Contacts of the helix formed by residues 191 - 207 (chain F) in PDB entry 3NO1
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 SER 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F LEU* 1.3 82.6 - - - +
192F ALA* 1.3 63.8 + - - +
193F ALA* 3.6 6.7 + - - +
194F GLU* 3.0 36.0 + - - +
195F ASP* 3.0 20.8 + - - +
220F TYR* 4.9 0.4 - - - -
224F VAL* 4.9 4.5 - - - -
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Residues in contact with ALA 192 (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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191F SER* 1.3 74.7 - - - +
193F ALA* 1.3 57.7 + - - +
196F ALA* 2.9 32.1 + - - +
220F TYR* 5.4 0.7 - - - -
224F VAL* 4.0 16.8 - - + +
227F ASP* 3.5 42.4 - - + +
228F LEU* 3.5 22.0 - - - +
231F ARG* 3.8 4.0 - - - +
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Residues in contact with ALA 193 (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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191F SER* 3.4 6.8 + - - +
192F ALA* 1.3 78.9 - - - +
194F GLU* 1.3 63.9 + - + +
196F ALA* 3.3 2.6 + - - +
197F ALA* 3.0 24.1 + - - +
231F ARG* 3.9 33.2 - - - +
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Residues in contact with GLU 194 (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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190F LEU* 3.0 33.2 - - + +
191F SER* 3.0 33.6 + - - +
193F ALA* 1.3 78.3 - - + +
195F ASP* 1.3 63.2 + - - +
197F ALA* 3.1 17.1 + - - +
198F ARG* 3.2 17.3 + - - +
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Residues in contact with ASP 195 (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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161F TYR* 2.7 27.5 + - - -
187F VAL* 4.1 8.7 - - + -
188F GLY 3.5 0.7 + - - -
190F LEU* 3.0 30.7 + - - +
191F SER 3.0 11.6 + - - +
194F GLU* 1.3 74.4 - - - +
196F ALA* 1.3 65.4 + - - +
198F ARG* 2.8 26.5 + - - +
199F ILE* 3.0 29.1 + - - +
220F TYR* 2.6 28.0 + - - +
228F LEU* 4.1 7.9 - - + -
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Residues in contact with ALA 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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192F ALA 2.9 21.9 + - - +
193F ALA* 3.5 4.9 - - - +
194F GLU 3.2 0.2 - - - -
195F ASP* 1.3 75.6 - - - +
197F ALA* 1.3 58.8 + - - +
199F ILE* 3.3 3.5 + - - +
200F THR* 2.9 35.0 + - - +
228F LEU* 3.6 15.2 - - + +
231F ARG* 3.9 25.8 - - + +
232F ILE* 4.3 9.9 - - + +
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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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193F ALA 3.0 13.2 + - - +
194F GLU* 3.4 11.2 - - - +
196F ALA* 1.3 78.3 - - - +
198F ARG* 1.3 57.3 + - + +
200F THR* 3.5 7.7 + - - -
201F ALA* 3.1 26.9 + - - +
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Residues in contact with ARG 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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159F GLY 2.7 30.5 + - - -
160F TYR 4.5 3.0 + - - -
161F TYR* 3.3 28.2 + - - -
163F GLU* 4.8 9.1 + - - +
168F ILE* 3.6 27.7 - - + +
185F PHE* 3.4 19.1 - - + -
186F LYS 3.1 21.4 + - - -
187F VAL* 3.8 5.1 - - - +
190F LEU* 4.0 14.6 - - - -
194F GLU 3.2 9.4 + - - +
195F ASP* 2.8 40.7 + - - +
197F ALA* 1.3 75.8 - - + +
199F ILE* 1.3 64.9 + - - +
201F ALA* 3.2 5.0 + - - +
202F ALA* 3.1 19.2 + - - +
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Residues in contact with ILE 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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185F PHE* 3.3 30.1 - - + -
187F VAL* 3.5 13.2 - - + -
195F ASP 3.0 17.1 + - - +
196F ALA* 3.6 8.7 - - - +
198F ARG* 1.3 75.0 - - - +
