Contacts of the helix formed by residues 196 - 212 (chain F) in PDB entry 3JSX
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 PRO 196 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194F HIS 3.6 7.2 - - - +
195F THR* 1.3 96.2 - - + +
197F ALA* 1.3 55.6 + - - +
198F ASP* 3.7 4.0 - - - +
199F ALA* 3.0 15.6 - - + +
200F ARG* 2.8 33.9 + - - +
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Residues in contact with ALA 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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196F PRO* 1.3 70.5 - - - +
198F ASP* 1.3 61.9 + - - +
200F ARG* 2.9 34.2 + - - +
201F ILE* 2.9 30.0 + - + +
601F FAD 5.0 0.3 - - - -
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Residues in contact with ASP 198 (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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196F PRO* 5.1 3.5 - - - +
197F ALA* 1.3 76.2 + - + +
199F ALA* 1.3 63.4 + - - +
200F ARG 3.2 0.2 - - - -
201F ILE* 3.5 21.5 - - + +
202F GLN* 2.9 43.6 + - + +
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Residues in contact with ALA 199 (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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195F THR* 3.4 20.2 - - + -
196F PRO* 3.0 28.4 + - + +
198F ASP* 1.3 84.3 + - - +
200F ARG* 1.3 57.4 + - - -
202F GLN* 3.4 10.3 + - - +
203F ILE* 3.2 25.3 + - + +
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Residues in contact with ARG 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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17F PHE* 3.9 10.7 - - + -
192F ILE* 4.2 24.2 + - + -
195F THR* 2.7 51.9 + - + +
196F PRO* 2.8 7.8 + - - +
197F ALA* 2.9 38.4 + - - +
199F ALA* 1.3 75.3 - - - +
201F ILE* 1.3 64.6 + - - +
203F ILE* 3.0 18.0 + - - +
204F LEU* 3.1 21.4 + - - +
601F FAD 3.0 60.9 + - - +
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Residues in contact with ILE 201 (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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197F ALA* 2.9 21.6 + - + +
198F ASP* 3.3 23.7 + - + +
200F ARG* 1.3 76.2 - - - +
202F GLN* 1.3 62.0 + - + +
204F LEU* 3.6 11.2 + - - +
205F GLU* 3.5 26.4 + - + +
601F FAD 4.7 12.3 - - + +
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Residues in contact with GLN 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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198F ASP* 2.9 27.8 + - + +
199F ALA* 3.8 10.2 - - - +
200F ARG 3.2 0.2 - - - -
201F ILE* 1.3 76.0 - - + +
203F ILE* 1.3 61.1 + - - +
205F GLU* 3.9 10.5 - - + +
206F GLY* 3.3 18.5 + - - -
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Residues in contact with ILE 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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17F PHE* 3.6 24.5 - - + -
21F MET* 4.1 11.9 - - + -
189F THR* 4.3 22.7 - - + +
190F TYR 6.0 0.2 - - - +
192F ILE* 4.6 3.4 - - + -
195F THR* 4.1 21.5 - - + +
199F ALA* 3.2 15.6 + - + +
200F ARG* 3.0 11.9 + - - +
202F GLN* 1.3 76.3 - - - +
204F LEU* 1.3 65.7 + - - +
205F GLU 3.0 1.1 - - - -
206F GLY* 3.3 2.3 + - - +
207F TRP* 3.1 21.7 + - - +
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Residues in contact with LEU 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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17F PHE* 3.1 33.0 - - + -
20F ALA* 3.7 30.7 - - + +
21F MET* 3.9 13.9 - - - +
24F ALA* 4.1 9.6 - - + +
200F ARG 3.1 28.7 + - - +
201F ILE* 3.7 10.5 - - - +
203F ILE* 1.3 77.7 - - - +
205F GLU* 1.3 63.2 - - - +
207F TRP* 3.6 5.9 + - - +
208F LYS* 2.9 32.4 + - + +
601F FAD 3.6 23.8 - - + +
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Residues in contact with GLU 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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201F ILE* 3.5 22.7 + - + +
