Contacts of the helix formed by residues 211 - 225 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210L GLN* 1.3 75.6 - - - +
212L ARG* 1.3 64.1 + - - +
213L SER* 3.0 32.6 + - - +
214L THR* 2.9 44.2 + - - +
215L VAL* 3.4 11.6 + - - +
237L THR* 3.8 1.6 - - - -
238L ALA* 4.7 1.6 - - - +
152O LYS* 4.7 9.8 - - + +
294O GLU* 3.5 20.0 - - - +
327O ALA 4.2 11.0 + - - +
328O HIS* 3.2 48.4 - - - +
329O LEU 4.4 3.6 - - - -
330O ASP* 3.3 26.1 + - - -
356O ARG* 4.3 4.0 - - - +
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Residues in contact with ARG 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L ILE* 6.3 0.8 - - - +
211L LYS* 1.3 71.1 - - - +
213L SER* 1.3 57.1 - - - +
215L VAL* 4.3 2.2 - - - +
216L ALA* 3.2 25.4 + - - +
237L THR* 3.1 35.7 + - + +
239L SER* 4.2 9.7 + - - -
240L GLU* 3.7 28.9 + - - +
121O PRO* 3.8 23.4 + - - +
122O PRO 3.5 25.1 + - - -
123O SER* 4.1 8.1 - - - +
124O PHE* 4.2 25.3 - - + +
127O GLN* 3.3 23.6 - - + +
294O GLU* 2.7 22.1 + - - +
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Residues in contact with SER 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L LYS* 3.0 25.2 + - - +
212L ARG* 1.3 77.3 - - - +
214L THR* 1.3 60.9 + - - +
216L ALA* 3.1 8.5 + - - +
217L GLN* 2.9 27.6 + - - +
127O GLN* 4.3 14.8 + - - +
128O SER 5.2 2.4 + - - -
129O THR* 3.9 13.7 - - - +
152O LYS* 6.0 3.4 - - - -
294O GLU* 4.6 1.9 + - - -
297O THR* 4.6 10.6 + - - -
330O ASP* 4.9 4.9 + - - -
356O ARG* 4.9 3.9 + - - -
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Residues in contact with THR 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L THR* 6.5 0.4 - - + -
210L GLN* 3.8 21.1 - - + +
211L LYS* 2.9 42.5 + - - +
213L SER* 1.3 78.7 - - - +
215L VAL* 1.3 57.4 + - - +
217L GLN* 2.9 23.9 + - + +
218L LEU* 2.9 16.2 + - + +
327O ALA 4.9 1.9 + - - -
356O ARG* 4.0 13.8 + - - +
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Residues in contact with VAL 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L TYR* 5.6 0.4 - - + -
207L ALA* 3.5 19.7 - - + -
210L GLN* 3.4 26.0 - - + +
211L LYS 3.4 13.3 + - - +
212L ARG 4.4 4.0 - - - +
214L THR* 1.3 75.4 - - - +
216L ALA* 1.3 59.4 + - - +
218L LEU* 3.3 11.6 + - + +
219L VAL* 3.2 24.2 + - + +
233L ILE* 3.9 28.3 - - + -
235L ALA* 4.1 11.7 - - + -
237L THR* 4.3 11.7 - - + -
124O PHE* 4.1 13.5 - - + -
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Residues in contact with ALA 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L ARG 3.2 20.2 + - - +
213L SER* 3.1 9.3 + - - +
215L VAL* 1.3 77.5 - - - +
217L GLN* 1.3 61.7 + - - +
219L VAL* 3.3 18.1 - - - +
220L GLN* 3.6 10.6 + - - +
124O PHE* 4.0 15.6 - - + +
127O GLN* 3.9 23.6 - - + -
129O THR* 4.3 10.9 + - + +
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Residues in contact with GLN 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L SER 2.9 11.7 + - - +
214L THR* 2.9 13.4 + - + +
216L ALA* 1.3 77.6 - - - +
218L LEU* 1.3 63.3 + - - +
220L GLN* 3.5 20.5 + - - +
221L THR* 3.4 29.7 + - - +
129O THR* 3.4 25.6 - - + +
130O SER 5.0 2.3 + - - +
356O ARG* 3.5 32.2 + - - +
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Residues in contact with LEU 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L THR* 4.5 21.5 - - + -