200F THR* 1.3 64.2 + - - +
202F ALA* 3.0 8.0 + - - +
203F ARG* 2.9 21.0 + - + +
212F ILE* 4.8 8.0 - - + +
214F ILE* 3.4 26.2 - - + -
228F LEU* 5.0 3.4 - - + -
232F ILE* 4.2 14.4 - - + -
235F LEU* 3.9 17.5 - - + -
237F ILE* 4.2 21.5 - - + -
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Residues in contact with THR 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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196F ALA* 2.9 20.3 + - - +
197F ALA* 3.7 8.2 - - - -
199F ILE* 1.3 77.0 - - - +
201F ALA* 1.3 56.8 + - - +
203F ARG* 3.1 4.3 + - + +
204F GLU* 2.8 33.9 + - + +
235F LEU* 3.6 27.6 - - + +
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Residues in contact with ALA 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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168F ILE* 3.9 22.7 - - + +
169F ALA* 5.0 1.0 - - - +
197F ALA 3.1 14.9 + - - +
198F ARG* 3.5 9.9 - - - +
199F ILE 3.2 0.2 - - - -
200F THR* 1.3 76.8 - - - +
202F ALA* 1.3 56.8 + - - +
204F GLU* 4.1 5.0 - - - +
205F ALA* 3.1 29.6 + - - +
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Residues in contact with ALA 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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168F ILE* 3.6 17.5 - - + +
172F MSE 3.9 20.8 - - - +
185F PHE* 4.2 14.1 - - + -
198F ARG 3.1 10.7 + - - +
199F ILE* 3.0 11.7 + - - +
201F ALA* 1.3 76.7 - - - +
203F ARG* 1.3 59.1 + - - +
206F ALA* 3.0 34.8 + - - +
212F ILE* 4.9 13.0 - - + -
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Residues in contact with ARG 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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199F ILE* 2.9 12.6 + - + +
200F THR* 3.5 7.9 - - + +
202F ALA* 1.3 77.2 - - - +
204F GLU* 1.3 63.6 + - - +
206F ALA* 5.1 0.4 - - - +
207F GLY* 3.0 53.1 + - - -
208F ASP* 3.5 24.7 + - - +
210F PHE* 2.7 30.9 + - - +
212F ILE* 3.6 23.3 - - + +
235F LEU* 2.5 67.3 + - + +
236F ASN* 3.6 17.1 + - - +
237F ILE* 5.2 1.3 - - + -
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Residues in contact with GLU 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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200F THR* 2.8 25.1 + - + +
201F ALA* 4.1 6.1 - - - +
203F ARG* 1.3 75.9 - - - +
205F ALA* 1.3 59.8 + - - +
207F GLY* 4.1 5.0 + - - -
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Residues in contact with ALA 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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169F ALA* 3.6 35.7 - - + +
172F MSE 4.5 5.4 - - + -
173F HIS* 3.1 30.8 + - + +
176F GLN* 4.2 0.7 - - - +
201F ALA 3.1 20.2 + - - +
202F ALA 4.0 1.8 - - - +
204F GLU* 1.3 79.9 - - - +
206F ALA* 1.3 60.8 + - - +
207F GLY 3.5 0.2 - - - -
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Residues in contact with ALA 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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172F MSE 4.0 10.1 - - + -
176F GLN* 2.8 31.1 + - - +
202F ALA 3.0 18.5 + - - +
203F ARG* 5.1 0.7 - - - +
205F ALA* 1.3 77.8 - - - +
207F GLY* 1.3 63.4 + - - +
209F ASP* 4.9 2.8 - - - +
210F PHE* 3.4 41.2 - - + +
212F ILE* 4.9 1.6 - - + -
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Residues in contact with GLY 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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203F ARG* 3.0 39.1 + - - -
204F GLU 4.1 3.7 + - - -
205F ALA 3.5 2.2 - - - -
206F ALA* 1.3 82.1 - - - +
208F ASP* 1.3 63.6 + - - -
209F ASP* 3.5 2.9 - - - -
210F PHE* 4.0 2.6 - - - +
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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