Contacts of the helix formed by residues 190 - 206 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C VAL* 5.1 1.3 - - + -
188C GLY 3.2 10.0 + - - +
189C VAL* 1.3 77.5 - - - +
191C MET* 1.3 59.0 + - - +
192C LEU* 3.1 4.0 - - - -
193C ASP* 2.8 40.0 + - - +
194C VAL* 3.7 4.6 + - - +
216C VAL* 5.2 3.3 + - - -
219C GLY 4.9 3.1 - - - -
220C HIS* 4.3 21.1 - - + -
278C PHE* 5.9 0.4 - - - -
295C CYS* 3.5 9.9 + - - +
296C ALA* 3.2 24.4 + - - +
297C PHE* 3.7 21.8 - - + +
309C ALA* 4.2 13.2 - - + +
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Residues in contact with MET 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C VAL* 3.5 7.9 - - + +
190C THR* 1.3 79.4 + - - +
192C LEU* 1.3 56.4 + - - +
194C VAL* 3.1 46.3 + - + +
195C VAL* 2.9 34.6 + - + +
198C ASN* 5.6 0.9 - - - +
274C ALA* 3.4 33.9 - - + +
277C LYS* 4.5 11.0 - - + -
278C PHE* 4.1 32.7 - - + +
294C GLU* 3.3 32.5 - - - +
295C CYS 4.7 5.6 + - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C VAL* 5.2 1.8 + - - +
190C THR 2.9 2.5 + - - +
191C MET* 1.3 78.0 - - - +
193C ASP* 1.3 57.7 + - - +
195C VAL* 4.2 9.4 - - + -
196C ARG* 2.9 72.9 + - + +
220C HIS* 5.1 4.5 - - + -
267C ALA* 4.1 4.9 - - + -
270C SER* 3.9 35.0 - - - +
271C MET* 3.8 32.7 - - - +
274C ALA* 3.7 13.0 - - + +
1313C CIT 3.9 16.2 - - + +
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Residues in contact with ASP 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C THR* 2.8 17.9 + - - +
192C LEU* 1.3 76.1 - - - +
194C VAL* 1.3 59.4 + - - +
196C ARG* 3.9 11.9 + - - +
197C ALA* 2.9 29.6 + - - +
216C VAL* 3.7 24.2 - - + +
219C GLY 4.0 2.8 - - - +
220C HIS* 2.5 51.2 + - - +
225C ILE* 3.5 25.7 - - + +
250C ILE* 4.2 7.8 - - - +
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C THR* 4.5 6.5 - - - +
191C MET* 3.1 35.1 + - + +
193C ASP* 1.3 75.6 - - - +
195C VAL* 1.3 60.2 + - - +
197C ALA* 3.2 1.6 + - - +
198C ASN* 2.8 50.0 + - - +
213C ASP* 4.4 10.5 - - - +
214C VAL 3.8 13.9 - - - +
216C VAL* 3.8 23.1 - - + -
294C GLU* 5.5 0.2 - - - +
295C CYS* 4.0 30.5 - - + +
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C MET* 2.9 31.5 + - + +
192C LEU* 3.7 16.2 - - + +
194C VAL* 1.3 76.5 - - - +
196C ARG* 1.3 62.4 + - - +
198C ASN* 3.3 4.2 + - - +
199C THR* 2.9 26.9 + - - -
273C TYR* 3.8 16.6 - - + -
274C ALA* 4.2 11.7 - - + -
277C LYS* 5.0 4.3 - - + -
90D HIS 3.2 18.8 - - - +
91D MET* 3.8 7.4 - - + -
92D ASP* 3.2 34.2 - - - +
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ARG* 4.5 0.4 - - - +
192C LEU* 2.9 43.0 + - + +
193C ASP* 4.0 14.7 + - - +
195C VAL* 1.3 78.0 - - - +
197C ALA* 1.3 62.5 + - - +
199C THR* 3.1 1.7 + - - -
200C PHE* 2.9 44.0 + - + -
220C HIS* 4.4 0.2 - - - -
225C ILE* 6.0 0.6 - - - +
250C ILE* 4.8 10.8 + - + -
253C GLY* 3.7 10.8 + - - -
254C GLY* 3.1 24.7 - - - +
257C VAL* 4.2 1.8 - - - +
267C ALA* 3.6 12.3 - - - +
270C SER* 4.7 0.4 + - - -
1313C CIT 2.7 43.4 + - - -
90D HIS* 2.8 50.3 + - + +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ASP 2.9 19.8 + - - +
194C VAL 3.6 4.0 - - - +
196C ARG* 1.3 76.2 - - - +
198C ASN* 1.3 57.5 + - - +
200C PHE 4.7 0.2 - - - +
201C VAL* 2.8 36.4 + - - +
214C VAL* 3.7 27.1 - - + -
216C VAL* 4.1 8.1 - - + -
250C ILE* 3.5 30.6 - - + +
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Residues in contact with ASN 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C MET* 5.6 1.2 - - - +
