Contacts of the helix formed by residues 190 - 206 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A VAL* 4.7 0.7 - - + -
188A GLY 3.1 3.4 + - - +
189A VAL* 1.3 73.2 - - - +
191A MET* 1.3 65.1 + - - +
192A LEU 3.2 3.1 - - - -
193A ASP* 2.9 26.1 + - - +
194A VAL* 3.6 5.0 + - - +
216A VAL* 5.5 2.6 + - - -
219A GLY 4.8 1.1 - - - +
220A HIS* 3.7 31.6 - - + -
278A PHE* 6.0 0.2 - - - -
295A CYS* 3.2 10.8 + - - +
296A ALA* 3.2 23.9 + - - +
297A PHE* 3.6 32.3 - - + +
309A ALA* 4.4 11.7 - - + +
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Residues in contact with MET 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.4 14.6 - - + -
190A THR* 1.3 78.5 + - - +
192A LEU* 1.3 63.7 + - - +
194A VAL* 3.0 36.5 + - + +
195A VAL* 2.9 26.0 + - + +
274A ALA* 3.4 33.0 - - + +
277A LYS* 4.1 20.2 - - + +
278A PHE* 4.0 21.5 - - + -
294A GLU* 3.6 30.7 - - + +
295A CYS 4.2 16.1 + - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL 5.2 0.2 + - - -
190A THR 3.1 1.2 + - - -
191A MET* 1.3 78.2 - - - +
193A ASP* 1.3 57.4 + - - +
195A VAL* 4.2 11.9 - - + -
196A ARG* 3.0 71.4 + - + +
220A HIS* 4.8 10.5 + - + +
267A ALA* 4.5 3.4 - - + -
270A SER* 3.7 38.1 - - - +
271A MET* 4.1 34.3 - - + +
274A ALA* 3.7 13.7 - - + +
90B HIS* 5.2 0.4 - - + -
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Residues in contact with ASP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR* 2.9 12.3 + - - +
192A LEU* 1.3 77.0 - - - +
194A VAL* 1.3 58.7 + - - +
196A ARG* 3.4 20.8 + - - +
197A ALA* 2.8 29.8 + - - +
216A VAL* 4.1 11.5 - - + +
219A GLY 3.9 3.6 - - - +
220A HIS* 2.8 39.9 + - - +
225A ILE* 3.5 45.2 - - + +
250A ILE* 4.1 6.8 - - + +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A THR* 3.6 6.2 + - - +
191A MET* 3.0 29.5 + - + +
193A ASP* 1.3 78.4 - - - +
195A VAL* 1.3 52.7 + - - +
197A ALA* 3.4 1.1 + - - +
198A ASN* 2.8 56.0 + - - +
213A ASP* 4.8 7.9 - - - +
214A VAL 3.9 14.1 - - - +
216A VAL* 3.8 24.5 - - + -
277A LYS* 5.3 3.6 - - - +
294A GLU* 5.4 2.0 - - - +
295A CYS* 3.9 30.1 - - + -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A MET* 2.9 24.0 + - + +
192A LEU* 3.6 19.1 - - + +
193A ASP 3.3 0.2 - - - -
194A VAL* 1.3 73.8 - - - +
196A ARG* 1.3 59.7 + - - +
198A ASN* 3.3 2.6 + - - +
199A THR* 2.9 33.4 + - - -
273A TYR* 3.8 16.2 - - + -
274A ALA* 4.1 13.7 - - + -
277A LYS* 4.5 7.6 - - - +
90B HIS 3.0 22.0 - - - +
91B MET* 3.8 5.6 - - + -
92B ASP* 3.5 36.5 - - - +
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Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.0 54.8 + - + +
193A ASP* 3.7 18.7 + - - +
195A VAL* 1.3 74.4 - - - +
197A ALA* 1.3 57.2 + - - +
199A THR* 3.1 1.9 + - - -
200A PHE* 2.7 54.9 + - + -
220A HIS* 6.0 0.4 + - - -
225A ILE* 5.8 2.0 - - - +
250A ILE* 4.6 11.2 + - + -
253A GLY* 4.1 14.9 + - - +
254A GLY* 3.6 34.1 - - - +
257A VAL* 4.8 0.8 - - - +
267A ALA* 3.8 17.6 - - - +
270A SER* 4.9 0.2 + - - -
90B HIS* 3.2 41.9 + - + +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASP 2.8 17.8 + - - +
194A VAL 3.6 4.3 - - - +
196A ARG* 1.3 75.6 - - - +
198A ASN* 1.3 58.3 + - - +
200A PHE* 4.1 0.2 - - - +
201A VAL* 2.8 35.5 + - - +
214A VAL* 3.7 25.8 - - + -
216A VAL* 4.0 9.0 - - + -
