Contacts of the helix formed by residues 190 - 206 (chain H) in PDB entry 1SMK
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 THR 190 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H VAL* 4.6 0.9 - - + -
188H GLY 3.1 2.5 + - - -
189H VAL* 1.3 75.9 - - - +
191H MET* 1.3 54.6 + - - +
192H LEU 3.1 2.9 - - - -
193H ASP* 2.8 42.8 + - - +
194H VAL* 3.6 4.0 + - - +
216H VAL 5.1 2.7 + - - -
219H GLY 4.5 7.6 - - - +
220H HIS* 4.0 28.3 - - + -
278H PHE* 5.9 0.2 - - - -
295H CYS* 3.7 9.6 + - - +
296H ALA* 3.5 21.2 + - - +
297H PHE* 3.7 30.1 - - + +
309H ALA* 4.6 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 191 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H VAL* 3.4 5.6 - - + +
190H THR* 1.3 78.4 + - - +
192H LEU* 1.3 54.5 + - - +
194H VAL* 2.7 55.1 + - + +
195H VAL* 2.8 19.8 + - + -
274H ALA* 3.4 33.4 - - + +
277H LYS* 4.2 23.3 - - + -
278H PHE* 4.1 21.5 - - + -
294H GLU* 3.1 32.8 - - + +
295H CYS 4.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G HIS* 5.2 0.2 - - + -
189H VAL* 5.3 2.0 + - - +
190H THR 3.0 1.2 + - - +
191H MET* 1.3 77.4 - - - +
193H ASP* 1.3 57.0 + - - +
195H VAL* 4.1 9.6 - - + -
196H ARG* 2.9 72.2 + - + +
220H HIS* 4.8 6.1 - - - +
267H ALA* 4.5 3.1 - - + -
270H SER* 3.5 37.7 - - - +
271H MET* 3.5 47.8 - - + +
274H ALA* 3.6 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 193 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H THR* 2.8 14.1 + - - +
192H LEU* 1.3 77.9 - - - +
194H VAL* 1.3 58.1 + - - +
196H ARG* 3.5 18.2 + - - +
197H ALA* 3.0 29.5 + - - +
216H VAL* 4.0 22.6 - - + +
219H GLY 3.8 6.4 - - - +
220H HIS* 2.6 41.1 + - - +
225H ILE* 3.3 30.5 - - + +
250H ILE* 4.3 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H THR* 4.3 6.7 - - - +
191H MET* 2.7 43.7 + - + +
193H ASP* 1.3 69.8 - - + +
195H VAL* 1.3 59.5 - - + +
197H ALA* 3.2 1.9 + - - +
198H ASN* 2.8 46.4 + - - +
213H ASP* 4.6 7.6 - - - +
214H VAL 3.9 12.8 - - - +
216H VAL* 4.1 18.8 - - + +
294H GLU* 5.2 1.8 - - - +
295H CYS* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G HIS 3.1 21.1 - - - +
91G MET* 3.7 7.2 - - + -
92G ASP* 3.4 36.5 - - - +
191H MET* 2.8 29.3 + - + +
192H LEU* 3.7 16.8 - - + +
194H VAL* 1.3 73.4 - - + +
196H ARG* 1.3 63.1 + - - +
198H ASN* 3.4 3.3 + - - +
199H THR* 2.9 26.2 + - - -
273H TYR* 3.9 12.6 - - + -
274H ALA* 3.8 19.3 - - + -
277H LYS* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G HIS* 3.1 42.5 + - + +
192H LEU* 2.9 53.3 + - + +
193H ASP* 3.9 18.1 + - - +
195H VAL* 1.3 76.7 - - - +
197H ALA* 1.3 53.4 + - - +
199H THR* 3.0 3.5 + - - -
200H PHE* 2.6 53.4 + - + -
220H HIS* 5.8 1.6 + - - -
250H ILE* 4.7 10.4 + - - +
253H GLY* 3.8 14.8 - - - +
254H GLY* 3.2 37.4 - - - +
257H VAL* 4.6 0.6 - - - +
267H ALA* 3.7 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H ASP 3.0 19.1 + - - +
194H VAL 3.2 4.9 + - - +
196H ARG* 1.3 76.9 - - - +
198H ASN* 1.3 53.2 + - - +
201H VAL* 2.7 40.0 + - - +
214H VAL* 3.7 21.3 - - + -
