Contacts of the helix formed by residues 182 - 194 (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 THR 182 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181F LEU* 1.3 77.4 - - - +
183F LEU* 1.3 65.2 + - - +
184F SER* 3.7 7.8 + - - -
185F GLN* 2.8 45.6 + - - +
186F ILE* 3.1 11.3 + - - +
228F ASN* 4.1 13.7 - - - +
233F LYS* 6.3 0.2 - - + -
234F SER* 3.9 13.7 - - - +
235F SER 3.4 15.7 - - - +
236F TRP* 3.7 25.6 - - + -
237F TRP* 4.3 1.1 - - - -
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Residues in contact with LEU 183 (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 3.8 40.4 - - + +
3D G 3.7 15.0 - - - +
182F THR* 1.3 72.6 - - - +
184F SER* 1.3 62.5 + - - +
186F ILE* 3.1 16.6 + - + +
187F TYR* 3.1 50.8 + - + +
213F ILE* 4.0 4.9 - - + -
214F ARG* 3.7 24.9 - - + -
217F LEU* 3.8 24.5 - - + -
234F SER* 4.4 3.4 + - - +
235F SER 4.2 1.4 + - - -
237F TRP* 3.9 12.8 - - - +
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Residues in contact with SER 184 (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 3.8 21.6 + - - -
182F THR* 3.9 9.2 - - - -
183F LEU* 1.3 81.6 - - - +
185F GLN* 1.3 61.0 + - - +
187F TYR* 3.4 16.4 + - - +
188F GLU* 3.1 21.1 + - - +
234F SER* 5.3 0.9 + - - -
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Residues in contact with GLN 185 (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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233C LYS* 6.3 0.6 - - - +
181F LEU* 3.3 31.0 - - + +
182F THR* 2.8 43.2 + - - +
184F SER* 1.3 76.3 - - - +
186F ILE* 1.3 61.7 + - - +
188F GLU* 3.3 8.1 + - - +
189F TRP* 2.9 28.4 + - - +
236F TRP* 3.4 16.3 - - - -
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Residues in contact with ILE 186 (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 ILE* 4.2 25.6 - - + -
172F ALA* 4.5 13.0 - - + -
173F ILE* 4.5 4.3 - - + -
181F LEU* 3.8 22.4 - - + +
182F THR 3.1 14.1 + - - +
183F LEU* 3.1 9.1 + - - +
185F GLN* 1.3 77.6 - - - +
187F TYR* 1.3 62.1 + - - +
189F TRP* 3.3 8.0 + - - +
190F MET* 3.0 33.9 + - + +
213F ILE* 4.0 22.2 - - + -
217F LEU* 4.2 17.7 - - + -
237F TRP* 4.1 25.4 - - + -
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Residues in contact with TYR 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D T 3.9 19.8 + - - +
183F LEU* 3.1 50.1 + - + +
184F SER* 3.5 14.8 - - - +
185F GLN 3.2 0.2 - - - -
186F ILE* 1.3 77.2 - - - +
188F GLU* 1.3 62.4 + - - +
190F MET* 3.0 13.9 + - - +
191F VAL* 3.0 19.3 + - + +
209F TRP* 3.9 18.6 - + + -
210F LYS* 3.4 50.9 - - + +
213F ILE* 3.9 16.2 - - + -
214F ARG* 2.9 29.1 + - - +
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Residues in contact with GLU 188 (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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184F SER 3.1 11.3 + - - +
185F GLN* 3.3 12.1 + - - +
187F TYR* 1.3 79.9 - - - +
189F TRP* 1.3 57.5 + - - +
191F VAL* 3.3 7.3 + - - +
192F LYS* 2.9 32.0 + - - +
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Residues in contact with TRP 189 (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 LEU* 3.5 9.6 - - + -
171F LYS* 3.7 44.9 - - + -
172F ALA* 3.4 24.9 - - + -
175F SER* 3.4 30.0 + - - -
181F LEU* 5.0 4.0 - - + -
185F GLN 2.9 16.9 + - - +
186F ILE* 3.6 4.7 - - - +
188F GLU* 1.3 76.5 - - - +
190F MET* 1.3 95.2 + - + +
192F LYS* 4.6 2.2 - - - +
193F SER* 2.8 63.7 + - - -
194F VAL* 3.9 13.2 - - + -
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Residues in contact with MET 190 (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* 5.4 0.9 - - - -
168F LEU* 3.3 44.6 - - + +
169F ILE* 5.4 0.7 - - - -
172F ALA* 5.3 0.4 - - + -
186F ILE* 3.0 22.3 + - + +
187F TYR 3.0 9.0 + - - +
189F TRP* 1.3 113.9 - - + +
191F VAL* 1.3 59.2 + - - +
194F VAL* 3.0 41.1 + - + +
197F PHE* 3.9 15.6 - - + +
209F TRP* 3.8 26.0 - - + -
213F ILE* 4.1 22.2 - - + -
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Residues in contact with VAL 191 (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* 3.0 14.4 + - + +
188F GLU* 3.7 9.2 - - - +
190F MET* 1.3 77.4 - - - +
192F LYS* 1.3 60.9 + - + +
194F VAL 4.3 1.0 - - - +
197F PHE* 4.1 10.8 - - + +
198F LYS* 3.2 40.4 + - - +
201F GLY* 3.9 20.0 - - - -
209F TRP* 3.9 24.2 - - + -
210F LYS* 6.1 0.4 - - - -
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Residues in contact with LYS 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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28B A 5.9 4.6 - - - +
188F GLU 2.9 17.0 + - - +
189F TRP* 4.4 2.9 - - - +
191F VAL* 1.3 80.0 - - + +
193F SER* 1.3 63.2 + - - +
194F VAL 3.9 0.7 - - - -
198F LYS* 6.0 0.2 - - - -
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Residues in contact with SER 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F TRP* 2.8 67.5 + - - -
192F LYS* 1.3 80.2 - - - +
194F VAL* 1.3 61.5 + - - +
195F PRO* 3.6 8.9 - - - +
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Residues in contact with VAL 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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160F TRP* 3.8 29.2 - - + +
168F LEU* 4.1 12.3 - - + -
189F TRP* 3.9 11.9 - - + -
190F MET* 3.0 40.5 + - + +
191F VAL 4.3 0.6 - - - +
192F LYS 5.4 0.4 - - - -
193F SER* 1.3 81.1 - - - +
195F PRO* 1.4 73.6 - - + +
196F TYR 4.1 3.1 - - - +
197F PHE* 2.8 38.0 + - + -
198F LYS* 3.2 10.1 + - - -
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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