 10.4 + - - +
207E ALA* 2.8 25.2 + - - +
208E VAL* 3.3 10.5 + - - +
501E NAD 4.7 1.8 - - - -
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Residues in contact with LYS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LYS* 3.2 36.8 - - - +
231D TYR* 4.8 11.4 - - + -
501D NAD 5.4 3.4 + - - -
204E ASP* 1.3 78.4 - - + +
206E GLU* 1.3 60.2 + - - +
208E VAL* 3.4 3.0 + - - +
209E ASP* 3.0 59.1 + - - +
231E TYR* 3.6 14.6 - - - -
501E NAD 3.1 58.8 + - + +
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Residues in contact with GLU 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D TYR* 5.9 8.7 - - + -
234D ARG* 4.2 14.0 - - - +
18E ARG* 2.9 23.3 + - - +
37E ALA 4.6 0.7 - - - +
38E SER* 3.2 35.0 - - - -
39E THR* 3.2 23.9 + - + +
204E ASP* 3.0 12.3 + - - +
205E LYS* 1.3 75.0 - - - +
207E ALA* 1.3 65.5 + - - +
209E ASP* 3.5 9.1 + - + +
210E ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ALA* 3.7 22.5 + - + +
38E SER 5.5 0.2 - - - -
42E VAL* 3.9 18.3 - - + +
172E LYS* 4.0 18.2 - - + -
201E VAL* 4.9 0.7 - - + -
202E ASN 4.8 0.7 - - - +
203E GLY* 4.1 5.2 - - - -
204E ASP* 2.8 18.8 + - - +
206E GLU* 1.3 78.6 - - - +
208E VAL* 1.3 62.1 + - - +
210E ALA* 3.3 6.4 + - - +
211E LEU* 3.2 25.8 + - - +
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Residues in contact with VAL 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E ILE* 3.8 23.6 - - + -
172E LYS* 3.7 24.2 - - + -
204E ASP 3.3 6.2 + - - +
205E LYS 3.5 7.4 - - - +
207E ALA* 1.3 74.1 - - - +
209E ASP* 1.3 66.0 + - - +
211E LEU* 3.0 13.7 + - - +
212E LEU* 2.9 26.6 + - + +
232E ILE* 3.4 33.0 - - + -
501E NAD 3.6 27.4 - - + +
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Residues in contact with ASP 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LYS* 4.1 6.9 - - - -
209D ASP* 4.4 2.9 - - - +
231D TYR* 4.3 7.3 + - - -
205E LYS* 3.0 44.5 + - - +
206E GLU* 3.9 8.2 - - + +
207E ALA 3.5 0.2 - - - -
208E VAL* 1.3 75.1 - - - +
210E ALA* 1.3 63.3 + - - +
212E LEU* 3.2 6.7 + - - +
213E HIS* 2.8 43.5 + - + +
231E TYR* 2.9 28.2 + - - -
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Residues in contact with ALA 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E THR* 4.0 27.7 - - - +
42E VAL* 3.7 26.2 - - + -
43E GLU* 6.1 1.8 - - + -
206E GLU 3.1 13.8 + - - +
207E ALA 3.3 11.2 - - - +
208E VAL 3.1 0.2 - - - -
209E ASP* 1.3 78.6 - - - +
211E LEU* 1.3 62.1 + - - +
213E HIS* 3.3 2.9 + - - -
214E ASP* 3.2 23.6 + - - +
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 4.0 15.9 - - + -
46E ILE* 4.2 10.8 - - + -
143E ALA* 4.0 29.2 - - + -
145E ILE* 4.5 11.4 - - + -
170E VAL* 3.8 32.8 - - + +
172E LYS* 3.8 30.1 - - + -
201E VAL* 5.1 1.8 - - + -
207E ALA 3.2 12.3 + - - +
208E VAL* 3.0 12.4 + - - +
210E ALA* 1.3 79.0 - - - +
212E LEU* 1.3 65.3 + - + +
213E HIS 3.4 0.2 + - - -
214E ASP 3.4 7.6 + - - -
217E VAL* 3.6 27.5 - - + +
220E VAL* 5.7 0.4 - - + -
241E LYS* 3.7 1.0 + - - -
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ILE* 5.0 2.0 - - + -
208E VAL* 2.9 23.6 + - + +
209E ASP* 3.7 11.9 - - - +
210E ALA 3.2 0.2 - - - -
211E LEU* 1.3 77.2 - - + +
213E HIS* 1.3 65.9 + - - +
214E ASP 3.5 0.2 - - - -
220E VAL* 4.0 34.5 - - + -
231E TYR* 4.2 9.4 - - + -
232E ILE* 3.9 33.0 - - + -
235E THR* 3.8 29.3 - - + +
236E ALA* 4.2 13.6 - - + +
239E ASN* 3.6 13.0 - - - +
241E LYS* 3.2 23.7 + - - +
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Residues in contact with HIS 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ASP* 5.5 5.6 - - - -
209E ASP* 2.8 41.3 + - + +
210E ALA* 3.8 3.8 - - - +
212E LEU* 1.3 79.7 - - + +
214E ASP* 1.3 58.7 + - - +
215E ASP* 3.8 9.3 + - - +
231E TYR* 4.9 2.9 - - - -
235E THR* 4.0 24.0 - - + +
239E ASN* 3.5 28.7 + - - +
241E LYS* 4.5 0.4 - - - -
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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