Contacts of the helix formed by residues 211 - 225 (chain S) 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 LYS 211 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210S GLN* 1.3 75.6 - - - +
212S ARG* 1.3 59.2 + - - +
213S SER* 3.0 31.5 + - - +
214S THR* 2.7 42.9 + - - +
215S VAL* 3.1 15.6 + - - +
238S ALA* 4.9 0.4 - - - -
152V LYS* 3.6 26.4 - - + +
294V GLU* 3.1 21.5 - - - +
327V ALA 5.0 4.9 + - - +
328V HIS* 3.9 23.3 - - - +
330V ASP* 3.5 26.5 + - - -
356V ARG* 3.8 13.2 - - - +
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Residues in contact with ARG 212 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211S LYS* 1.3 70.9 - - - +
213S SER* 1.3 60.9 + - - +
214S THR 3.4 0.4 - - - -
215S VAL* 4.0 6.1 - - - -
216S ALA* 3.2 26.5 + - - +
237S THR* 3.1 32.7 + - + +
239S SER* 4.3 13.8 + - - -
240S GLU* 3.6 31.7 + - - +
121V PRO* 4.4 13.1 + - - +
122V PRO 2.8 37.2 + - - -
123V SER* 3.5 13.2 + - - +
124V PHE* 4.1 24.8 - - + +
127V GLN* 3.6 24.2 - - + +
294V GLU* 3.2 14.0 + - - +
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Residues in contact with SER 213 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211S LYS* 3.0 27.9 - - - +
212S ARG* 1.3 80.1 - - - +
214S THR* 1.3 58.0 + - - +
216S ALA* 4.4 1.8 - - - +
217S GLN* 3.1 28.6 + - - +
127V GLN* 3.3 8.1 + - - -
152V LYS* 5.1 6.9 + - - +
294V GLU* 4.7 3.5 + - - -
297V THR* 3.2 27.0 + - - -
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Residues in contact with THR 214 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178S THR* 6.6 0.2 - - + -
210S GLN* 5.1 11.4 - - - +
211S LYS* 2.7 42.9 + - - +
213S SER* 1.3 76.5 - - - +
215S VAL* 1.3 59.1 + - - +
217S GLN* 3.0 9.0 + - + +
218S LEU* 2.8 35.9 + - + +
356V ARG* 3.8 13.5 + - - +
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Residues in contact with VAL 215 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109S VAL* 5.5 0.4 - - + -
205S TYR* 6.2 0.7 - - + -
207S ALA* 3.6 26.5 - - + -
210S GLN* 3.9 12.1 - - + +
211S LYS 3.1 17.1 + - - +
212S ARG* 4.2 3.8 - - - -
214S THR* 1.3 75.6 - - - +
216S ALA* 1.3 58.0 + - - +
218S LEU* 3.0 25.0 + - + +
219S VAL* 3.1 13.6 + - + +
233S ILE* 4.4 16.4 - - + -
235S ALA* 4.2 17.7 - - + -
237S THR* 3.9 16.2 - - + -
124V PHE* 3.5 22.7 - - + -
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Residues in contact with ALA 216 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212S ARG 3.2 18.0 + - - +
213S SER 4.4 2.0 - - - +
215S VAL* 1.3 79.0 - - - +
217S GLN* 1.3 63.5 + - - +
219S VAL* 3.5 3.4 + - - +
220S GLN* 3.2 24.7 + - - +
124V PHE* 3.5 27.3 - - + +
127V GLN* 3.9 23.6 - - + +
128V SER 6.1 1.6 - - - -
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Residues in contact with GLN 217 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213S SER 3.1 22.1 + - - +
214S THR* 3.0 15.1 + - + +
216S ALA* 1.3 78.2 - - - +
218S LEU* 1.3 50.9 + - - +
220S GLN* 3.8 20.9 + - - +
221S THR* 2.7 34.6 + - - +
128V SER 5.0 3.1 - - - +
130V SER 3.0 35.2 + - - +
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Residues in contact with LEU 218 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178S THR* 5.0 11.9 - - + -
