Contacts of the helix formed by residues 202 - 220 (chain F) in PDB entry 3COA
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 202 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ASP 3.6 15.1 - - - +
201F GLY* 1.3 79.2 + - - +
203F SER* 1.3 70.6 + - - +
204F ASN* 3.0 7.6 + - - +
205F SER* 2.6 42.2 + - - -
206F SER* 3.0 16.3 + - - -
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Residues in contact with SER 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F GLY 3.7 2.0 + - - -
202F ASP* 1.3 72.6 - - - +
204F ASN* 1.3 67.8 + - - +
206F SER* 3.3 13.0 + - - -
207F ALA* 4.0 5.2 + - - +
210F LYS* 5.8 1.3 - - - +
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Residues in contact with ASN 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ASP* 3.0 8.8 + - - +
203F SER* 1.3 83.7 - - - +
205F SER* 1.3 56.2 + - - +
206F SER 3.2 3.3 + - - -
207F ALA* 3.8 12.8 + - - +
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Residues in contact with SER 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F ASP 4.3 1.7 + - - -
200F LYS* 3.8 24.2 - - - +
202F ASP* 2.6 35.3 + - - -
204F ASN* 1.3 68.7 - - - +
206F SER* 1.3 58.2 + - - +
207F ALA 3.6 0.9 - - - -
208F GLY 5.0 1.9 + - - -
209F TRP* 3.6 13.3 + - - -
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Residues in contact with SER 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F LYS 3.3 16.8 - - - -
201F GLY 4.0 2.9 - - - -
202F ASP 3.0 16.3 + - - -
203F SER* 3.3 9.0 + - - -
204F ASN 3.2 0.6 + - - -
205F SER* 1.3 78.0 - - - +
207F ALA* 1.3 67.7 + - - +
208F GLY 3.3 2.6 + - - -
209F TRP* 3.2 13.6 + - - +
210F LYS* 2.9 57.8 + - - +
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Residues in contact with ALA 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 SER 4.0 3.3 + - - +
204F ASN 3.8 12.0 + - - +
205F SER 3.6 0.6 - - - -
206F SER* 1.3 78.8 + - - +
208F GLY* 1.3 65.4 + - - +
210F LYS* 3.9 4.1 - - - +
211F ASN* 3.0 25.6 + - - +
214F ARG* 5.0 1.4 + - - -
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Residues in contact with GLY 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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18E A 5.7 4.0 - - - +
19E A 4.4 17.9 - - - -
165F TYR* 5.3 0.4 - - - -
205F SER 5.0 2.2 + - - -
206F SER 3.3 0.4 - - - -
207F ALA* 1.3 78.8 - - - +
209F TRP* 1.3 62.6 + - - +
211F ASN* 3.2 9.5 + - - +
212F SER* 3.1 21.2 + - - -
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Residues in contact with TRP 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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165F TYR* 3.7 20.5 - + + +
187F TYR* 3.7 40.8 - + - -
190F MET* 3.8 26.2 - - + -
191F VAL* 3.9 17.5 - - + -
197F PHE* 3.6 39.5 - + + -
200F LYS* 2.8 35.1 + - + +
201F GLY* 4.5 0.7 - - - -
205F SER 3.6 7.9 - - - -
206F SER* 3.2 23.3 + - - +
208F GLY* 1.3 74.8 - - - +
210F LYS* 1.3 79.8 + - + +
212F SER* 3.2 4.6 + - - -
213F ILE* 3.0 40.3 + - + +
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Residues in contact with LYS 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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187F TYR* 3.4 52.9 + - + +
191F VAL* 6.1 0.4 - - - -
201F GLY* 4.0 12.4 + - - -
202F ASP 5.7 0.2 - - - -
203F SER* 5.8 1.6 - - - +
206F SER* 2.9 45.3 + - - +
207F ALA* 3.9 3.8 - - - +
209F TRP* 1.3 91.3 - - + +
211F ASN* 1.3 66.4 + - - +
213F ILE* 3.0 12.7 + - - +
214F ARG* 3.0 32.4 + - - +
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Residues in contact with ASN 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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4D T 4.6 2.9 - - - +
19E A 3.1 35.0 + - - +
20E A 3.1 35.3 + - - +
21E A 4.6 2.8 + - - -
207F ALA 3.0 19.2 + - - +
208F GLY* 3.5 6.9 + - - +
210F LYS* 1.3 75.7 - - - +
212F SER* 1.3 60.7 + - - +
214F ARG* 3.3 28.1 + - - +
215F HIS* 2.9 30.4 + - - +
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Residues in contact with SER 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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17E C 4.6 1.0 - - - +