202F GLN* 4.1 9.6 - - + +
203F ILE 3.0 0.8 - - - -
204F LEU* 1.3 79.6 - - - +
206F GLY* 1.3 53.8 + - - +
208F LYS* 3.4 30.1 + - - +
209F LYS* 2.7 34.7 + - - +
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Residues in contact with GLY 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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187F GLN* 5.3 3.5 + - - +
202F GLN 3.3 11.5 + - - -
203F ILE* 3.3 6.5 + - - -
205F GLU* 1.3 80.7 - - - +
207F TRP* 1.3 54.6 + - - +
209F LYS* 3.1 10.8 - - - +
210F ARG* 3.0 27.2 + - - +
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Residues in contact with TRP 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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21F MET* 3.5 46.2 + - + +
24F ALA* 4.4 3.8 - - + -
25F ALA* 3.2 23.3 - - + +
98F ILE* 4.0 20.9 - - + -
100F GLN* 4.3 2.0 + - - -
143F VAL* 4.3 19.7 - - + -
145F SER* 3.9 14.4 - - - -
187F GLN* 3.1 50.5 - - + -
203F ILE 3.1 14.9 + - - +
204F LEU 3.8 3.8 - - - +
205F GLU 3.2 0.2 - - - -
206F GLY* 1.3 73.6 - - - +
208F LYS* 1.3 56.2 + - - +
209F LYS 3.1 4.3 - - - -
210F ARG* 3.4 17.6 + - - -
211F LEU* 2.9 62.6 + - + +
214F ILE* 4.9 0.7 - - + -
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Residues in contact with LYS 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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24F ALA* 3.8 29.0 + - + +
27F ALA* 4.3 13.5 - - - +
28F ALA* 3.5 38.9 - - + +
31F LYS* 6.4 1.3 - - - -
204F LEU* 2.9 24.2 + - + +
205F GLU* 3.5 27.2 + - - +
207F TRP* 1.3 72.5 - - - +
209F LYS* 1.3 60.4 + - - +
211F LEU* 4.0 4.3 - - - +
212F GLU* 3.1 28.2 + - - +
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Residues in contact with LYS 209 (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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205F GLU 2.7 15.3 + - - +
206F GLY* 3.1 17.3 - - - +
207F TRP 3.1 0.2 - - - -
208F LYS* 1.3 74.9 - - - +
210F ARG* 1.3 66.4 + - - +
212F GLU* 3.2 43.4 + - - +
213F ASN* 4.1 4.5 + - - +
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Residues in contact with ARG 210 (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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143F VAL* 4.2 1.6 - - - +
184F LEU* 4.0 6.9 - - - +
185F GLU* 2.6 47.7 + - - +
186F PRO 4.0 1.8 + - - -
187F GLN* 2.7 51.9 + - - +
206F GLY 3.0 12.1 + - - +
207F TRP* 3.8 14.8 - - + +
209F LYS* 1.3 79.9 - - - +
211F LEU* 1.3 63.7 + - - +
212F GLU 2.9 1.6 + - - -
213F ASN* 3.1 14.1 + - - +
214F ILE* 3.3 24.9 + - + +
217F GLU* 3.1 40.9 + - - +
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Residues in contact with LEU 211 (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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25F ALA* 3.4 29.2 - - + -
28F ALA* 4.5 9.8 - - + +
29F LEU* 4.2 29.1 - - + +
32F LYS* 5.4 0.3 - - - +
34F TRP* 4.6 4.9 + - - -
98F ILE* 4.3 9.9 - - + -
207F TRP* 2.9 69.7 + - + +
208F LYS* 4.0 9.2 - - - +
209F LYS 3.3 0.4 - - - -
210F ARG* 1.3 74.8 - - - +
212F GLU* 1.3 62.7 + - - +
213F ASN 3.2 0.6 + - - -
214F ILE* 3.7 38.2 + - + +
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Residues in contact with GLU 212 (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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28F ALA* 5.5 4.7 - - + +
31F LYS* 5.5 6.8 - - - +
32F LYS* 3.5 51.9 + - + +
34F TRP* 5.4 1.4 + - - -
208F LYS 3.1 19.6 + - - +
209F LYS* 3.2 32.6 + - - +
210F ARG 2.9 0.8 + - - -
211F LEU* 1.3 78.1 - - - +
213F ASN* 1.3 74.8 + - - +
214F ILE 3.7 0.2 - - - -
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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