182S LEU* 4.0 39.9 - - + -
205S TYR* 3.8 45.8 - - + +
214S THR* 2.8 17.4 + - + +
215S VAL* 3.0 13.7 + - + +
217S GLN* 1.3 74.7 - - - +
219S VAL* 1.3 58.8 + - + +
220S GLN 3.0 1.3 - - - -
221S THR* 2.8 26.2 + - - +
222S LEU* 3.0 24.3 + - + +
233S ILE* 5.2 5.6 - - + -
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Residues in contact with VAL 219 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109S VAL* 3.8 27.6 - - + -
215S VAL 3.1 12.8 + - - +
216S ALA 3.5 5.8 + - - +
218S LEU* 1.3 76.6 - - + +
220S GLN* 1.3 60.8 + - - +
222S LEU* 3.5 7.7 + - - +
223S GLU* 3.2 24.2 + - - +
228S MET* 3.8 29.6 - - + +
233S ILE* 4.3 21.3 - - + -
124V PHE* 4.1 15.0 - - + -
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Residues in contact with GLN 220 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216S ALA 3.2 17.1 + - - +
217S GLN* 3.8 28.6 + - - +
218S LEU 3.0 0.6 - - - -
219S VAL* 1.3 78.3 - - - +
221S THR* 1.3 59.4 + - - +
223S GLU* 3.7 8.5 - - + +
224S GLN* 3.5 29.3 + - - +
128V SER 5.1 10.3 - - - -
130V SER 4.7 5.9 + - - -
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Residues in contact with THR 221 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182S LEU* 4.9 7.4 - - + -
186S LEU* 4.7 2.3 - - + +
217S GLN* 2.7 27.4 + - - +
218S LEU* 2.8 10.2 + - - +
220S GLN* 1.3 76.3 - - - +
222S LEU* 1.3 61.2 + - - +
223S GLU 3.1 5.5 + - - -
224S GLN* 3.5 16.9 + - - +
225S HIS* 2.9 39.9 + - + +
435S TYR* 3.4 39.9 + - + +
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Residues in contact with LEU 222 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182S LEU* 3.5 29.4 - - + -
185S ILE* 4.6 14.8 - - + -
186S LEU* 4.0 15.5 - - + -
205S TYR* 6.1 1.1 - - + -
218S LEU* 3.0 25.2 + - + +
219S VAL* 3.5 4.5 + - - +
221S THR* 1.3 75.8 - - - +
223S GLU* 1.3 58.7 + - - +
225S HIS* 4.0 1.6 - - - +
226S ASP 3.2 1.6 + - - -
227S ALA* 2.7 39.7 + - + +
228S MET* 2.8 27.9 + - + +
231S SER* 3.7 22.7 - - - +
233S ILE* 3.8 21.8 - - + -
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Residues in contact with GLU 223 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120S LYS* 4.7 12.6 + - - -
219S VAL* 3.2 15.4 + - - +
220S GLN* 3.7 11.4 - - + +
221S THR 3.1 0.2 - - - -
222S LEU* 1.3 77.0 - - - +
224S GLN* 1.3 63.6 + - + +
225S HIS 3.1 1.8 - - - -
226S ASP* 3.2 13.2 + - - +
228S MET* 3.8 29.8 - - - +
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Residues in contact with GLN 224 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220S GLN* 3.5 21.5 + - + +
221S THR* 3.5 21.2 + - - +
223S GLU* 1.3 77.1 - - + +
225S HIS* 1.3 68.0 + - + +
226S ASP 3.4 0.2 - - - -
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Residues in contact with HIS 225 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186S LEU* 3.8 28.6 - - + +
189S LYS* 3.2 40.4 + - - +
221S THR* 2.9 30.7 + - + +
222S LEU 3.8 0.2 + - - -
223S GLU 3.1 0.4 - - - -
224S GLN* 1.3 86.5 - - + +
226S ASP* 1.3 71.7 + - - +
227S ALA* 4.4 4.7 - - + +
435S TYR* 4.0 42.9 + + - +
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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