Contacts of the helix formed by residues 190 - 206 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B VAL* 4.8 0.9 - - + -
188B GLY 3.2 1.8 + - - -
189B VAL* 1.3 73.9 - - - +
191B MET* 1.3 54.8 + - - +
192B LEU 3.1 3.1 - - - -
193B ASP* 2.8 41.9 + - - +
194B VAL* 3.6 5.2 + - - +
216B VAL* 5.2 3.2 + - - -
219B GLY 4.9 1.3 - - - +
220B HIS* 3.6 28.3 - - + -
295B CYS* 3.5 10.8 + - - +
296B ALA* 3.4 22.3 + - - +
297B PHE* 3.6 34.1 - - + +
309B ALA* 4.3 11.8 - - + +
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Residues in contact with MET 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.3 15.1 - - + -
190B THR* 1.3 77.3 + - - +
192B LEU* 1.3 56.6 + - - +
194B VAL* 3.1 21.7 + - - +
195B VAL* 2.9 30.9 + - + +
274B ALA* 3.2 29.2 - - + +
277B LYS* 3.5 16.8 - - + +
278B PHE* 3.3 43.3 - - + +
294B GLU* 3.8 33.9 - - - +
295B CYS 4.6 6.1 + - - +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 5.1 0.2 - - + -
189B VAL* 5.0 2.0 + - - +
190B THR 3.1 1.6 + - - -
191B MET* 1.3 75.6 - - - +
193B ASP* 1.3 64.8 + - - +
194B VAL 3.2 0.2 - - - -
195B VAL* 3.8 14.8 - - + -
196B ARG* 3.1 64.0 + - + +
220B HIS* 4.9 9.2 - - + +
267B ALA* 4.5 2.9 - - + -
270B SER* 3.6 37.7 - - - +
271B MET* 4.0 37.0 - - + -
274B ALA* 3.7 12.7 - - + +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 2.8 15.3 + - - +
192B LEU* 1.3 79.1 - - - +
194B VAL* 1.3 58.3 + - - +
196B ARG* 4.0 17.6 + - - +
197B ALA* 3.1 27.4 + - - +
216B VAL* 3.8 23.1 - - + +
219B GLY 3.9 2.9 - - - +
220B HIS* 2.7 38.8 + - - -
225B ILE* 3.6 34.6 - - + +
250B ILE* 4.0 8.4 - - + +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 4.2 9.2 - - - +
191B MET* 3.1 22.8 + - - +
193B ASP* 1.3 76.4 - - - +
195B VAL* 1.3 60.0 + - + +
197B ALA* 3.4 1.4 + - - +
198B ASN* 2.9 44.0 + - - +
213B ASP* 4.8 7.6 - - - +
214B VAL 3.6 14.6 - - - +
216B VAL* 3.9 20.6 - - + -
294B GLU* 6.0 1.3 - - - +
295B CYS* 3.9 33.7 - - + +
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Residues in contact with VAL 195 (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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90A HIS 3.0 22.4 - - - +
91A MET* 3.7 6.7 - - + -
92A ASP* 3.5 36.8 - - - +
191B MET* 2.9 26.7 + - + +
192B LEU* 3.8 17.9 - - + +
194B VAL* 1.3 77.3 - - + +
196B ARG* 1.3 62.8 + - - +
198B ASN* 3.3 1.5 + - - +
199B THR* 2.9 26.0 + - - -
273B TYR* 4.0 11.2 - - + -
274B ALA* 3.9 18.2 - - + -
277B LYS* 5.0 4.0 - - + -
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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
----------------------------------------------------------
90A HIS* 3.0 44.4 + - + +
192B LEU* 3.1 50.8 + - + +
193B ASP* 4.0 19.8 + - - +
195B VAL* 1.3 78.8 - - - +
197B ALA* 1.3 54.0 + - - +
199B THR* 3.0 4.0 + - - -
200B PHE* 2.7 54.4 + - + -
220B HIS* 5.8 1.6 + - - -
225B ILE* 6.0 1.0 - - - +
250B ILE* 4.9 9.2 + - + -
253B GLY* 3.8 14.2 + - - +
254B GLY* 3.4 37.1 - - - +
257B VAL* 4.6 0.6 - - - +
267B ALA* 3.9 16.2 - - - +
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Residues in contact with ALA 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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193B ASP 3.1 17.3 + - - +
194B VAL 3.6 4.5 - - - +
196B ARG* 1.3 79.4 - - - +
198B ASN* 1.3 57.3 + - - +
201B VAL* 2.7 38.1 + - - +
214B VAL* 3.8 22.4 - - + -
216B VAL* 4.1 9.2 - - + -
250B ILE* 3.5 31.7 - - + +
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Residues in contact with ASN 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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92A ASP* 3.3 28.1 + - + +
194B VAL* 2.9 35.6 + - - +