182L LEU* 4.3 26.4 - - + +
205L TYR* 3.4 46.7 - - + +
210L GLN* 5.9 0.4 - - - +
214L THR* 2.9 14.2 + - + +
215L VAL* 3.5 15.3 - - + +
216L ALA 3.3 0.4 - - - -
217L GLN* 1.3 74.0 - - - +
219L VAL* 1.3 66.2 + - + +
221L THR* 3.1 7.3 + - - -
222L LEU* 2.9 41.9 + - + +
233L ILE* 4.6 5.8 - - + -
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Residues in contact with VAL 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L VAL* 4.0 24.2 - - + -
215L VAL* 3.4 13.9 - - + +
216L ALA* 3.3 19.1 - - - +
218L LEU* 1.3 76.7 - - + +
220L GLN* 1.3 65.6 + - + +
222L LEU* 4.2 0.9 - - - -
223L GLU* 3.1 28.9 + - - +
228L MET* 3.4 29.4 - - + +
233L ILE* 4.3 18.4 - - + -
124O PHE* 4.3 13.0 - - + -
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Residues in contact with GLN 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L ALA 3.6 9.2 - - - +
217L GLN* 3.5 26.4 + - - +
218L LEU 3.1 0.6 - - - -
219L VAL* 1.3 84.8 - - + +
221L THR* 1.3 60.4 + - - +
223L GLU* 3.6 8.4 + - - +
224L GLN* 3.0 45.1 + - + +
129O THR* 2.8 36.7 + - - +
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Residues in contact with THR 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182L LEU* 5.0 7.9 - - + -
186L LEU* 5.3 1.8 - - + -
217L GLN* 3.4 22.4 + - - +
218L LEU* 3.1 8.8 + - - -
220L GLN* 1.3 75.4 - - - +
222L LEU* 1.3 67.3 + - - +
224L GLN* 3.1 22.8 + - - +
225L HIS* 3.0 41.9 - - + +
435L TYR* 3.7 31.6 + - + +
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Residues in contact with LEU 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182L LEU* 3.9 26.2 - - + +
185L ILE* 4.0 18.6 - - + -
186L LEU* 4.0 6.7 - - + -
205L TYR* 5.7 2.5 - - + -
218L LEU* 2.9 32.9 + - + +
219L VAL* 4.4 1.1 - - - -
221L THR* 1.3 76.9 - - - +
223L GLU* 1.3 56.4 + - - +
225L HIS* 3.2 2.4 + - - -
226L ASP 3.1 2.9 + - - -
227L ALA* 2.7 57.2 + - + +
228L MET* 3.5 32.5 - - + +
231L SER* 4.4 3.8 - - - +
233L ILE* 3.8 20.0 - - + -
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Residues in contact with GLU 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L LYS* 4.0 19.2 + - - -
219L VAL* 3.1 24.8 + - - +
220L GLN* 3.8 7.6 - - - +
222L LEU* 1.3 71.5 - - - +
224L GLN* 1.3 59.9 + - - +
225L HIS 3.0 2.2 - - - -
226L ASP* 2.8 24.5 + - - +
228L MET* 3.7 30.2 - - + +
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Residues in contact with GLN 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L GLN* 3.0 42.9 + - + +
221L THR* 3.1 24.0 + - - +
223L GLU* 1.3 76.1 - - + +
225L HIS* 1.3 65.2 + - + +
226L ASP 3.3 0.6 + - - -
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Residues in contact with HIS 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L LEU* 3.6 36.2 - - + +
189L LYS* 3.7 22.3 + - + +
221L THR* 3.0 36.5 + - + +
222L LEU 3.2 3.1 + - - +
223L GLU 3.0 0.6 - - - -
224L GLN* 1.3 83.6 + - + +
226L ASP* 1.3 71.0 + - - +
227L ALA* 3.2 2.0 + - + +
435L TYR* 3.8 39.6 - + + -
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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
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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