Contacts of the helix formed by residues 190 - 206 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164E VAL* 4.9 0.4 - - + -
188E GLY 3.2 2.1 + - - +
189E VAL* 1.3 74.3 - - - +
191E MET* 1.3 54.5 + - - +
192E LEU 3.2 2.7 - - - -
193E ASP* 2.8 41.5 + - - +
194E VAL* 3.4 5.6 + - - +
216E VAL* 5.1 5.0 + - - -
219E GLY 4.6 1.3 - - - +
220E HIS* 3.7 30.5 - - + +
295E CYS* 3.6 12.0 + - - +
296E ALA* 3.5 20.8 + - - -
297E PHE* 3.7 30.5 + - + +
309E ALA* 4.3 12.4 - - + +
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Residues in contact with MET 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E VAL* 3.3 21.8 - - + +
190E THR* 1.3 76.7 + - - +
192E LEU* 1.3 51.6 + - - +
194E VAL* 2.8 28.9 + - + +
195E VAL* 2.6 46.8 + - + +
198E ASN* 5.8 1.8 - - - +
274E ALA* 3.4 29.4 - - + +
277E LYS* 3.4 31.4 - - + -
278E PHE* 4.0 19.7 - - + +
294E GLU* 3.4 27.4 - - - +
295E CYS 4.7 8.0 + - - +
92F ASP* 5.8 0.9 - - - +
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E VAL 5.2 0.8 + - - +
190E THR 3.1 0.8 + - - -
191E MET* 1.3 78.9 - - - +
193E ASP* 1.3 54.4 + - - +
195E VAL* 3.9 11.9 - - + -
196E ARG* 2.7 84.9 + - + +
220E HIS* 4.8 10.5 - - + +
267E ALA* 4.5 3.6 - - + -
270E SER* 3.7 35.7 - - - +
271E MET* 3.7 38.4 - - + +
274E ALA* 3.6 10.5 - - + +
90F HIS* 4.9 1.1 - - + -
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Residues in contact with ASP 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E THR* 2.8 22.9 + - - +
192E LEU* 1.3 71.8 - - - +
194E VAL* 1.3 52.0 + - - +
196E ARG* 3.4 16.9 + - - +
197E ALA* 2.7 35.8 + - - +
216E VAL* 4.0 21.6 - - + +
219E GLY 4.1 2.1 - - - +
220E HIS* 2.5 41.4 + - - -
225E ILE* 3.1 35.8 - - + +
250E ILE* 4.1 5.8 - - - +
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Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E THR* 3.4 8.0 + - - +
191E MET* 2.8 29.7 + - + +
193E ASP* 1.3 73.8 - - - +
195E VAL* 1.3 58.7 + - - +
197E ALA* 3.0 7.1 + - - +
198E ASN* 2.7 51.4 + - - +
213E ASP* 5.2 2.7 - - - +
214E VAL 3.7 15.7 - - - +
215E PRO* 5.7 0.4 - - + -
216E VAL* 4.0 17.0 - - + -
295E CYS* 3.8 30.7 - - + +
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E MET* 2.6 45.8 + - + +
192E LEU* 3.5 13.7 - - + +
194E VAL* 1.3 73.3 - - - +
196E ARG* 1.3 56.9 + - - +
198E ASN* 3.4 1.9 + - - +
199E THR* 2.7 32.1 + - - -
273E TYR* 3.7 16.8 - - + -
274E ALA* 3.8 19.7 - - + -
277E LYS* 4.9 1.6 - - + -
90F HIS 3.4 16.4 - - - +
91F MET* 3.7 3.1 - - - -
92F ASP* 3.5 33.3 - - - +
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Residues in contact with ARG 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E LEU* 2.7 59.4 + - + +
193E ASP* 3.6 18.5 + - - +
195E VAL* 1.3 70.0 - - - +
197E ALA* 1.3 58.6 + - - +
199E THR* 3.1 2.5 + - - -
200E PHE* 2.8 55.7 + - + -
220E HIS* 5.7 2.4 - - - -
225E ILE* 5.7 1.6 - - - +
250E ILE* 4.8 7.9 + - + -
253E GLY* 3.8 14.1 + - - +
254E GLY* 3.5 35.4 - - - +
257E VAL* 4.9 0.6 - - - +
267E ALA* 3.8 17.2 - - - +
270E SER* 5.0 0.2 + - - -
90F HIS* 2.9 46.1 + - + +
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E ASP 2.7 23.0 + - - +
194E VAL* 3.3 5.8 - - - +
196E ARG* 1.3 73.3 - - - +
198E ASN* 1.3 60.9 + - - +
200E PHE* 4.1 0.7 - - - +
201E VAL* 2.8 34.3 + - - +
214E VAL* 3.9 14.1 - - + -
216E VAL* 3.7 22.4 - - + -
250E ILE* 3.7 24.8 - - + +
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Residues in contact with ASN 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E MET* 5.8 1.8 - - - +
194E VAL* 2.7 36.2 + - - +
195E VAL* 3.8 3.6 - - - +
197E ALA* 1.3 71.2 - - - +
