Contacts of the helix formed by residues 195 - 210 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLY* 3.5 13.8 + - - +
194A GLY* 1.3 71.6 - - - -
196A ARG* 1.3 63.1 + - - +
197A ILE 3.1 2.7 - - - -
198A LEU* 2.7 58.4 + - + +
199A ASN* 3.0 14.3 + - - +
219A SER 4.3 2.4 + - - -
261A ARG* 4.1 24.9 - - + +
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Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLN* 5.5 3.6 + - - +
194A GLY 3.6 18.9 + - - -
195A ALA* 1.3 72.6 - - - +
197A ILE* 1.3 76.5 + - + +
199A ASN* 3.2 13.4 + - - +
200A GLN* 3.0 33.5 + - + +
261A ARG* 2.9 32.7 - - - +
282A PHE* 4.1 18.7 - - - -
307A GLN* 5.6 0.7 - - - -
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA 2.9 2.9 + - - +
196A ARG* 1.3 85.4 - - + +
198A LEU* 1.3 73.0 + - + +
200A GLN* 3.3 5.8 + - + +
201A THR* 2.8 45.2 + - - +
261A ARG* 3.7 29.8 - - - +
280A VAL* 4.7 2.9 - - + -
307A GLN* 3.5 35.7 - - + +
310A LEU* 3.3 29.8 - - + +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 3.9 24.0 - - + -
189A VAL 3.6 24.2 - - - +
190A GLY* 4.6 1.1 - - - -
195A ALA* 2.7 31.0 + - + +
197A ILE* 1.3 84.4 - - + +
199A ASN* 1.3 64.5 + - - +
201A THR* 4.4 5.2 - - + +
202A MET* 3.1 27.5 + - + +
217A HIS* 3.3 11.0 - - - -
259A VAL* 3.8 31.9 - - + +
260A CYS* 4.2 9.4 - - - -
261A ARG* 5.0 2.9 - - + +
280A VAL* 4.2 19.3 - - + -
310A LEU* 6.4 1.6 - - + -
315A VAL* 6.5 1.1 - - + -
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Residues in contact with ASN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLY* 5.9 0.3 - - - -
194A GLY* 4.7 0.8 - - - -
195A ALA 3.0 20.8 + - - +
196A ARG* 3.2 12.5 + - - +
198A LEU* 1.3 79.3 - - - +
200A GLN* 1.3 68.2 + - - +
203A PRO* 3.4 20.8 - - - +
217A HIS* 2.8 25.5 + - - -
218A GLN 4.5 1.2 - - - +
219A SER* 2.9 29.7 + - - +
223A SER* 3.9 16.4 + - - -
227A VAL* 3.6 23.3 - - + +
230A ALA* 4.9 4.0 - - - +
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Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 3.0 22.0 + - + +
197A ILE* 3.8 5.8 - - + +
198A LEU 3.1 0.2 - - - -
199A ASN* 1.3 90.5 + - - +
201A THR* 1.3 62.3 + - - +
202A MET 3.8 0.2 - - - -
203A PRO* 3.8 6.6 - - - +
204A GLN* 2.9 28.8 + - - +
226A SER* 5.6 4.4 + - - -
227A VAL* 5.9 1.0 - - - +
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 2.8 36.6 + - - +
198A LEU* 3.4 6.0 + - + -
200A GLN* 1.3 78.8 - - - +
202A MET* 1.3 69.3 + - - +
203A PRO 3.4 0.4 - - - -
204A GLN* 3.2 10.4 + - - +
205A VAL* 3.1 33.3 + - + +
310A LEU* 4.3 6.8 - - + +
311A SER* 4.3 2.1 - - - -
312A VAL* 4.0 23.7 + - + +
315A VAL* 4.1 16.6 - - + -
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.3 15.9 - - + -
188A VAL* 3.8 35.0 - - + -
198A LEU* 3.1 23.8 + - + +
201A THR* 1.3 73.7 - - - +
203A PRO* 1.3 65.5 - - + +
205A VAL* 3.5 22.3 - - + +
206A ALA* 2.8 29.5 + - - +
215A ILE* 4.5 11.4 - - + +
217A HIS* 3.8 2.0 - - - +
