Contacts of the helix formed by residues 190 - 205 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164G VAL* 4.9 0.7 - - + -
188G GLY 3.3 16.5 + - - +
189G VAL* 1.3 76.8 - - - +
191G MET* 1.3 60.1 + - - +
192G LEU 3.0 3.8 - - - -
193G ASP* 2.8 40.7 + - - +
194G VAL* 3.6 4.4 + - - +
216G VAL* 5.2 2.4 + - - +
219G GLY 5.1 1.1 - - - +
220G HIS* 3.7 24.0 - - + +
278G PHE* 5.9 0.6 - - - -
295G CYS* 3.8 10.3 + - - +
296G ALA* 3.7 19.3 + - - +
297G PHE* 3.6 23.3 - - + +
309G ALA* 4.4 10.9 - - + +
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Residues in contact with MET 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G VAL* 3.5 14.1 - - + +
190G THR* 1.3 78.9 + - - +
192G LEU* 1.3 57.2 + - - +
194G VAL* 3.2 25.4 + - + +
195G VAL* 2.8 44.4 + - + +
274G ALA* 3.3 27.1 - - - +
277G LYS* 4.5 13.7 - - + -
278G PHE* 4.1 22.6 - - + -
294G GLU* 3.2 31.9 - - + +
295G CYS 3.9 22.3 + - - +
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Residues in contact with LEU 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G THR 2.9 0.8 + - - -
191G MET* 1.3 78.9 - - - +
193G ASP* 1.3 57.9 + - - +
195G VAL* 3.6 8.4 - - + +
196G ARG* 2.9 74.4 + - + +
220G HIS* 4.5 15.0 - - + +
267G ALA* 5.2 3.4 - - + +
270G SER* 3.6 38.8 - - - +
271G MET* 3.6 36.2 - - + +
274G ALA* 3.9 11.9 - - + +
90H HIS* 5.1 0.9 - - + -
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Residues in contact with ASP 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G THR* 2.8 17.0 + - - +
192G LEU* 1.3 78.3 - - - +
194G VAL* 1.3 52.7 + - - +
196G ARG* 3.2 16.1 + - - +
197G ALA* 2.7 35.7 + - - +
216G VAL* 3.8 22.7 - - + +
219G GLY 4.1 2.6 - - - +
220G HIS* 2.5 38.9 + - - -
225G ILE* 3.3 35.6 - - + +
250G ILE* 4.3 7.6 - - - +
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Residues in contact with VAL 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G THR* 4.1 7.9 - - - +
191G MET* 3.2 25.3 + - + +
193G ASP* 1.3 73.4 - - - +
195G VAL* 1.3 62.3 + - + +
197G ALA* 3.0 0.9 + - - +
198G ASN* 2.8 50.6 + - - +
213G ASP* 4.1 10.1 - - - +
214G VAL 3.4 17.7 - - - +
216G VAL* 3.7 20.4 - - + -
294G GLU* 5.8 0.7 - - - +
295G CYS* 3.8 32.3 - - + -
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Residues in contact with VAL 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G MET* 2.8 33.5 + - + +
192G LEU* 3.6 13.2 - - + +
194G VAL* 1.3 75.5 - - + +
196G ARG* 1.3 58.8 + - - +
198G ASN* 3.4 0.6 + - - +
199G THR* 2.7 32.4 + - - -
273G TYR* 4.0 9.4 - - + -
274G ALA* 3.9 15.9 - - + -
277G LYS* 4.9 5.2 - - + +
90H HIS 3.0 20.9 - - - +
91H MET* 3.6 6.3 - - + -
92H ASP* 3.1 42.1 - - - +
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Residues in contact with ARG 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G LEU* 2.9 60.0 + - + +
193G ASP* 3.4 15.4 + - - +
195G VAL* 1.3 75.5 - - - +
197G ALA* 1.3 64.5 + - - +
199G THR* 3.1 2.1 + - - -
200G PHE* 2.9 46.6 + - + -
220G HIS* 5.8 2.2 - - - -
250G ILE* 4.7 11.6 + - + -
253G GLY* 3.8 15.0 + - - -
254G GLY* 3.4 35.5 - - - +
257G VAL* 4.3 0.4 - - - +
267G ALA* 4.0 17.8 - - - +
90H HIS* 2.6 48.0 + - + +
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Residues in contact with ALA 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G ASP 2.7 21.2 + - - +
194G VAL 3.3 4.9 - - - +
196G ARG* 1.3 72.9 - - - +
198G ASN* 1.3 56.7 + - - +
200G PHE* 4.3 0.2 - - - -
201G VAL* 2.9 35.2 + - - +
214G VAL* 3.7 15.7 - - + -
216G VAL* 3.7 21.8 - - + -
250G ILE* 3.4 29.9 - - + +
