Contacts of the helix formed by residues 211 - 225 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210K GLN* 1.3 72.9 - - - +
212K ARG* 1.3 66.7 + - - +
213K SER* 3.7 18.3 + - - +
214K THR* 3.1 32.6 + - - +
215K VAL* 3.2 16.4 + - - +
238K ALA* 5.2 0.2 - - - -
152N LYS* 3.9 19.6 - - - +
294N GLU* 3.2 12.3 - - - +
327N ALA 4.0 8.7 + - - +
328N HIS* 3.3 56.6 + - + +
329N LEU 5.1 0.4 + - - -
330N ASP* 3.5 26.7 + - - -
356N ARG* 5.3 2.8 - - - +
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Residues in contact with ARG 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K ILE* 5.5 10.3 - - - +
210K GLN 3.6 1.0 + - - -
211K LYS* 1.3 71.7 - - - +
213K SER* 1.3 63.1 + - - +
215K VAL* 3.4 3.8 + - - +
216K ALA* 3.1 21.9 + - - +
237K THR* 3.6 32.0 + - + +
239K SER* 4.8 8.0 + - - -
240K GLU* 4.1 18.7 + - - -
121N PRO* 3.3 23.7 + - - +
122N PRO 3.3 26.9 + - - -
123N SER* 4.2 5.8 + - - +
124N PHE* 3.5 39.5 - - + +
127N GLN* 4.2 16.2 - - + +
294N GLU* 2.7 23.9 + - + +
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Residues in contact with SER 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K LYS* 3.7 23.9 + - - +
212K ARG* 1.3 77.1 - - - +
214K THR* 1.3 73.7 + - - +
216K ALA* 2.9 17.7 + - - +
217K GLN* 3.0 29.2 + - - +
127N GLN* 3.9 9.4 + - - -
128N SER 5.4 4.0 - - - -
152N LYS* 5.9 0.7 - - - -
294N GLU* 4.7 2.8 + - - -
297N THR* 3.9 22.4 - - - -
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Residues in contact with THR 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K GLN* 4.6 15.3 - - + +
211K LYS* 3.1 37.8 + - - +
213K SER* 1.3 83.8 + - - +
215K VAL* 1.3 58.5 + - - +
217K GLN* 3.5 8.8 + - - +
218K LEU* 3.0 30.4 + - + +
356N ARG* 5.6 9.4 + - - +
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Residues in contact with VAL 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205K TYR* 5.3 3.6 - - + -
207K ALA* 3.6 22.7 - - + -
210K GLN* 3.3 29.4 - - + +
211K LYS 3.2 14.9 + - - +
212K ARG* 3.8 6.3 - - - +
214K THR* 1.3 74.1 - - - +
216K ALA* 1.3 59.4 + - - +
218K LEU* 3.2 10.2 + - + +
219K VAL* 2.9 29.2 + - + +
233K ILE* 4.3 15.3 - - + -
235K ALA* 4.2 11.7 - - + -
237K THR* 4.6 8.1 - - + -
124N PHE* 3.9 15.7 - - + -
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Residues in contact with ALA 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K ARG 3.1 13.5 + - - +
213K SER* 2.9 10.2 + - - +
215K VAL* 1.3 77.1 - - - +
217K GLN* 1.3 62.6 + - - +
219K VAL* 3.1 6.4 + - - +
220K GLN* 3.1 20.4 + - - +
124N PHE* 3.6 19.9 - - + +
127N GLN* 4.0 24.5 - - + +
128N SER 4.3 11.0 - - - +
129N THR* 4.5 10.7 - - + +
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Residues in contact with GLN 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K SER* 3.0 25.0 + - - +
214K THR* 4.0 6.7 - - - +
216K ALA* 1.3 72.8 - - - +
218K LEU* 1.3 62.1 + - - +
220K GLN* 3.3 2.6 + - - +
221K THR* 2.8 29.6 + - - -
128N SER 4.2 6.3 + - - +
129N THR 3.6 27.8 - - - +
130N SER 4.0 1.6 - - - -
131N ALA* 3.2 42.0 - - - +
356N ARG* 4.6 15.8 + - - +
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Residues in contact with LEU 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K THR* 4.3 11.7 - - + -
182K LEU* 4.3 19.7 - - + +