231A TYR* 3.3 19.8 + - - +
259A VAL* 4.5 15.0 - - + -
315A VAL* 4.1 19.5 - - - -
319A LEU* 4.3 9.9 - - + -
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Residues in contact with PRO 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU 4.0 0.9 - - - +
199A ASN 3.4 26.2 - - - +
200A GLN* 3.8 5.2 - - - +
201A THR 3.5 3.6 - - - -
202A MET* 1.3 93.2 - - + +
204A GLN* 1.3 64.4 + - + +
206A ALA* 3.2 5.0 + - - +
207A ALA 3.2 16.8 + - - -
217A HIS* 4.7 0.4 - - + -
227A VAL* 4.6 1.8 - - + +
230A ALA* 3.8 39.9 - - + +
231A TYR* 3.6 29.4 - - + +
234A ALA* 3.4 13.6 - - + +
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLN* 2.9 26.6 + - - +
201A THR 3.2 7.1 + - - +
202A MET 3.2 0.2 - - - -
203A PRO* 1.3 75.7 - - + +
205A VAL* 1.3 63.5 + - - +
207A ALA* 3.2 8.0 + - - -
208A LYS* 2.8 40.6 + - - +
234A ALA* 5.0 2.9 - - + -
312A VAL* 3.6 30.1 - - + +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR* 3.1 27.4 + - + +
202A MET* 3.5 25.4 - - + +
204A GLN* 1.3 74.0 - - - +
206A ALA* 1.3 67.7 + - - +
208A LYS* 3.1 3.9 + - - +
209A LEU* 3.0 36.2 + - + +
213A VAL* 6.2 0.2 - - + -
215A ILE* 5.9 1.1 - - + -
312A VAL* 3.6 27.8 - - + +
315A VAL* 3.9 17.7 - - + -
316A ALA* 3.9 22.4 - - - +
319A LEU* 4.3 4.0 - - + -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET 2.8 13.6 + - - +
203A PRO 3.3 10.5 - - - +
205A VAL* 1.3 77.7 - - - +
207A ALA* 1.3 56.6 + - - +
209A LEU* 4.2 4.0 - - - +
210A GLY* 2.8 32.7 + - - +
213A VAL* 5.1 2.0 - - - -
215A ILE* 3.9 9.2 - - + +
231A TYR* 3.7 21.3 - - + -
236A GLN* 3.8 10.5 - - + +
239A HIS* 3.8 21.0 + - + +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PRO 3.2 8.1 + - - +
204A GLN* 3.3 12.6 - - - +
205A VAL 3.2 0.4 - - - -
206A ALA* 1.3 81.3 - - - +
208A LYS* 1.3 73.2 + - + +
210A GLY* 3.8 6.6 + - - -
234A ALA* 3.7 28.3 - - + +
236A GLN* 4.2 7.5 + - - +
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLN* 2.8 40.2 + - - +
205A VAL 3.1 7.0 + - - +
207A ALA* 1.3 89.3 - - + +
209A LEU* 1.3 63.6 + - + +
210A GLY 3.8 0.2 + - - -
312A VAL* 4.2 16.1 - - + +
313A ASP* 4.8 11.7 - - - +
316A ALA* 4.4 16.2 - - + -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.0 36.1 + - + +
206A ALA 4.2 0.4 - - - +
208A LYS* 1.3 83.4 - - + +
210A GLY* 1.3 65.8 + - - +
211A ASP 3.3 0.5 + - - -
212A SER* 2.6 33.9 + - - +
213A VAL* 3.6 35.2 - - + -
316A ALA* 3.9 22.7 - - + +
319A LEU* 4.0 23.3 - - + -
320A ALA* 3.9 17.9 - - + +
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Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA 2.8 17.3 + - - +
207A ALA 3.8 4.1 + - - -
208A LYS 3.5 2.6 + - - -
209A LEU* 1.3 76.7 - - - +
211A ASP* 1.3 63.1 + - - -
212A SER 3.2 0.7 + - - -
213A VAL* 3.4 19.8 + - - +
236A GLN* 4.1 24.9 - - - +
238A GLN* 5.3 0.5 + - - -
239A HIS* 4.9 1.9 + - - -
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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