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Residues in contact with ASN 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G VAL* 2.8 37.3 + - - +
195G VAL* 3.9 2.9 - - - +
197G ALA* 1.3 70.1 - - - +
199G THR* 1.3 58.4 + - - +
201G VAL* 3.8 0.5 - - - +
202G ALA* 2.8 38.1 + - - +
209G PRO* 4.1 3.6 - - - +
212G VAL* 3.3 32.4 + - + +
213G ASP* 2.9 9.2 + - - -
214G VAL* 2.5 33.5 + - - +
92H ASP* 3.5 26.1 + - + -
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Residues in contact with THR 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G VAL 2.7 16.3 + - - -
196G ARG* 3.5 4.3 - - - -
198G ASN* 1.3 77.5 - - - +
200G PHE* 1.3 66.0 + - + +
202G ALA* 3.3 3.1 + - - +
203G GLU* 2.8 44.1 + - + +
209G PRO* 4.2 16.6 - - + +
65H LYS* 6.1 0.2 - - - +
89H SER 3.4 25.4 - - - +
90H HIS 2.7 23.0 + - - +
91H MET 4.3 4.5 - - - +
92H ASP* 3.1 14.0 - - - -
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Residues in contact with PHE 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G ARG* 2.9 42.0 + - + +
197G ALA 4.3 1.3 - - - +
199G THR* 1.3 80.9 - - + +
201G VAL* 1.3 65.9 + - - +
203G GLU* 2.9 35.0 + - - +
204G VAL* 3.0 17.8 + - - +
245G TYR* 5.9 0.7 - - + -
246G LEU* 3.7 18.2 - - + -
249G ARG* 3.2 55.6 - - + +
250G ILE* 3.8 21.3 - - + -
253G GLY* 5.0 0.4 - - - -
256G GLU* 4.4 0.4 - - - -
89H SER 5.0 1.1 - - - -
90H HIS* 3.6 33.4 - + - -
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Residues in contact with VAL 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G ALA* 2.9 27.4 + - - +
198G ASN 3.8 2.7 - - - +
200G PHE* 1.3 76.0 - - - +
202G ALA* 1.3 63.5 + - - +
204G VAL* 3.3 2.9 + - - +
205G LEU* 3.1 45.1 + - + +
212G VAL* 4.0 14.4 - - + -
214G VAL* 3.5 16.8 - - + -
229G LEU* 3.9 22.2 - - + -
232G VAL* 4.0 7.2 - - + -
238G PHE* 3.8 12.6 - - + -
246G LEU* 4.0 17.5 - - + -
250G ILE* 5.0 0.9 - - + -
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Residues in contact with ALA 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G ASN 2.8 19.8 + - - +
199G THR 3.6 4.5 - - - +
201G VAL* 1.3 76.9 - - - +
203G GLU* 1.3 61.4 + - - +
205G LEU* 4.8 0.2 - - - -
206G GLY* 3.1 2.3 + - - -
207G LEU* 2.7 52.5 + - - +
209G PRO* 3.5 25.4 - - + -
212G VAL* 3.8 15.7 - - + +
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Residues in contact with GLU 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199G THR* 2.8 33.9 + - + +
200G PHE* 2.9 23.3 + - - +
202G ALA* 1.3 76.2 - - - +
204G VAL* 1.3 66.5 + - + +
206G GLY* 3.3 11.3 + - - -
209G PRO* 5.8 2.0 - - + -
245G TYR* 6.0 0.3 - - - -
249G ARG* 2.8 33.2 + - - -
89H SER* 4.9 2.8 - - - +
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Residues in contact with VAL 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E GLU* 6.0 0.5 - - - +
333E ARG* 3.3 41.1 + - - +
200G PHE 3.0 14.8 + - - +
201G VAL 3.3 5.8 + - - +
203G GLU* 1.3 78.2 - - + +
205G LEU* 1.3 66.7 + - + +
206G GLY 3.3 1.3 + - - -
238G PHE* 4.8 0.7 - - + -
242G GLU* 3.3 29.0 - - + +
245G TYR* 4.5 5.8 - - + -
246G LEU* 3.5 30.7 - - + -
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Residues in contact with LEU 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G VAL* 3.1 36.5 + - + +
202G ALA* 5.2 0.2 - - - -
204G VAL* 1.3 80.6 - - + +
206G GLY* 1.3 64.9 + - - +
207G LEU* 3.0 33.0 + - + +
212G VAL* 5.3 0.9 - - + -
232G VAL* 4.9 4.3 - - + -
234G PRO* 5.2 0.7 - - + +
236G SER* 3.7 30.1 - - - +
237G SER 4.7 4.0 - - - +
238G PHE* 3.4 27.8 - - + -
242G GLU* 5.5 1.8 - - - +
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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