Contacts of the helix formed by residues 190 - 205 (chain V) in PDB entry 3FKS
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 ARG 190 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166U ARG* 4.6 4.5 - - - +
309U GLU* 4.1 4.9 - - - -
345U ILE 4.6 1.2 + - - -
346U SER* 3.1 26.3 + - - +
347U ILE 3.7 7.4 + - - +
348U THR 3.6 18.0 + - - -
349U ASP* 3.4 19.6 + - - +
375U ARG* 3.1 49.5 - - - +
189V GLU* 1.3 83.2 + - - +
191V THR* 1.3 66.9 + - - +
192V ARG* 3.1 7.4 - - + -
193V GLU* 2.8 50.1 + - + +
194V GLY 3.2 8.1 + - - -
221V GLN* 3.3 2.8 + - - -
222V MET* 4.1 13.7 - - + -
260V ARG* 4.3 10.8 - - - +
311V TYR* 4.7 6.1 + - - -
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Residues in contact with THR 191 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136U PRO 3.6 11.0 - - - +
137U GLY* 4.0 1.8 - - - +
138U ILE* 3.5 23.5 - - + +
141U ARG* 3.3 27.6 - - - +
309U GLU* 2.8 32.8 + - - -
189V GLU 3.3 3.2 + - - -
190V ARG* 1.3 70.7 - - - +
192V ARG* 1.3 62.6 + - - +
194V GLY* 3.2 11.3 + - - -
195V ASN* 3.2 11.3 + - - +
221V GLN* 3.1 29.0 - - + +
223V ASN* 3.3 6.1 + - - +
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Residues in contact with ARG 192 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141U ARG* 3.7 22.0 - - + +
142U ARG 5.9 2.5 - - - +
144U VAL* 4.8 20.3 - - + +
164U GLY 5.1 5.8 - - - -
166U ARG* 4.1 13.8 - - - +
349U ASP* 2.9 44.4 + - - +
375U ARG* 3.9 18.6 + - - +
376U VAL* 4.2 19.5 - - - +
190V ARG* 3.1 4.1 - - + +
191V THR* 1.3 79.5 - - - +
193V GLU* 1.3 86.9 + - + +
195V ASN* 3.2 9.7 + - - +
196V ASP* 3.0 50.0 + - - +
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Residues in contact with GLU 193 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375U ARG* 3.6 13.7 + - - +
164V THR* 2.9 38.8 + - + +
168V GLN* 4.9 3.1 + - - -
189V GLU* 3.1 24.1 - - - +
190V ARG* 2.8 41.2 + - + +
192V ARG* 1.3 104.7 + - - +
194V GLY* 1.3 63.9 + - - +
196V ASP* 3.3 11.1 + - - +
197V LEU* 3.1 21.3 + - - +
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Residues in contact with GLY 194 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138U ILE* 4.1 10.3 - - - +
189V GLU* 5.6 0.6 + - - +
190V ARG 3.2 6.6 + - - -
191V THR 3.2 8.2 + - - -
193V GLU* 1.3 77.8 - - - +
195V ASN* 1.3 61.3 - - - +
197V LEU* 3.3 6.0 + - - +
198V TYR* 3.2 21.3 + - - +
219V PHE* 3.6 34.8 - - - -
221V GLN* 4.4 0.9 - - - +
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Residues in contact with ASN 195 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138U ILE* 3.1 25.9 - - - +
139U LEU* 4.0 4.0 - - - +
141U ARG* 3.0 51.2 + - + +
142U ARG* 3.5 13.5 + - - +
143U SER* 4.4 1.2 + - - +
191V THR 3.2 10.4 + - - +
192V ARG* 3.4 10.2 + - - +
194V GLY* 1.3 75.4 - - - +
196V ASP* 1.3 67.1 + - - +
198V TYR* 3.6 19.2 + - - +
199V ARG* 3.7 8.7 + - - +
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Residues in contact with ASP 196 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142U ARG 5.0 0.7 - - - +
143U SER* 4.2 20.4 + - - -
164V THR* 6.4 0.7 - - + -
168V GLN* 4.5 8.3 - - - +
192V ARG* 3.0 40.3 + - - +
193V GLU* 3.6 12.6 - - - +
194V GLY 3.2 0.2 - - - -
195V ASN* 1.3 86.7 + - - +
197V LEU* 1.3 62.7 + - - +
199V ARG* 3.6 12.1 + - - +
200V GLU* 3.1 31.0 + - + +
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Residues in contact with LEU 197 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164V THR* 5.9 0.2 - - + -
167V ILE* 5.2 4.7 - - + -
168V GLN* 3.3 37.0 - - + +
171V ILE* 5.8 5.8 - - + -
184V PHE* 3.7 51.8 - - + -