195B VAL* 3.7 4.8 - - - +
197B ALA* 1.3 74.5 - - - +
199B THR* 1.3 57.2 + - - +
202B ALA* 2.8 34.4 + - - +
209B PRO* 4.0 4.7 - - - +
212B VAL* 3.1 31.9 + - + +
213B ASP* 3.3 4.1 + - - +
214B VAL* 2.8 30.0 + - - +
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Residues in contact with THR 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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89A SER 3.4 24.0 - - - +
90A HIS* 2.8 23.8 + - - +
91A MET 4.4 3.6 - - - +
92A ASP* 3.2 14.1 - - - -
195B VAL 2.9 6.8 + - - -
196B ARG* 3.0 8.4 + - - -
198B ASN* 1.3 76.1 - - - +
200B PHE* 1.3 63.2 + - + +
202B ALA* 3.2 2.6 + - - +
203B GLU* 2.9 46.5 + - + +
209B PRO* 3.9 13.6 - - + +
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Residues in contact with PHE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER 5.4 0.4 - - - -
90A HIS* 3.7 34.3 - + - -
196B ARG* 2.7 44.4 + - + +
197B ALA* 4.0 2.5 - - - +
199B THR* 1.3 81.7 - - + +
201B VAL* 1.3 62.1 + - - +
203B GLU* 3.3 16.1 + - - +
204B VAL* 3.1 26.0 + - - +
245B TYR* 4.8 3.1 + - - +
246B LEU* 3.7 17.5 - - + -
249B ARG* 3.3 73.1 - - + -
250B ILE* 3.8 17.3 - - + -
253B GLY* 4.9 0.4 - - - -
256B GLU* 4.2 0.7 - - - -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 2.7 27.7 + - - +
198B ASN 4.0 1.3 - - - +
200B PHE* 1.3 72.2 - - - +
202B ALA* 1.3 63.2 + - - +
204B VAL* 3.2 4.8 + - - +
205B LEU* 2.9 33.8 + - + +
212B VAL* 4.0 12.3 - - + -
214B VAL* 3.6 17.7 - - + -
229B LEU* 3.8 25.1 - - + -
232B VAL* 4.1 7.9 - - + -
238B PHE* 3.7 22.7 - - + -
246B LEU* 4.1 15.0 - - + -
250B ILE* 4.8 2.2 - - + -
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Residues in contact with ALA 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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198B ASN 2.8 23.9 + - - +
199B THR 3.7 3.1 - - - +
201B VAL* 1.3 73.9 - - - +
203B GLU* 1.3 52.8 + - - +
205B LEU* 3.3 1.5 + - - +
206B GLY 2.7 30.5 + - - -
207B LEU* 2.8 31.2 + - - +
209B PRO* 3.4 24.9 - - + -
212B VAL* 3.8 17.9 - - + -
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Residues in contact with GLU 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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89A SER* 5.0 3.3 - - - +
199B THR* 2.9 33.9 + - + +
200B PHE* 3.3 17.6 - - - +
202B ALA* 1.3 76.0 - - - +
204B VAL* 1.3 64.3 + - + +
206B GLY* 2.9 14.9 + - - -
207B LEU 5.1 0.7 - - - -
245B TYR* 4.3 5.0 + - - +
249B ARG* 3.7 21.6 + - - -
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Residues in contact with VAL 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 PHE 3.1 13.4 + - - +
201B VAL 3.4 7.4 - - - +
203B GLU* 1.3 81.7 - - + +
205B LEU* 1.3 62.8 - - + +
206B GLY* 3.3 0.3 + - - -
238B PHE* 4.1 17.0 - - + -
242B GLU* 3.5 36.4 - - + +
245B TYR* 3.8 16.8 - - + -
246B LEU* 3.6 25.8 - - + -
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Residues in contact with LEU 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 VAL* 2.9 37.4 + - + +
202B ALA 4.0 1.1 - - - +
204B VAL* 1.3 76.5 - - + +
206B GLY* 1.3 64.9 + - - +
207B LEU* 3.7 35.0 - - + +
212B VAL* 4.6 6.3 - - + -
232B VAL* 4.7 4.3 - - + -
234B PRO* 4.9 1.8 - - + -
236B SER* 3.4 32.5 - - - +
237B SER 4.7 4.5 - - - +
238B PHE* 3.5 25.1 - - + -
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Residues in contact with GLY 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 ALA 2.7 12.7 + - - -
203B GLU* 2.9 12.1 + - - -
204B VAL 3.1 1.2 + - - -
205B LEU* 1.3 75.3 - - - +
207B LEU* 1.3 64.4 + - - +
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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