Contacts of the helix formed by residues 195 - 208 (chain F) in PDB entry 3ZXR
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 TYR 195 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ILE* 3.9 54.1 + - + -
140F ASP* 4.9 1.2 + - - -
157F ALA* 4.1 4.2 - - - +
158F ILE* 3.8 10.8 - - + +
159F SER* 2.8 44.9 + - - -
193F ASP* 3.2 2.6 + - - -
194F GLN* 1.3 92.1 - - + +
196F VAL* 1.3 59.6 + - - +
197F ASP 3.5 2.5 - - - -
198F LEU* 3.2 15.1 + - + +
199F ARG* 2.9 44.8 + - - +
218F HIS* 4.0 13.9 - + - -
223F GLY 4.0 1.4 - - - -
224F GLY* 3.4 23.0 + - - -
258F LYS* 4.3 17.9 - - - -
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E HIS* 4.0 12.6 - - + -
84E ARG* 3.4 50.5 - - + +
190F ALA* 4.2 13.5 - - + -
193F ASP* 3.4 38.8 + - + +
194F GLN 3.7 1.6 - - - -
195F TYR* 1.3 76.5 - - - +
197F ASP* 1.3 58.4 + - - +
199F ARG* 3.9 10.5 - - - +
200F ASP* 3.0 28.1 + - - +
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Residues in contact with ASP 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PHE 4.8 3.8 - - - +
84E ARG* 3.7 15.5 - - - +
85E ALA* 3.6 31.8 + - - +
86E ALA 5.1 0.2 + - - -
255E GLN* 5.3 4.2 + - - -
195F TYR 3.5 0.2 - - - -
196F VAL* 1.3 75.3 - - - +
198F LEU* 1.3 65.3 + - - +
200F ASP* 3.2 9.3 + - - +
201F LYS* 3.1 33.5 + - - +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F ILE* 3.7 35.7 - - + -
195F TYR* 3.2 19.1 + - + +
197F ASP* 1.3 77.6 - - - +
199F ARG* 1.3 64.1 + - - +
201F LYS* 3.0 20.3 + - + +
202F MET* 3.0 25.2 + - + +
252F THR* 4.1 13.9 - - + +
253F ALA* 4.5 1.6 - - - -
256F ASN* 3.8 35.9 - - + +
258F LYS* 3.7 22.0 - - + -
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E HIS* 4.1 11.1 - - - -
36E THR* 5.4 3.2 + - - -
138F ILE* 4.3 17.0 - - + -
193F ASP* 2.7 44.1 + - - -
195F TYR* 2.9 29.1 + - - +
196F VAL* 4.0 11.4 + - - +
198F LEU* 1.3 71.6 - - - +
200F ASP* 1.3 62.4 + - - +
202F MET* 3.2 14.8 + - - +
203F LEU* 2.8 38.1 + - + +
216F GLY* 4.5 2.6 + - - -
217F HIS* 3.5 23.8 - - - +
218F HIS* 3.4 25.3 - - - +
226F ALA* 3.7 26.1 - - + +
227F GLU 4.9 2.0 - - - -
228F ILE* 4.2 9.5 - - + +
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Residues in contact with ASP 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 3.4 19.0 + - + -
84E ARG* 2.8 49.1 + - - +
86E ALA* 3.9 22.6 - - + +
196F VAL 3.0 16.2 + - - +
197F ASP* 3.4 14.5 - - - +
198F LEU 3.2 0.4 - - - -
199F ARG* 1.3 76.7 - - - +
201F LYS* 1.3 56.9 + - + +
203F LEU* 3.3 13.9 + - - +
204F THR* 2.9 34.4 + - - -
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Residues in contact with LYS 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E ALA* 6.4 2.2 - - - -
197F ASP* 3.1 24.0 + - - +
198F LEU* 3.0 13.0 + - - +
200F ASP* 1.3 77.3 - - + +
202F MET* 1.3 55.5 + - - +
204F THR* 3.3 6.1 + - - -
205F ASN* 2.9 38.0 + - - +
252F THR* 4.0 13.0 - - + -
256F ASN* 3.1 34.5 + - - +
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Residues in contact with MET 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F PHE* 3.9 24.0 - - + -
