Contacts of the helix formed by residues 190 - 205 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166J ARG* 4.0 10.8 - - - +
309J GLU* 4.1 3.4 - - - +
345J ILE 4.4 1.8 + - - -
346J SER* 2.7 29.2 + - - +
347J ILE 3.1 25.6 + - - +
348J THR 3.4 9.3 + - - -
349J ASP* 3.8 15.3 - - - +
375J ARG* 3.2 30.7 - - - +
188N GLY 3.6 1.2 + - - +
189N GLU* 1.3 80.6 - - - +
191N THR* 1.3 59.9 + - - +
193N GLU* 3.1 42.8 + - + +
194N GLY* 2.9 23.7 + - - -
222N MET* 3.8 17.5 - - - -
260N ARG* 4.8 5.1 - - - +
610N PO4 3.2 27.9 + - - -
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Residues in contact with THR 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ALA* 5.5 0.6 - - + +
136J PRO 3.4 24.2 - - - +
137J GLY* 3.8 12.6 - - - +
138J ILE* 3.9 5.9 - - + +
141J ARG* 3.4 18.9 + - - -
309J GLU* 3.1 16.8 + - - +
189N GLU 3.4 2.1 + - - -
190N ARG* 1.3 72.7 - - - +
192N ARG* 1.3 61.1 + - - +
194N GLY* 3.5 3.1 + - - +
195N ASN* 3.4 19.1 + - - +
221N GLN* 3.6 37.3 + - - +
222N MET* 5.0 0.4 + - - +
223N ASN* 3.9 13.9 + - - -
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Residues in contact with ARG 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J ARG* 3.2 24.2 - - + +
142J ARG 6.1 0.4 - - - +
143J SER* 6.2 1.8 - - - -
144J VAL* 4.0 28.6 - - + +
164J GLY 5.0 6.1 - - - -
165J GLN* 5.3 0.7 - - - +
166J ARG* 4.1 11.4 - - - +
309J GLU* 4.1 0.8 + - - -
312J ALA* 5.6 4.7 - - + -
313J LYS 6.2 0.7 - - - +
349J ASP* 3.0 44.2 + - - +
375J ARG* 4.2 14.8 - - - +
376J VAL* 3.5 24.1 - - - +
190N ARG* 3.1 0.8 - - + -
191N THR* 1.3 75.4 - - - +
193N GLU* 1.3 92.3 + - - +
195N ASN* 3.3 6.8 + - - +
196N ASP* 3.2 31.0 + - + +
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Residues in contact with GLU 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375J ARG* 2.7 40.4 + - - -
189N GLU* 3.7 20.6 - - - +
190N ARG* 3.1 39.8 + - - +
192N ARG* 1.3 94.1 + - - +
194N GLY* 1.3 58.9 + - - +
195N ASN 3.3 0.2 - - - -
196N ASP* 3.8 8.4 - - + +
197N LEU* 2.9 32.1 + - - +
610N PO4 4.8 3.3 + - - -
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Residues in contact with GLY 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ILE* 3.5 10.6 - - - +
189N GLU* 4.0 1.3 + - - -
190N ARG 2.9 15.8 + - - -
191N THR* 3.9 4.7 - - - -
192N ARG 3.1 0.6 - - - -
193N GLU* 1.3 78.1 - - - +
195N ASN* 1.3 56.2 + - - +
197N LEU* 3.9 0.2 - - - +
198N TYR* 3.1 28.6 + - - +
219N PHE* 3.6 33.3 - - - -
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Residues in contact with ASN 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ILE* 3.1 37.2 + - + +
139J LEU* 4.1 8.1 + - - +
141J ARG* 2.9 35.4 + - + +
142J ARG 4.3 0.2 - - - -
143J SER* 4.1 16.6 + - - -
191N THR 3.4 6.5 + - - +
192N ARG 3.3 8.6 + - - +
194N GLY* 1.3 75.8 - - - +
196N ASP* 1.3 60.1 + - - +
198N TYR* 3.2 7.3 + - - +
199N ARG* 2.9 40.8 + - - +
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Residues in contact with ASP 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J SER* 3.0 29.3 + - - +
192N ARG* 3.2 24.3 + - + +
193N GLU* 4.0 8.5 - - - +
194N GLY 3.4 0.2 - - - -
195N ASN* 1.3 79.7 + - - +
197N LEU* 1.3 57.6 + - - +
199N ARG* 3.1 19.9 + - - -
200N GLU* 2.9 36.3 + - - +
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Residues in contact with LEU 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N THR* 3.7 30.3 - - + +
167N ILE* 6.1 2.7 - - + -
168N GLN* 5.2 0.2 - - - +
184N PHE* 3.4 43.5 - - + -
189N GLU* 4.9 4.3 - - - +
193N GLU 2.9 18.6 + - - +
194N GLY 3.9 2.5 - - - +
196N ASP* 1.3 76.0 - - - +
198N TYR* 1.3 58.8 + - - +