194C VAL* 2.8 35.8 + - - +
195C VAL* 3.5 5.3 - - - +
197C ALA* 1.3 77.0 - - - +
199C THR* 1.3 56.8 + - - +
201C VAL 3.9 0.2 - - - -
202C ALA* 2.9 34.1 + - - +
209C PRO* 4.1 5.3 - - - +
212C VAL* 3.2 31.6 + - - +
213C ASP* 3.4 3.3 + - - +
214C VAL* 2.9 29.6 + - - +
92D ASP* 3.2 27.8 + - + +
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C VAL 2.9 5.1 + - - -
196C ARG 3.5 6.1 - - - -
198C ASN* 1.3 77.2 - - - +
200C PHE* 1.3 65.6 + - + +
202C ALA* 3.5 2.3 - - - +
203C GLU* 2.9 50.2 + - + +
209C PRO* 4.2 11.0 - - + -
89D SER 3.4 24.7 - - - +
90D HIS* 2.5 25.1 + - - +
91D MET 4.2 4.3 - - - +
92D ASP* 3.0 18.1 - - - -
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Residues in contact with PHE 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ARG* 2.9 40.0 + - + +
197C ALA 4.2 1.1 - - - +
199C THR* 1.3 78.4 - - + +
201C VAL* 1.3 66.6 + - - +
203C GLU* 3.4 16.9 + - - +
204C VAL* 3.0 28.6 + - - +
245C TYR* 5.5 2.0 - - + -
246C LEU* 3.5 18.4 - - + -
249C ARG* 3.6 65.1 - - + +
250C ILE* 3.8 17.9 - - + -
89D SER 5.0 1.3 - - - -
90D HIS* 3.6 39.9 - + - -
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ALA* 2.8 25.7 + - - +
198C ASN 4.0 1.3 - - - +
200C PHE* 1.3 68.4 - - - +
202C ALA* 1.3 68.6 + - - +
204C VAL* 3.3 1.9 + - - +
205C LEU* 3.0 46.1 + - + +
212C VAL* 3.9 18.4 - - + -
214C VAL* 3.7 11.0 - - + -
229C LEU* 3.6 30.3 - - + -
232C VAL* 4.1 6.5 - - + -
238C PHE* 3.9 8.7 - - + -
246C LEU* 3.8 19.1 - - + -
250C ILE* 5.1 1.1 - - + -
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ASN 2.9 20.0 + - - +
199C THR 3.5 4.3 - - - +
201C VAL* 1.3 78.1 - - - +
203C GLU* 1.3 56.6 + - + +
206C GLY* 2.8 9.7 + - - -
207C LEU* 2.8 43.9 + - - +
208C ASP 4.0 1.8 - - - -
209C PRO* 3.3 32.3 - - + -
212C VAL* 4.2 11.7 - - + -
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ARG* 5.2 2.0 + - - -
199C THR* 2.9 36.1 + - + +
200C PHE* 3.7 23.2 - - - +
201C VAL 3.2 0.2 - - - -
202C ALA* 1.3 78.6 - - + +
204C VAL* 1.3 62.6 + - + +
206C GLY* 3.4 10.3 + - - -
207C LEU 5.2 0.4 - - - -
209C PRO* 6.5 0.2 - - + -
245C TYR* 5.5 0.3 + - - -
249C ARG* 4.4 6.8 + - - -
89D SER* 4.6 4.7 - - - +
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ARG* 3.9 30.2 + - - +
200C PHE 3.0 20.7 + - - +
201C VAL* 3.8 5.4 - - - +
203C GLU* 1.3 78.5 - - + +
205C LEU* 1.3 67.1 + - + +
206C GLY 3.6 0.3 + - - -
238C PHE* 4.8 4.0 - - + -
242C GLU* 3.2 46.4 - - + +
245C TYR* 4.0 24.5 - - + -
246C LEU* 4.2 8.5 - - + -
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C VAL* 3.0 29.5 + - + +
204C VAL* 1.3 80.5 - - + +
206C GLY* 1.3 62.3 + - - +
207C LEU* 3.5 27.5 + - + +
232C VAL* 5.3 1.6 - - + -
236C SER* 3.5 31.0 - - - +
237C SER 4.1 15.3 - - - +
238C PHE* 3.7 31.2 - - + -
242C GLU* 4.8 5.8 - - - +
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Residues in contact with GLY 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ALA 2.8 6.7 + - - -
203C GLU* 3.4 6.8 + - - -
204C VAL 3.3 4.2 + - - -
205C LEU* 1.3 79.0 - - - +
207C LEU* 1.3 63.2 + - - +
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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
------------------------------------------------------------
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