Contacts of the helix formed by residues 195 - 210 (chain B) in PDB entry 1F0K
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 ALA 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B GLY* 3.5 16.2 + - - +
194B GLY* 1.3 71.4 - - - -
196B ARG* 1.3 78.0 + - - +
197B ILE* 3.3 1.1 - - + -
198B LEU* 3.0 33.5 + - + +
199B ASN* 2.9 26.5 + - - +
219B SER 4.3 2.4 + - - -
261B ARG* 4.6 16.6 - - + +
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLN* 5.6 4.4 - - - +
194B GLY 3.8 15.7 + - - -
195B ALA* 1.3 79.0 - - - +
197B ILE* 1.3 76.5 + - + +
199B ASN* 3.2 10.8 + - - +
200B GLN* 3.0 39.4 + - - +
261B ARG* 3.0 34.7 - - - +
282B PHE* 4.5 15.4 - - - -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ALA 4.8 1.1 - - - +
196B ARG* 1.3 86.3 - - + +
198B LEU* 1.3 74.0 + - + +
200B GLN* 3.4 15.1 + - + +
201B THR* 2.8 52.1 + - - +
261B ARG* 4.0 32.3 - - - +
280B VAL* 4.5 4.3 - - + -
310B LEU* 4.0 24.9 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B VAL* 4.0 23.3 - - + -
189B VAL 3.7 19.3 - - - +
190B GLY* 4.8 0.4 - - - -
195B ALA* 3.0 28.5 + - + +
197B ILE* 1.3 82.8 - - + +
199B ASN* 1.3 68.4 + - - +
200B GLN 3.1 1.6 - - - -
201B THR* 4.3 4.5 - - - +
202B MET* 3.0 30.4 + - + +
217B HIS* 3.4 10.0 - - - -
259B VAL* 3.9 29.6 - - + +
260B CYS* 4.2 10.8 - - - -
261B ARG* 5.0 2.7 - - + +
280B VAL* 4.1 19.1 - - + -
310B LEU* 6.0 2.5 - - + -
315B VAL* 6.4 1.8 - - + -
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Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLY* 5.8 0.5 - - - -
194B GLY* 4.8 0.6 - - - -
195B ALA 2.9 24.7 + - - +
196B ARG* 3.2 10.3 + - - +
198B LEU* 1.3 77.7 - - - +
200B GLN* 1.3 59.8 + - + +
203B PRO* 3.3 22.1 - - - +
217B HIS* 2.8 25.8 + - - -
218B GLN 4.4 1.7 - - - +
219B SER* 2.9 30.3 + - - +
223B SER* 3.9 16.0 + - - -
227B VAL* 3.7 23.0 - - + +
230B ALA* 4.8 4.0 - - - +
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Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ARG* 3.0 26.6 + - - +
197B ILE* 3.8 19.8 - - + +
199B ASN* 1.3 82.3 - - + +
201B THR* 1.3 63.2 + - - +
203B PRO* 3.7 6.8 - - - +
204B GLN* 3.1 26.0 + - - +
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 2.8 44.8 + - - +
198B LEU* 4.3 5.4 - - - -
200B GLN* 1.3 74.1 - - - +
202B MET* 1.3 68.8 + - - +
204B GLN* 3.1 19.4 + - - +
205B VAL* 3.1 25.2 + - + +
310B LEU* 3.9 7.6 - - + +
311B SER 4.3 1.3 - - - +
312B VAL* 4.0 24.8 - - + +
315B VAL* 4.2 16.4 - - + -
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B VAL* 4.6 6.1 - - + -
188B VAL* 3.8 34.1 - - + -
198B LEU* 3.0 24.0 + - + +
201B THR* 1.3 77.2 - - - +
203B PRO* 1.3 63.9 - - + +
205B VAL* 3.0 27.7 + - + +
206B ALA* 2.8 24.1 + - - +
215B ILE* 4.5 12.7 - - + +
217B HIS* 3.8 2.9 - - - +
231B TYR* 3.3 20.2 - - - +
259B VAL* 4.4 14.8 - - + -