200N GLU* 3.3 6.3 + - - +
201N MET* 2.8 60.3 + - + +
217N LEU* 4.4 3.4 - - + -
219N PHE* 4.0 18.8 - - + -
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Residues in contact with TYR 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ILE* 5.0 8.3 - - + -
139J LEU* 4.9 19.1 - - + -
93N GLY 4.7 5.9 + - - -
95N ILE* 3.2 35.4 - - + +
104N ASP* 4.4 14.6 + - + +
106N ARG* 4.6 4.5 + - - -
194N GLY 3.1 16.5 + - - +
195N ASN* 3.6 13.0 - - - +
197N LEU* 1.3 79.8 - - - +
199N ARG* 1.3 65.7 + - + +
201N MET* 3.0 14.8 + - - +
202N LYS* 3.2 44.8 + - + +
207N ILE* 4.6 11.2 - - + -
209N LEU* 4.0 18.2 - - - +
217N LEU* 3.6 20.2 - - + -
219N PHE* 5.1 2.5 - - + -
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Residues in contact with ARG 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J SER* 3.2 25.9 + - - +
195N ASN* 2.9 29.0 + - - +
196N ASP* 3.1 24.2 + - - +
198N TYR* 1.3 75.4 - - - +
200N GLU* 1.3 66.5 + - - +
202N LYS* 3.6 18.4 + - - +
203N GLU* 3.4 51.2 + - - +
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Residues in contact with GLU 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N THR* 3.2 36.1 + - - +
165N VAL* 4.5 8.8 - - - +
168N GLN* 3.7 14.4 - - - +
196N ASP* 2.9 29.9 + - - +
197N LEU* 3.5 4.6 - - - +
198N TYR 3.1 0.4 - - - -
199N ARG* 1.3 86.8 - - - +
201N MET* 1.3 62.3 + - - +
203N GLU* 3.3 12.2 + - - +
204N THR* 3.1 22.4 + - - +
424N PHE* 4.8 21.4 - - + -
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Residues in contact with MET 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167N ILE* 5.2 2.7 - - + -
168N GLN* 3.6 18.6 - - + +
171N ILE* 4.1 24.7 - - + -
184N PHE* 4.7 9.4 - - + -
197N LEU* 2.8 43.7 + - + +
198N TYR* 3.0 5.1 + - - +
200N GLU* 1.3 73.4 - - - +
202N LYS* 1.3 65.6 + - - +
203N GLU 3.1 1.3 - - - -
204N THR* 2.9 23.0 + - - +
205N GLY 3.2 5.5 + - - -
206N VAL* 3.8 5.6 - - + -
207N ILE* 3.5 25.9 + - + -
215N VAL* 4.1 14.4 - - + -
217N LEU* 3.7 33.7 - - + -
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Residues in contact with LYS 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J LEU* 6.0 3.0 - - - +
198N TYR* 3.2 32.3 + - + +
199N ARG* 4.0 22.2 - - - +
201N MET* 1.3 77.1 - - - +
203N GLU* 1.3 62.4 + - - +
205N GLY* 3.7 6.4 + - - -
207N ILE* 3.3 39.0 - - + +
209N LEU* 3.6 39.5 - - + +
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Residues in contact with GLU 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199N ARG* 3.4 36.6 + - - +
200N GLU* 3.3 12.7 + - - +
201N MET 3.1 0.6 - - - -
202N LYS* 1.3 81.0 - - - +
204N THR* 1.3 59.0 + - - +
205N GLY 3.5 0.4 + - - -
423N VAL* 4.1 19.7 - - + +
424N PHE* 4.3 21.7 - - + -
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Residues in contact with THR 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N GLN* 3.4 33.6 + - - +
200N GLU* 3.1 7.4 + - - +
201N MET* 2.9 23.1 - - - +
203N GLU* 1.3 79.6 - - - +
205N GLY* 1.3 56.1 + - - +
206N VAL* 3.6 15.9 + - + +
420N VAL* 3.1 45.2 + - - +
423N VAL* 4.4 16.6 - - - +
424N PHE* 5.1 6.5 - - - -
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Residues in contact with GLY 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201N MET 3.2 5.0 + - - -
202N LYS 3.7 6.8 + - - -
203N GLU 3.5 2.4 - - - -
204N THR* 1.3 78.7 - - - +
206N VAL* 1.3 64.2 + - - +
207N ILE 3.2 7.8 + - - -
208N ASN* 4.6 7.3 + - - +
212N GLU 5.2 2.1 - - - +
214N LYS* 4.1 11.3 + - - -
420N 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
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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