199E THR* 1.3 58.7 + - - +
201E VAL* 3.3 1.9 + - - +
202E ALA* 2.8 32.8 + - - +
209E PRO* 4.0 11.0 - - - +
212E VAL* 3.3 23.7 + - - +
213E ASP* 2.9 19.9 + - - -
214E VAL* 2.7 32.2 + - - -
92F ASP* 3.3 21.7 + - + -
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Residues in contact with THR 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E VAL 2.7 13.5 + - - -
196E ARG* 3.1 4.4 + - - -
198E ASN* 1.3 77.6 - - - +
200E PHE* 1.3 64.4 + - + +
202E ALA* 3.5 1.7 + - - +
203E GLU* 2.8 47.2 + - + +
209E PRO* 3.9 16.2 - - + -
89F SER 3.5 24.0 - - - +
90F HIS* 2.7 24.0 + - - +
91F MET 3.8 7.0 - - - +
92F ASP* 3.2 13.0 - - - -
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Residues in contact with PHE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ARG* 2.8 51.3 + - + +
197E ALA 4.1 1.8 - - - +
199E THR* 1.3 76.8 - - + +
201E VAL* 1.3 65.7 + - - +
203E GLU* 3.4 10.3 + - - +
204E VAL* 3.2 26.9 + - - +
246E LEU* 3.4 17.2 - - + +
249E ARG* 3.2 65.0 + - + +
250E ILE* 3.5 32.1 - - + -
253E GLY* 4.9 0.4 - - - -
256E GLU* 4.6 0.2 - - - -
89F SER 5.8 0.4 - - - -
90F HIS* 3.8 31.2 - + - -
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Residues in contact with VAL 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E ALA* 2.8 25.7 + - - +
198E ASN 3.7 2.9 - - - +
200E PHE* 1.3 77.4 - - - +
202E ALA* 1.3 56.9 + - - +
204E VAL* 3.2 3.6 + - - +
205E LEU* 2.9 57.3 + - + +
212E VAL* 4.0 5.8 - - + -
214E VAL* 3.4 19.3 - - + -
229E LEU* 3.7 22.9 - - + -
232E VAL* 3.9 18.6 - - + -
238E PHE* 4.0 9.0 - - + -
246E LEU* 4.2 12.1 - - + -
250E ILE* 4.8 2.0 - - + -
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Residues in contact with ALA 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ASN 2.8 17.8 + - - +
199E THR 3.8 4.3 - - - +
201E VAL* 1.3 77.7 - - - +
203E GLU* 1.3 52.5 + - + +
205E LEU* 3.2 1.0 + - - -
206E GLY 2.6 31.4 + - - -
207E LEU* 2.6 39.8 + - - +
208E ASP 3.9 0.7 - - - -
209E PRO* 3.5 24.7 - - + -
212E VAL* 4.2 9.6 - - + +
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Residues in contact with GLU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E THR* 2.8 38.8 + - + +
200E PHE* 3.6 12.0 - - - +
201E VAL 3.3 0.4 - - - -
202E ALA* 1.3 76.3 - - + +
204E VAL* 1.3 64.7 + - + +
206E GLY* 3.3 10.9 + - - -
207E LEU 5.0 0.7 - - - -
209E PRO* 6.2 1.8 - - + -
249E ARG* 2.9 33.7 + - - +
89F SER* 4.9 4.2 - - - +
96F VAL* 6.0 2.3 - - - +
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Residues in contact with VAL 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PHE 3.2 2.7 + - - +
201E VAL 3.2 7.5 + - - +
202E ALA 3.2 0.2 - - - -
203E GLU* 1.3 80.7 - - + +
205E LEU* 1.3 61.4 + - + +
206E GLY* 3.0 4.7 + - - -
238E PHE* 4.6 8.3 - - + -
242E GLU* 3.5 36.6 - - + +
245E TYR* 4.3 15.3 - - + -
246E LEU* 3.4 44.6 - - + -
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E VAL* 2.9 42.8 + - + +
202E ALA 3.9 0.9 - - - +
204E VAL* 1.3 76.7 - - + +
206E GLY* 1.3 64.3 + - - +
207E LEU* 3.3 38.2 + - + +
212E VAL* 4.7 4.0 - - + -
232E VAL* 4.5 6.7 - - + -
234E PRO* 5.1 0.9 - - + +
236E SER* 3.7 29.4 - - - +
237E SER 5.4 2.2 - - - +
238E PHE* 3.5 26.0 - - + -
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Residues in contact with GLY 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ALA 2.6 12.2 + - - -
203E GLU* 3.3 8.4 + - - -
204E VAL 3.0 6.4 + - - -
205E LEU* 1.3 75.3 - - - +
207E LEU* 1.3 61.0 + - - +
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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