205K TYR* 3.5 53.6 - - + +
210K GLN* 4.7 6.3 - - - +
214K THR* 3.0 19.7 + - + +
215K VAL* 3.3 14.1 - - + +
217K GLN* 1.3 78.6 - - - +
219K VAL* 1.3 61.6 + - + +
221K THR* 3.6 7.0 + - - -
222K LEU* 3.2 39.7 + - + +
233K ILE* 4.9 4.9 - - + -
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Residues in contact with VAL 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K VAL* 4.1 16.4 - - + -
215K VAL* 2.9 25.6 + - + +
216K ALA 3.1 7.8 + - - +
218K LEU* 1.3 74.1 - - + +
220K GLN* 1.3 60.8 + - - +
221K THR 3.1 2.2 - - - -
222K LEU* 2.9 27.3 + - - +
223K GLU* 3.2 34.0 + - + +
228K MET* 4.5 13.7 - - + -
233K ILE* 4.9 12.3 - - + -
124N PHE* 3.6 24.0 - - + -
129N THR* 6.4 0.9 - - + -
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Residues in contact with GLN 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ARG* 4.2 25.0 + - - +
216K ALA 3.1 4.6 + - - +
217K GLN 3.3 8.3 + - - +
219K VAL* 1.3 80.9 - - - +
221K THR* 1.3 58.1 + - - +
223K GLU* 3.6 15.6 + - - +
224K GLN* 3.2 39.8 + - - +
129N THR* 3.5 52.0 + - + +
130N SER* 5.0 4.0 - - - +
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Residues in contact with THR 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K LEU* 5.0 7.2 - - + -
186K LEU* 4.6 3.6 - - + +
217K GLN* 2.8 17.8 + - - +
218K LEU* 3.9 8.0 - - - -
219K VAL 3.1 1.0 - - - -
220K GLN* 1.3 77.3 - - - +
222K LEU* 1.3 61.7 + - - +
223K GLU 3.3 0.2 - - - -
224K GLN* 3.8 9.8 + - - +
225K HIS* 2.8 57.3 + - + +
435K TYR* 4.0 27.9 + - + +
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Residues in contact with LEU 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K LEU* 4.2 16.2 - - + -
185K ILE* 4.5 13.5 - - + -
186K LEU* 3.7 24.5 - - + -
205K TYR* 5.8 2.5 - - + -
218K LEU* 3.2 36.8 - - + +
219K VAL* 2.9 9.0 + - - +
221K THR* 1.3 77.1 - - + +
223K GLU* 1.3 55.6 - - - +
225K HIS 4.0 1.1 - - - -
226K ASP 3.5 0.2 + - - -
227K ALA* 2.7 39.4 + - + -
228K MET* 2.7 23.3 + - + +
231K SER* 4.6 5.6 - - - +
233K ILE* 4.0 25.4 - - + -
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Residues in contact with GLU 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ARG* 4.5 15.0 + - - +
212E GLU* 5.6 2.3 - - - +
120K LYS* 5.6 6.2 + - - -
219K VAL* 3.2 33.5 + - - +
220K GLN* 4.0 18.3 - - - +
221K THR 3.3 0.2 - - - -
222K LEU* 1.3 75.5 - - - +
224K GLN* 1.3 64.3 + - - +
225K HIS 3.2 1.8 - - - -
226K ASP* 3.3 12.4 + - - +
228K MET* 3.8 27.4 - - + +
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Residues in contact with GLN 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K GLN* 3.2 31.5 + - - +
221K THR* 3.6 11.8 + - - +
222K LEU 3.4 0.2 - - - -
223K GLU* 1.3 75.9 - - - +
225K HIS* 1.3 70.6 + - + +
226K ASP 3.4 0.9 - - - -
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Residues in contact with HIS 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K LEU* 3.9 30.3 - - + +
189K LYS* 3.3 28.1 - - + +
221K THR* 2.8 45.0 + - + +
222K LEU 4.0 0.2 + - - -
223K GLU 3.2 0.2 - - - -
224K GLN* 1.3 90.5 - - + +
226K ASP* 1.3 71.8 + - - +
227K ALA* 3.2 2.8 + - - +
435K TYR* 4.1 25.6 + + + +
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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