138F ILE* 4.1 21.5 - - + -
198F LEU* 3.0 22.5 + - + +
199F ARG* 3.4 16.6 - - - +
201F LYS* 1.3 72.8 - - - +
203F LEU* 1.3 65.1 + - - +
205F ASN* 3.4 2.1 + - - +
206F LEU* 3.0 30.7 + - - +
228F ILE* 3.7 11.7 - - + -
248F ILE* 4.4 1.0 - - - +
249F ILE* 3.7 40.8 - - + +
252F THR* 3.6 23.1 - - + -
253F ALA* 4.0 21.8 - - + +
260F VAL* 4.3 0.2 - - + -
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 3.3 36.1 - - + +
36E THR* 4.2 15.5 - - + +
38E PRO* 5.8 3.1 - - + -
199F ARG* 2.8 27.5 + - + +
200F ASP* 3.5 15.9 - - - +
202F MET* 1.3 72.9 - - - +
204F THR* 1.3 56.9 + - - +
206F LEU* 3.2 7.5 + - - +
207F ILE* 2.9 32.3 + - + +
213F LEU* 3.8 18.0 - - + +
215F LYS* 4.4 9.0 - - - +
216F GLY* 4.4 10.1 - - - +
228F ILE* 3.7 34.7 - - + +
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Residues in contact with THR 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E GLU* 4.2 12.5 + - - +
20E TYR* 2.6 25.6 + - - -
86E ALA* 5.1 2.1 - - - +
200F ASP 2.9 14.9 + - - -
201F LYS* 3.7 7.2 - - - -
202F MET 3.3 0.2 - - - -
203F LEU* 1.3 74.4 - - - +
205F ASN* 1.3 59.9 + - - +
207F ILE* 3.3 7.4 + - + +
208F ASN* 2.9 47.8 + - - +
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Residues in contact with ASN 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F PRO* 4.5 17.5 - - + +
83F PHE* 3.7 15.2 - - - -
201F LYS* 2.9 20.7 + - - +
202F MET 3.9 1.3 - - - +
204F THR* 1.3 80.3 - - - +
206F LEU* 1.3 59.8 + - - +
208F ASN* 3.6 9.4 + - - +
209F SER* 2.9 28.4 + - - -
248F ILE* 3.8 18.1 - - + +
252F THR* 2.8 30.1 + - - +
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Residues in contact with LEU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F MET 3.0 23.7 + - - +
203F LEU* 3.4 5.4 - - - +
205F ASN* 1.3 73.2 - - - +
207F ILE* 1.3 66.1 + - - +
209F SER 2.9 11.1 + - - -
211F PHE* 3.2 52.3 + - + -
213F LEU* 3.8 16.2 - - + -
228F ILE* 3.7 29.6 - - + -
230F TYR* 5.6 0.7 - - + -
245F TYR* 3.9 30.1 - - + +
248F ILE* 3.9 23.8 - - + -
249F ILE* 4.2 7.0 - - + -
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Residues in contact with ILE 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E GLU 5.5 1.3 - - - +
20E TYR* 3.8 28.7 - - + +
38E PRO* 4.3 15.7 - - + -
40E SER* 5.7 1.8 - - - +
203F LEU 2.9 22.3 + - - +
204F THR* 3.6 8.3 - - + +
206F LEU* 1.3 71.2 - - - +
208F ASN* 1.3 67.0 + - - +
210F GLY* 2.9 22.0 + - - -
211F PHE 3.9 10.9 - - - +
213F LEU* 3.5 19.5 - - + +
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Residues in contact with ASN 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ILE* 5.3 4.7 - - - +
82F PRO* 5.9 4.3 - - + -
204F THR* 2.9 41.1 + - - +
205F ASN* 4.0 10.2 + - - +
206F LEU 3.3 0.2 - - - -
207F ILE* 1.3 79.1 - - - +
209F SER* 1.3 56.8 + - - +
210F GLY 3.3 2.2 + - - -
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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