Contacts of the helix formed by residues 193 - 207 (chain A) in PDB entry 1UFK
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 TYR 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 1.3 87.2 - - + +
194A ALA* 1.3 68.6 + - - +
195A GLU* 3.6 23.1 - - + +
196A LEU* 3.0 61.1 + - + +
197A HIS* 3.1 16.6 + - - -
218A GLY 3.3 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 1.3 72.1 - - - +
195A GLU* 1.3 69.3 + - - +
197A HIS* 3.2 7.1 + - - +
198A ALA* 3.0 23.1 + - - +
218A GLY 3.9 5.5 + - - -
219A ILE* 4.2 10.0 - - + +
220A LEU 5.0 0.6 - - - +
223A ARG* 3.5 45.5 - - + +
226A LEU* 4.7 4.0 - - + -
227A VAL* 3.7 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 3.1 22.8 + - + +
194A ALA* 1.3 80.1 + - - +
196A LEU* 1.3 61.2 + - - +
198A ALA* 3.5 8.1 + - - +
199A ALA* 3.2 21.5 + - - +
223A ARG* 3.5 30.2 + - - +
226A LEU* 4.1 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.8 29.8 - - + -
193A TYR* 3.0 47.6 + - + +
195A GLU* 1.3 75.2 - - - +
197A HIS* 1.3 67.7 + - - +
199A ALA* 3.2 7.4 + - + +
200A LEU* 3.0 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 3.1 29.3 + - + -
192A LEU* 3.8 13.3 + - + +
193A TYR 3.1 28.5 + - - -
194A ALA* 3.5 4.9 - - - +
196A LEU* 1.3 77.1 - - - +
198A ALA* 1.3 64.7 + - - +
200A LEU* 3.1 1.7 + - - +
201A ALA* 2.9 24.8 + - - +
204A TYR* 2.8 36.6 + - + +
216A LEU* 3.4 24.1 - - + +
217A THR 2.7 24.2 + - - -
219A ILE* 3.7 22.9 - - + -
227A VAL* 4.3 10.8 - - + -
231A MET* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 3.0 14.0 + - - +
195A GLU* 3.6 12.6 - - - +
196A LEU 3.2 0.2 - - - -
197A HIS* 1.3 79.0 - - - +
199A ALA* 1.3 61.6 + - - +
201A ALA* 3.4 14.7 + - - +
202A PRO* 4.1 2.6 - - - +
226A LEU* 4.2 17.9 - - + +
227A VAL* 5.0 1.7 - - - +
230A ALA* 3.5 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU 3.2 9.4 + - - +
196A LEU* 3.2 13.1 + - + +
198A ALA* 1.3 79.5 - - - +
200A LEU* 1.3 70.2 + - + +
201A ALA 3.6 0.2 + - - -
202A PRO* 3.6 10.0 - - - +
203A ARG* 5.4 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 4.1 14.8 - - + -
175A SER* 5.7 3.4 - - - +
176A LEU* 4.5 12.8 - - + -
192A LEU* 4.4 1.3 - - + -
196A LEU* 3.0 47.7 + - + +
197A HIS 3.1 0.2 + - - -
199A ALA* 1.3 81.4 - - + +
201A ALA* 1.3 66.7 + - - +
202A PRO* 3.2 3.4 - - - -
203A ARG* 2.7 38.7 + - + +
204A TYR* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A HIS 2.9 11.9 + - - +
198A ALA 3.5 11.2 - - - +
200A LEU* 1.3 74.7 - - - +
202A PRO* 1.3 71.0 - - + +
204A TYR* 3.1 22.8 + - - +
205A ARG 3.3 8.8 + - - -
230A ALA* 3.5 33.4 - - + +
231A MET* 3.9 10.8 - - - -
234A ALA* 3.8 5.8 - - + +
236A PHE* 3.7 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA 4.1 2.9 - - - +
199A ALA 3.6 12.1 - - - +
200A LEU 3.4 3.8 - - - -
201A ALA* 1.3 96.7 - - + +
203A ARG* 1.3 62.0 + - + +
205A ARG* 3.4 14.7 + - + +
206A GLU* 3.5 21.2 + - - +
234A ALA* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 5.6 2.6 + - - -
176A LEU* 3.6 23.6 - - + +
177A GLU* 2.6 44.5 + - - +
180A LEU* 5.5 1.1 - - + +
199A ALA 5.4 3.5 + - - -
200A LEU* 2.7 35.1 + - - +
202A PRO* 1.3 74.8 - - + +
204A TYR* 1.3 63.6 - - - +
205A ARG 3.2 0.4 - - - -
206A GLU* 3.2 23.1 + - - +
207A ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.9 15.3 - - + -
176A LEU* 4.1 7.0 - - + -
188A LEU* 3.5 30.5 - - + -
190A ALA* 4.0 0.9 - - - +
192A LEU* 3.7 8.3 - - - +
197A HIS* 2.8 48.4 + - - -
200A LEU* 2.9 42.9 + - + +
201A ALA* 3.1 19.5 + - - +
203A ARG* 1.3 76.7 - - - +
205A ARG* 1.3 64.9 + - - +
207A ALA* 3.0 12.2 + - - +
208A LEU* 3.3 17.9 + - + +
214A ALA* 5.1 1.8 - - + -
216A LEU* 4.0 22.0 - - + -
231A MET* 4.1 13.0 - - + -
236A PHE* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA 3.3 4.4 + - - +
202A PRO* 3.5 11.9 - - + +
203A ARG 3.2 0.2 - - - -
204A TYR* 1.3 81.2 - - - +
206A GLU* 1.3 62.5 + - + +
208A LEU* 3.3 7.6 + - - +
234A ALA* 2.9 27.0 + - - +
235A GLY* 4.5 10.9 + - - -
236A PHE* 3.5 20.8 - - + -
254A ARG* 3.0 81.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 5.0 5.9 - - + +
184A PRO* 5.0 5.7 - - - +
202A PRO* 3.6 16.2 - - - +
203A ARG* 3.2 26.9 + - - +
204A TYR 3.2 0.4 - - - -
205A ARG* 1.3 79.9 - - + +
207A ALA* 1.3 59.3 + - - +
208A LEU 3.4 3.8 + - - +
254A ARG* 4.8 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 5.0 0.2 - - + -
176A LEU* 4.1 16.6 - - + -
180A LEU* 3.9 25.9 - - + +
184A PRO* 3.5 6.5 - - - +
185A PHE* 2.9 36.2 + - + +
188A LEU* 4.2 12.1 - - + -
203A ARG 3.1 12.5 + - - +
204A TYR 3.0 9.7 + - - +
206A GLU* 1.3 76.7 - - - +
208A LEU* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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