18E A 4.0 27.5 + - - +
19E A 6.2 0.2 - - - -
165F TYR* 3.7 34.8 + - - -
208F GLY 3.1 12.8 + - - -
209F TRP* 3.4 9.2 - - - -
210F LYS 3.2 0.2 - - - -
211F ASN* 1.3 81.4 + - - +
213F ILE* 1.3 61.3 + - - +
215F HIS* 3.4 8.2 + - - +
216F ASN* 2.8 32.8 + - - -
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Residues in contact with ILE 213 (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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165F TYR* 4.0 24.0 - - + +
169F ILE* 3.9 23.5 - - + +
183F LEU* 4.0 9.9 - - + -
186F ILE* 4.0 18.6 - - + -
187F TYR* 3.9 7.0 - - + -
190F MET* 4.1 20.4 - - + -
209F TRP* 3.0 37.7 + - + +
210F LYS* 3.0 8.2 + - - +
212F SER* 1.3 77.9 - - - +
214F ARG* 1.3 64.0 + - - +
216F ASN* 3.2 3.8 + - - +
217F LEU* 3.0 38.7 + - + +
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Residues in contact with ARG 214 (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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2D T 3.7 26.3 + - - +
3D G 3.6 32.6 + - + +
4D T 3.5 22.2 + - + +
183F LEU* 3.7 23.1 - - + -
187F TYR* 2.9 30.9 + - - +
207F ALA 5.0 1.6 + - - -
210F LYS* 3.0 23.8 + - - +
211F ASN* 3.4 36.3 + - - +
213F ILE* 1.3 73.9 - - - +
215F HIS* 1.3 63.5 + - - +
217F LEU* 3.3 10.8 + - - +
218F SER* 3.1 20.3 + - - -
237F TRP* 5.8 0.2 - - - -
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Residues in contact with HIS 215 (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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4D T 4.0 2.4 - - - +
5D T 3.1 32.2 + - - +
6D T 2.9 24.2 + + + -
7D T 4.4 1.3 - - - -
17E C 4.9 8.3 + + - -
18E A 3.5 30.4 + - - -
19E A 3.5 9.5 + - - +
20E A 4.6 1.3 - - - +
211F ASN* 2.9 19.1 + - - +
212F SER* 3.5 8.1 - - - +
214F ARG* 1.3 77.1 - - - +
216F ASN* 1.3 71.8 + - - +
219F LEU* 2.8 66.2 + - + +
220F HIS* 5.6 0.4 - - - -
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Residues in contact with ASN 216 (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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16E G 6.0 0.2 - - - +
17E C 4.4 9.8 + - - -
165F TYR* 3.7 27.4 - - - +
166F ALA* 3.8 13.5 + - - +
169F ILE* 3.7 19.3 - - + -
212F SER* 2.8 30.3 + - - +
215F HIS* 1.3 85.0 - - - +
217F LEU* 1.3 68.8 + - - +
219F LEU* 4.4 0.2 - - - -
220F HIS* 3.0 57.2 + - + -
223F PHE* 3.5 6.7 - - + -
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Residues in contact with LEU 217 (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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2F CA 2.9 19.1 - - - -
169F ILE* 3.7 30.3 - - + -
183F LEU* 3.8 29.2 - - + -
186F ILE* 4.2 6.1 - - + -
213F ILE* 3.0 24.6 + - + +
214F ARG* 3.3 8.0 + - - +
216F ASN* 1.3 79.4 - - - +
218F SER* 1.3 58.8 + - - +
220F HIS 3.7 4.9 - - - +
223F PHE* 3.7 16.3 - - + +
237F TRP* 3.7 62.3 - - + +
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Residues in contact with SER 218 (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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3D G 3.2 18.2 - - - +
4D T 2.6 46.3 + - - +
5D T 3.7 25.3 + - - -
2F CA 3.2 11.7 - - - -
214F ARG 3.1 12.4 + - - -
217F LEU* 1.3 76.6 - - - +
219F LEU* 1.3 64.6 + - - +
237F TRP* 4.5 0.9 - - - -
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Residues in contact with LEU 219 (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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5D T 3.9 8.7 - - + +
6D T 4.5 12.8 - - + -
215F HIS* 2.8 54.3 + - + +
216F ASN 3.3 1.5 + - - +
218F SER* 1.3 76.6 - - - +
220F HIS* 1.3 84.4 + - + +
221F SER 3.7 2.1 + - - -
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Residues in contact with HIS 220 (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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2F CA 3.1 16.1 - - - -
166F ALA* 4.3 8.8 - - + +
215F HIS* 5.6 0.2 + - - -
216F ASN* 3.0 55.1 + - + +
217F LEU 3.7 3.1 - - - +
219F LEU* 1.3 101.1 - - + +
221F SER* 1.3 59.6 + - - +
222F LYS* 3.0 18.6 + - + +
223F PHE* 3.1 24.9 + + + +
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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