Contacts of the helix formed by residues 204 - 214 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18L ARG* 3.0 39.9 + - - -
20L GLN* 4.9 5.1 - - - +
36L LEU* 4.2 8.9 - - + +
37L ALA 5.2 0.3 - - - +
172L LYS* 4.5 2.7 - - - +
175L GLU* 3.8 17.3 - - - +
203L GLY* 1.3 75.8 - - - +
205L LYS* 1.3 56.8 + - - +
206L GLU* 3.6 9.4 + - - +
207L ALA* 2.8 25.6 + - - +
208L VAL* 3.2 15.7 + - - +
501L NAD 4.8 2.9 - - - -
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Residues in contact with LYS 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L ASP* 1.3 78.4 - - + +
206L GLU* 1.3 56.1 + - - +
208L VAL* 3.8 0.4 - - - +
209L ASP* 2.9 51.9 + - - +
231L TYR* 3.5 33.2 - - - -
501L NAD 3.2 46.9 + - + +
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Residues in contact with GLU 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG* 2.7 32.5 + - - +
37L ALA 4.8 0.7 - - - +
38L SER* 3.1 32.2 - - - -
39L THR* 3.2 26.6 + - + +
204L ASP* 3.0 12.4 + - - +
205L LYS* 1.3 75.1 - - - +
207L ALA* 1.3 65.4 + - - +
209L ASP* 3.8 5.3 + - - +
210L ALA* 3.2 21.5 + - - +
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Residues in contact with ALA 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L ALA* 3.8 17.2 + - + +
42L VAL* 3.9 20.3 - - + +
172L LYS* 4.0 21.3 - - + -
201L VAL* 4.8 1.8 - - + -
202L ASN 4.7 2.2 - - - +
203L GLY* 4.1 13.5 - - - +
204L ASP* 2.8 9.5 + - - +
206L GLU* 1.3 76.3 - - - +
208L VAL* 1.3 67.4 + - - +
210L ALA* 3.2 5.5 + - - +
211L LEU* 3.2 23.7 + - - +
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Residues in contact with VAL 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ILE* 3.8 22.9 - - + -
172L LYS* 3.5 27.1 - - + +
204L ASP 3.2 6.1 + - - +
205L LYS 3.8 1.6 - - - +
207L ALA* 1.3 77.4 - - - +
209L ASP* 1.3 63.6 + - - +
211L LEU* 3.0 14.2 + - - +
212L LEU* 3.0 25.8 + - + +
232L ILE* 3.3 33.7 - - + -
501L NAD 3.4 32.5 - - + +
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Residues in contact with ASP 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L LYS* 2.9 49.3 + - - +
206L GLU* 4.2 5.8 - - - +
208L VAL* 1.3 74.2 - - - +
210L ALA* 1.3 62.5 + - - +
212L LEU* 3.3 6.0 + - - +
213L HIS* 2.9 44.3 + - + +
231L TYR* 2.5 34.6 + - - -
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Residues in contact with ALA 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L THR* 3.9 23.9 - - - +
42L VAL* 3.5 27.6 - - + -
43L GLU* 5.5 2.6 - - + +
46L ILE* 4.5 0.4 - - - +
206L GLU 3.2 12.4 + - - +
207L ALA 3.2 10.9 + - - +
208L VAL 3.1 0.6 - - - -
209L ASP* 1.3 78.2 - - - +
211L LEU* 1.3 61.9 + - - +
213L HIS* 3.4 2.8 + - - +
214L ASP* 3.2 27.4 + - - +
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Residues in contact with LEU 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L VAL* 3.9 14.1 - - + -
46L ILE* 4.1 10.5 - - + -
143L ALA* 4.3 20.9 - - + -
144L GLY 4.8 0.2 - - - +
145L ILE* 4.5 10.1 - - + -
170L VAL* 3.8 37.5 - - + +
172L LYS* 3.9 29.6 - - + -
201L VAL* 4.9 1.8 - - + -
207L ALA 3.2 11.9 + - - +
208L VAL* 3.0 11.3 + - - +
210L ALA* 1.3 79.2 - - - +
212L LEU* 1.3 63.5 + - + +
213L HIS 3.4 0.3 + - - -
214L ASP 3.8 1.2 + - - -
217L VAL* 3.4 38.8 - - + +
241L LYS* 3.8 2.9 + - - -
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Residues in contact with LEU 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ILE* 4.6 4.3 - - + -
208L VAL* 3.0 23.3 + - + +
209L ASP* 3.3 7.6 + - - +
211L LEU* 1.3 78.1 - - + +
213L HIS* 1.3 58.8 + - - +
214L ASP 3.6 0.2 - - - -
220L VAL* 3.7 37.5 - - + -
231L TYR* 4.1 8.3 - - + -
232L ILE* 3.7 35.0 - - + -
235L THR* 3.8 36.9 - - + +
236L ALA* 4.4 8.9 - - + -
239L ASN* 3.5 12.7 - - - +
241L LYS* 3.2 24.4 + - - +
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Residues in contact with HIS 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L ASP* 2.9 43.4 + - + +
210L ALA* 3.9 2.9 - - - +
211L LEU 3.3 0.2 - - - -
212L LEU* 1.3 77.2 - - + +
214L ASP* 1.3 62.8 + - - +
215L ASP* 3.6 11.4 + - - +
231L TYR* 4.7 2.0 - - - -
235L THR* 3.8 23.5 - - + +
239L ASN* 3.5 28.7 + - - +
241L LYS* 4.3 1.3 - - - -
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Residues in contact with ASP 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L GLU* 3.8 18.1 - - + +
46L ILE* 3.7 20.6 - - + +
210L ALA 3.2 15.6 + - - +
211L LEU 3.8 2.4 + - - +
212L LEU 3.6 0.8 - - - -
213L HIS* 1.3 76.9 - - - +
215L ASP* 1.3 62.0 + - - +
216L ARG* 2.9 64.6 + - - +
217L VAL* 3.2 8.5 + - + +
241L LYS* 2.7 25.1 + - - -
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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