Contacts of the helix formed by residues 190 - 205 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166S ARG* 4.4 1.8 - - - +
309S GLU* 4.6 3.4 - - - +
345S ILE 4.1 2.6 + - - -
346S SER* 3.0 33.8 + - - +
347S ILE 3.4 20.2 + - - +
348S THR 3.4 13.7 + - - -
349S ASP* 4.1 13.0 - - - -
375S ARG* 4.1 16.4 - - - +
188W GLY 3.6 2.5 + - - +
189W GLU* 1.3 74.3 - - - +
191W THR* 1.3 54.1 + - - +
192W ARG* 4.3 7.2 - - + +
193W GLU* 2.9 52.6 + - + +
194W GLY* 2.8 32.2 + - - -
222W MET* 3.6 24.0 - - - -
260W ARG* 5.0 10.9 - - - +
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Residues in contact with THR 191 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135S ALA* 5.6 0.2 - - - +
136S PRO 3.2 26.5 - - - +
137S GLY* 3.4 19.3 - - - +
138S ILE* 3.6 15.9 - - + +
141S ARG* 3.7 9.4 - - - -
309S GLU* 2.7 27.9 + - - +
189W GLU 3.1 4.2 + - - -
190W ARG* 1.3 70.7 - - - +
192W ARG* 1.3 62.1 + - - +
194W GLY 3.2 0.9 + - - -
195W ASN* 3.0 21.5 + - - +
221W GLN* 3.3 27.2 - - - +
223W ASN* 3.7 7.8 + - - +
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Residues in contact with ARG 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141S ARG* 3.5 26.0 - - - +
144S VAL* 5.1 11.0 - - + -
164S GLY 5.7 2.2 - - - -
166S ARG* 3.9 11.5 - - - +
312S ALA* 6.5 0.2 - - + -
349S ASP* 3.2 35.4 + - - -
375S ARG* 3.2 36.3 - - - +
376S VAL* 4.3 21.7 - - - +
190W ARG* 4.5 3.8 - - + +
191W THR* 1.3 78.5 - - - +
193W GLU* 1.3 83.8 + - - +
195W ASN* 3.1 7.0 + - - +
196W ASP* 3.0 43.9 + - + +
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Residues in contact with GLU 193 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375S ARG* 2.8 29.6 + - - +
189W GLU* 3.6 29.1 - - - +
190W ARG* 2.9 51.1 + - + +
192W ARG* 1.3 94.3 + - - +
194W GLY* 1.3 64.6 + - - +
196W ASP* 3.3 7.9 + - - +
197W LEU* 3.0 25.5 + - - +
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Residues in contact with GLY 194 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 3.6 19.0 - - - +
189W GLU* 4.3 2.8 - - - +
190W ARG 2.8 17.3 + - - -
191W THR 3.2 4.6 + - - -
193W GLU* 1.3 72.3 - - - +
195W ASN* 1.3 60.3 + - - +
197W LEU* 3.6 3.9 + - - +
198W TYR* 3.3 17.7 + - - +
219W PHE* 3.6 32.7 - - - -
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Residues in contact with ASN 195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 2.8 38.0 + - + +
139S LEU* 4.1 4.2 + - - +
141S ARG* 3.5 35.7 + - + +
142S ARG* 4.4 7.8 + - - -
143S SER* 4.6 6.9 + - - -
191W THR 3.0 12.0 + - - +
192W ARG* 3.1 10.5 + - - +
194W GLY* 1.3 73.6 - - - +
196W ASP* 1.3 67.1 + - - +
197W LEU 3.0 5.9 + - - -
198W TYR* 3.2 6.9 + - - +
199W ARG* 3.2 26.0 + - - +
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Residues in contact with ASP 196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S SER* 3.1 26.1 + - - -
164W THR* 6.2 0.2 - - - -
192W ARG* 3.0 32.4 + - - +
193W GLU* 3.3 8.9 + - - +
195W ASN* 1.3 79.7 + - - +
197W LEU* 1.3 60.6 + - - +
199W ARG* 3.5 26.3 + - - +
200W GLU* 3.6 20.8 + - - +
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Residues in contact with LEU 197 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164W THR* 3.6 31.0 - - + +
167W ILE* 6.0 3.1 - - + -
168W GLN* 5.1 3.6 - - + +
184W PHE* 3.4 50.3 - - + -
189W GLU* 5.8 2.7 - - + +
193W GLU 3.0 16.6 + - - +
194W GLY* 3.8 3.8 - - - +
195W ASN 3.0 0.8 - - - -
196W ASP* 1.3 75.6 - - - +
198W TYR* 1.3 67.7 + - - +
199W ARG 3.1 1.8 - - - -
200W GLU* 2.8 15.4 + - - +
201W MET* 2.8 38.1 + - + +