193V GLU 3.1 12.4 + - - +
194V GLY* 3.3 10.5 + - - +
196V ASP* 1.3 75.1 - - - +
198V TYR* 1.3 64.4 + - - +
200V GLU* 3.3 4.8 + - + +
201V MET* 3.3 49.5 + - + +
217V LEU* 4.8 1.6 - - + -
219V PHE* 4.3 9.9 - - + -
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Residues in contact with TYR 198 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138U ILE* 5.4 4.9 - - + +
139U LEU* 4.5 20.9 - - + +
93V GLY 5.6 3.5 + - - -
95V ILE* 3.4 37.0 - - + -
104V ASP* 4.2 6.6 + - - +
106V ARG* 4.1 20.8 - - - -
194V GLY 3.2 12.6 + - - +
195V ASN* 3.6 18.4 - - - +
197V LEU* 1.3 79.8 - - - +
199V ARG* 1.3 60.8 + - + +
201V MET* 4.5 5.6 - - + +
202V LYS* 3.0 73.7 + - + +
207V ILE* 5.9 2.9 - - + +
209V LEU* 4.5 2.4 - - - +
217V LEU* 3.9 17.7 - - + -
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Residues in contact with ARG 199 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143U SER* 4.3 17.7 + - - -
195V ASN 3.7 8.1 + - - +
196V ASP* 3.6 11.9 + - - +
197V LEU 3.3 0.2 - - - -
198V TYR* 1.3 78.9 - - + +
200V GLU* 1.3 107.4 + - - +
202V LYS* 3.5 6.0 + - - -
203V GLU* 3.4 55.2 + - + +
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Residues in contact with GLU 200 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168V GLN* 4.3 23.1 - - + +
196V ASP* 3.1 24.9 + - + +
197V LEU* 3.3 8.7 + - + +
199V ARG* 1.3 111.2 + - - +
201V MET* 1.3 58.3 + - + +
203V GLU* 3.5 3.2 + - - +
204V THR* 3.1 31.4 + - - +
420V VAL* 5.8 4.0 - - - +
423V VAL* 6.0 2.4 - - - +
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Residues in contact with MET 201 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171V ILE* 4.6 20.4 - - + -
184V PHE* 5.8 2.5 - - - -
197V LEU* 3.3 36.7 + - + +
198V TYR* 4.6 2.7 - - - +
200V GLU* 1.3 73.0 - - + +
202V LYS* 1.3 58.9 + - + +
203V GLU 3.0 11.3 + - - -
204V THR* 3.3 11.8 - - + +
206V VAL* 3.2 46.8 + - + -
207V ILE* 3.4 8.1 + - + -
215V VAL* 3.6 28.5 - - + -
217V LEU* 3.5 39.3 - - + -
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Residues in contact with LYS 202 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198V TYR* 3.0 66.0 + - + +
199V ARG* 4.0 5.8 - - - +
200V GLU 3.4 0.4 - - - -
201V MET* 1.3 76.4 - - + +
203V GLU* 1.3 63.2 + - + +
205V GLY 5.1 0.2 - - - -
207V ILE* 3.5 40.9 - - + +
209V LEU* 3.6 42.7 - - - +
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Residues in contact with GLU 203 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199V ARG* 3.4 50.4 + - + +
200V GLU* 4.1 3.3 - - - +
201V MET 3.0 0.6 - - - -
202V LYS* 1.3 84.7 - - + +
204V THR* 1.3 64.8 + - - +
205V GLY* 3.3 3.1 + - - -
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Residues in contact with THR 204 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171V ILE* 5.8 2.5 - - + -
172V ASN* 2.8 30.6 + - + -
176V LYS* 3.8 13.4 + - + +
200V GLU 3.1 20.6 + - - +
201V MET* 3.3 18.6 - - + +
203V GLU* 1.3 78.7 - - - +
205V GLY* 1.3 59.4 + - - +
206V VAL* 3.5 16.4 - - + -
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Residues in contact with GLY 205 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176V LYS* 4.1 16.6 - - - +
201V MET 3.5 0.4 + - - -
202V LYS 5.1 0.4 - - - -
203V GLU 3.3 3.7 - - - -
204V THR* 1.3 79.3 - - - +
206V VAL* 1.3 65.8 + - - +
207V ILE 5.7 0.4 - - - -
214V LYS* 4.6 7.6 + - - +
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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
------------------------------------------------------------
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