216H VAL* 3.8 12.8 - - + -
250H ILE* 3.5 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ASP* 3.3 27.2 + - + -
194H VAL* 2.8 36.9 + - - +
195H VAL 3.6 4.0 - - - +
197H ALA* 1.3 72.6 - - - +
199H THR* 1.3 57.7 + - - +
202H ALA* 3.0 31.5 + - - +
209H PRO* 4.2 3.8 - - - +
212H VAL* 3.3 33.4 + - - +
213H ASP* 3.1 8.7 + - - +
214H VAL* 2.6 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G SER 3.5 23.6 - - - +
90G HIS 2.8 22.9 + - - +
91G MET 4.2 3.1 - - - +
92G ASP* 3.0 21.1 - - - -
195H VAL 2.9 5.2 + - - -
196H ARG 3.4 7.2 - - - -
198H ASN* 1.3 77.1 - - - +
200H PHE* 1.3 64.5 + - + +
202H ALA* 3.4 3.8 + - - +
203H GLU* 2.8 47.2 + - + +
209H PRO* 4.1 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G SER 5.3 0.4 - - - -
90G HIS* 3.6 41.7 - + - -
196H ARG* 2.6 37.9 + - + +
197H ALA 4.1 1.6 - - - +
199H THR* 1.3 82.9 - - + +
201H VAL* 1.3 65.4 + - - +
203H GLU* 3.3 13.1 + - - +
204H VAL* 3.2 19.1 + - - +
245H TYR* 5.5 0.8 - - + -
246H LEU* 3.4 20.4 - - + +
249H ARG* 3.4 70.4 - - + +
250H ILE* 4.1 20.0 - - + -
253H GLY* 4.3 3.8 - - - -
256H GLU* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H ALA 2.7 25.2 + - - +
198H ASN 4.2 1.6 - - - +
200H PHE* 1.3 71.9 - - - +
202H ALA* 1.3 57.9 + - - +
204H VAL* 3.3 2.8 + - - +
205H LEU* 2.9 50.7 + - + +
212H VAL* 4.0 5.8 - - + -
214H VAL* 3.6 17.5 - - + -
229H LEU* 3.6 26.2 - - + -
232H VAL* 4.0 14.6 - - + -
238H PHE* 3.7 13.2 - - + -
246H LEU* 3.9 17.3 - - + -
250H ILE* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198H ASN 3.0 21.2 + - - +
199H THR 3.5 4.7 - - - +
201H VAL* 1.3 75.9 - - - +
203H GLU* 1.3 60.3 + - + +
205H LEU* 3.3 0.4 + - - -
206H GLY* 2.9 9.2 + - - -
207H LEU* 2.8 36.3 + - - +
209H PRO* 3.5 34.3 - - + -
212H VAL* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B PRO* 5.0 0.9 - - - +
89G SER* 4.8 4.0 - - - +
199H THR* 2.8 36.9 + - + +
200H PHE* 3.3 15.9 + - - +
202H ALA* 1.3 75.2 - - + +
204H VAL* 1.3 63.9 + - + +
206H GLY* 3.1 12.7 + - - -
207H LEU 5.1 0.4 - - - -
249H ARG* 2.8 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ARG* 4.3 16.1 + - - +
200H PHE 3.2 4.7 + - - +
201H VAL 3.7 7.0 - - - +
203H GLU* 1.3 77.9 - - + +
205H LEU* 1.3 62.9 + - + +
206H GLY 3.5 0.7 + - - -
238H PHE* 4.5 7.4 - - + -
242H GLU* 3.6 39.0 - - + +
245H TYR* 3.7 21.8 - - + -
246H LEU* 3.4 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H VAL* 2.9 40.6 + - + +
202H ALA 4.0 1.3 - - - +
204H VAL* 1.3 80.8 - - + +
206H GLY* 1.3 63.1 + - - +
207H LEU* 3.2 30.4 + - + +
212H VAL* 5.1 2.2 - - + -
232H VAL* 4.7 5.2 - - + -
234H PRO* 5.2 0.4 - - + +
236H SER* 3.6 29.2 - - - +
237H SER 5.0 4.7 - - - +
238H PHE* 3.5 28.9 - - + -
242H GLU* 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ALA 2.9 5.6 + - - -
203H GLU* 3.1 11.7 + - - -
204H VAL 3.2 1.4 + - - -
205H LEU* 1.3 78.9 - - - +
207H LEU* 1.3 65.7 + - - +
----------------------------------------------------------
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