315B VAL* 3.9 23.6 - - + -
319B LEU* 4.4 9.2 - - + -
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Residues in contact with PRO 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU 4.0 0.4 - - - +
199B ASN 3.3 26.2 - - - +
200B GLN 3.7 6.1 - - - +
201B THR 3.5 3.8 - - - -
202B MET* 1.3 92.9 - - + +
204B GLN* 1.3 62.5 + - + +
206B ALA* 3.3 4.0 + - - +
207B ALA 3.2 15.2 + - - -
217B HIS* 4.7 0.7 - - + -
227B VAL* 4.7 2.2 - - + -
230B ALA* 3.6 40.4 - - + +
231B TYR* 3.6 29.1 - - + +
234B ALA* 3.3 16.2 - - + +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLN* 3.1 23.9 + - - +
201B THR* 3.1 6.5 + - - +
203B PRO* 1.3 76.5 - - + +
205B VAL* 1.3 65.8 + - - +
207B ALA* 3.2 4.0 + - - -
208B LYS* 2.6 44.9 + - - +
234B ALA* 5.0 1.8 - - + -
312B VAL* 3.6 28.3 - - + +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B THR* 3.1 27.2 + - + +
202B MET* 3.0 27.3 + - + +
204B GLN* 1.3 77.8 - - - +
206B ALA* 1.3 57.0 + - - +
208B LYS* 3.1 6.3 + - - +
209B LEU* 2.9 50.5 + - + +
215B ILE* 5.7 1.3 - - + -
312B VAL* 3.9 15.7 - - + +
315B VAL* 3.8 27.4 - - + -
316B ALA* 4.0 12.3 - - - +
319B LEU* 4.3 1.3 - - + -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B MET 2.8 11.9 + - - +
203B PRO 3.4 10.5 - - - +
204B GLN 3.2 0.2 - - - -
205B VAL* 1.3 78.7 - - - +
207B ALA* 1.3 56.7 + - - +
209B LEU* 4.5 3.4 - - - +
210B GLY* 2.8 27.9 + - - +
213B VAL* 5.2 2.7 - - - -
215B ILE* 3.8 16.8 - - + +
231B TYR* 3.7 21.8 - - + -
236B GLN* 3.5 14.5 - - + +
239B HIS* 3.9 15.0 - - + +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B PRO 3.2 9.0 + - - +
204B GLN* 3.5 10.3 - - - +
205B VAL 3.2 0.2 - - - -
206B ALA* 1.3 79.1 - - - +
208B LYS* 1.3 75.6 + - + +
210B GLY* 4.0 5.7 + - - -
234B ALA* 3.6 29.2 - - + +
236B GLN* 4.1 8.4 + - - +
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Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLN* 2.6 48.5 + - - +
205B VAL* 3.1 6.1 + - - +
207B ALA* 1.3 90.8 - - + +
209B LEU* 1.3 63.7 + - + +
312B VAL* 4.2 15.3 - - + +
313B ASP* 5.2 8.1 - - - +
316B ALA* 4.3 16.2 - - + -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B VAL* 2.9 37.9 + - + +
206B ALA 4.4 0.4 - - - +
208B LYS* 1.3 80.0 - - - +
210B GLY* 1.3 63.4 + - - +
211B ASP 3.3 0.5 + - - -
212B SER* 2.6 36.0 + - - +
213B VAL* 3.9 32.1 - - + -
316B ALA* 3.6 26.2 - - + +
319B LEU* 4.1 20.6 - - + -
320B ALA* 3.9 17.7 - - + +
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA 2.8 18.7 + - - +
207B ALA 4.0 2.8 + - - -
208B LYS 3.5 2.2 - - - -
209B LEU* 1.3 76.6 - - - +
211B ASP* 1.3 60.2 + - - -
212B SER 3.1 5.2 + - - -
213B VAL* 3.4 19.9 + - - +
236B GLN* 3.9 24.2 - - - +
238B GLN* 5.3 0.7 + - - -
239B HIS* 4.9 2.6 + - - -
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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