250A ILE* 3.5 32.4 - - + +
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Residues in contact with ASN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A VAL* 2.8 41.8 + - - +
195A VAL* 3.6 3.8 - - - +
197A ALA* 1.3 72.4 - - - +
199A THR* 1.3 58.5 + - - +
201A VAL 3.9 0.2 - - - -
202A ALA* 2.9 32.4 + - - +
209A PRO* 4.2 4.9 - - - +
212A VAL* 3.2 33.8 + - + +
213A ASP* 3.4 3.5 + - - +
214A VAL* 2.8 30.5 + - - +
277A LYS* 4.4 5.7 - - - +
92B ASP* 3.3 27.2 + - + +
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A VAL 2.9 18.1 + - - -
196A ARG 3.5 4.0 - - - -
198A ASN* 1.3 76.9 - - - +
200A PHE* 1.3 68.4 + - + +
202A ALA* 3.2 3.6 + - - +
203A GLU* 2.8 48.9 + - + +
209A PRO* 4.3 13.5 - - + -
89B SER 3.5 21.3 - - - +
90B HIS 2.9 16.4 + - - +
91B MET 4.4 3.4 - - - +
92B ASP* 2.9 18.7 - - - -
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Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ARG* 2.7 39.3 + - + +
197A ALA 4.1 1.3 - - - +
199A THR* 1.3 82.3 - - + +
201A VAL* 1.3 62.7 + - - +
203A GLU* 3.3 12.8 + - - +
204A VAL* 3.1 19.9 + - - +
245A TYR* 5.6 0.3 - - - -
246A LEU* 3.4 22.6 - - + +
249A ARG* 3.2 75.1 + - + +
250A ILE* 3.8 17.5 - - + -
253A GLY* 4.6 2.2 - - - -
256A GLU* 4.2 1.6 - - - -
89B SER 5.2 0.2 - - - -
90B HIS* 3.5 40.4 - + - -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ALA 2.8 25.5 + - - +
198A ASN 4.0 2.2 - - - +
200A PHE* 1.3 71.4 - - - +
202A ALA* 1.3 59.7 + - - +
204A VAL* 3.2 2.6 + - - +
205A LEU* 2.9 52.4 + - + +
212A VAL* 3.9 15.0 - - + -
214A VAL* 3.6 17.9 - - + -
229A LEU* 3.6 24.2 - - + -
232A VAL* 4.2 5.4 - - + -
238A PHE* 3.9 12.8 - - + -
246A LEU* 3.8 16.8 - - + -
250A ILE* 4.7 3.6 - - + -
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASN 2.9 19.7 + - - +
199A THR 3.2 4.2 + - - +
201A VAL* 1.3 77.9 - - - +
203A GLU* 1.3 52.7 + - - +
205A LEU* 4.5 0.7 - - - +
206A GLY* 2.7 31.0 + - - -
207A LEU* 2.8 32.5 + - - +
208A ASP 3.9 2.7 - - - +
209A PRO* 3.5 26.9 - - + -
212A VAL* 4.2 11.0 - - + +
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A THR* 2.8 43.4 + - + +
200A PHE* 3.6 6.3 - - - +
202A ALA* 1.3 78.8 - - + +
204A VAL* 1.3 62.2 + - + +
206A GLY* 3.4 8.8 + - - -
207A LEU 5.3 0.2 - - - -
209A PRO* 5.7 3.1 - - + -
249A ARG* 2.8 34.1 + - - +
89B SER* 4.4 5.5 - - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE 3.1 13.9 + - - +
201A VAL 3.2 6.0 + - - +
203A GLU* 1.3 78.5 - - + +
205A LEU* 1.3 65.8 + - + +
206A GLY 3.5 0.7 + - - -
238A PHE* 4.9 1.6 - - + -
242A GLU* 3.4 43.1 - - + +
245A TYR* 3.8 32.5 - - + -
246A LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL* 2.9 39.0 + - + +
202A ALA 4.2 0.7 - - - +
204A VAL* 1.3 80.3 - - + +
206A GLY* 1.3 62.7 + - - +
207A LEU* 3.8 31.2 - - + +
212A VAL* 5.2 2.2 - - + -
232A VAL* 5.5 1.8 - - + -
234A PRO* 5.9 0.4 - - + -
236A SER* 3.6 30.7 - - - +
237A SER 4.5 6.7 - - - +
238A PHE* 3.8 28.0 - - + -
242A GLU* 5.3 2.7 - - - +
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA 2.7 9.4 + - - -
203A GLU 3.4 7.0 + - - -
204A VAL 3.2 5.3 + - - -
205A LEU* 1.3 79.9 - - - +
207A LEU* 1.3 64.1 + - - +
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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