217W LEU* 4.7 1.6 - - + -
219W PHE* 4.3 12.1 - - + -
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Residues in contact with TYR 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 4.5 13.2 - - + -
139S LEU* 4.3 22.7 - - + -
93W GLY 4.7 3.9 + - - -
95W ILE* 3.3 35.3 - - + +
104W ASP* 4.2 10.3 + - + +
106W ARG* 4.8 3.5 + - - -
194W GLY 3.3 10.1 + - - +
195W ASN* 3.2 11.1 + - - +
197W LEU* 1.3 79.5 - - - +
199W ARG* 1.3 62.9 + - - +
201W MET* 3.2 7.7 + - - +
202W LYS* 3.1 57.2 + - + +
207W ILE* 4.2 15.3 - - + -
209W LEU* 3.6 23.0 - - - +
217W LEU* 3.6 20.9 - - + -
219W PHE* 5.9 1.1 - - + -
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Residues in contact with ARG 199 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143S SER* 3.4 23.4 + - - -
195W ASN* 3.2 17.6 + - - +
196W ASP* 3.5 29.4 + - - +
197W LEU 3.1 0.2 - - - -
198W TYR* 1.3 79.6 - - - +
200W GLU* 1.3 67.6 + - - +
202W LYS* 3.3 18.4 + - - +
203W GLU* 3.0 40.0 + - + +
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Residues in contact with GLU 200 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164W THR* 3.1 32.6 + - + +
165W VAL* 4.1 12.5 - - - +
168W GLN* 3.3 20.7 - - - +
196W ASP 3.6 11.8 + - - +
197W LEU* 2.8 11.3 + - - +
199W ARG* 1.3 85.4 + - - +
201W MET* 1.3 60.1 + - - +
203W GLU* 3.4 8.0 + - - +
204W THR* 2.9 33.4 + - - +
424W PHE* 4.1 29.3 - - + -
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Residues in contact with MET 201 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ILE* 5.7 1.1 - - + -
168W GLN* 3.3 22.9 - - + +
171W ILE* 4.1 16.4 - - + -
184W PHE* 5.4 4.5 - - + -
197W LEU* 2.8 38.1 + - + +
198W TYR* 3.2 5.6 + - - +
200W GLU* 1.3 77.2 - - - +
202W LYS* 1.3 60.2 + - - +
204W THR* 3.0 17.7 - - - +
205W GLY 3.4 0.7 + - - -
206W VAL* 3.5 20.2 - - + -
207W ILE* 3.2 45.3 + - + -
215W VAL* 3.5 22.0 - - + -
217W LEU* 3.8 23.3 - - + -
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Residues in contact with LYS 202 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139S LEU* 5.8 2.6 - - - +
198W TYR* 3.1 55.2 + - + +
199W ARG* 3.6 17.3 - - - +
200W GLU 3.2 0.2 - - - -
201W MET* 1.3 78.6 - - - +
203W GLU* 1.3 63.3 + - - +
204W THR 3.1 1.4 + - - -
205W GLY* 3.5 8.0 + - - -
207W ILE* 3.5 24.3 - - + +
209W LEU* 3.8 29.4 - - + +
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Residues in contact with GLU 203 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199W ARG* 3.0 29.5 + - + +
200W GLU* 3.9 7.3 - - - +
202W LYS* 1.3 79.5 - - - +
204W THR* 1.3 59.9 + - - +
423W VAL* 3.8 17.5 - - + +
424W PHE* 4.1 25.1 - - + -
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Residues in contact with THR 204 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168W GLN* 3.3 21.2 + - - +
200W GLU 2.9 17.1 + - - +
201W MET 3.0 17.5 - - - +
203W GLU* 1.3 79.7 - - - +
205W GLY* 1.3 68.5 + - - +
206W VAL* 3.5 18.6 - - + +
420W VAL* 3.2 44.0 + - - +
423W VAL* 4.2 16.8 - - - +
424W PHE* 4.7 9.8 - - - -
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Residues in contact with GLY 205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201W MET 3.4 3.0 + - - -
202W LYS 3.5 8.9 + - - -
204W THR* 1.3 80.7 - - - +
206W VAL* 1.3 65.5 + - - +
207W ILE 3.4 4.0 - - - -
208W ASN* 4.6 14.9 + - - +
212W GLU 5.1 0.9 - - - +
214W LYS* 3.6 17.7 + - - -
420W VAL* 6.2 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
------------------------------------------------------------
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