Contacts of the helix formed by residues 190 - 206 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D VAL* 4.8 0.9 - - + -
188D GLY 3.2 13.5 + - - +
189D VAL* 1.3 74.3 - - - +
191D MET* 1.3 59.0 + - - +
192D LEU 3.2 2.7 - - - -
193D ASP* 2.8 32.5 + - - +
194D VAL* 3.6 5.0 + - - +
216D VAL* 5.1 3.2 + - - -
219D GLY 4.9 1.3 - - - -
220D HIS* 3.5 35.0 - - + +
295D CYS* 3.6 8.7 + - - +
296D ALA* 3.4 22.2 + - - +
297D PHE* 3.7 21.8 - - + +
309D ALA* 4.3 13.5 - - + +
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Residues in contact with MET 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D VAL* 3.4 18.4 - - + -
190D THR* 1.3 76.8 + - - +
192D LEU* 1.3 57.4 + - - +
194D VAL* 2.8 38.9 + - + +
195D VAL* 2.8 32.6 + - + +
274D ALA* 3.4 31.2 - - + +
277D LYS* 4.5 17.9 - - + -
278D PHE* 4.3 15.9 - - + -
294D GLU* 3.6 29.8 - - + +
295D CYS 4.3 16.8 + - - +
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Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C HIS* 5.0 0.2 - - + -
189D VAL* 5.1 1.6 + - - +
190D THR 3.2 0.8 + - - -
191D MET* 1.3 79.0 - - - +
193D ASP* 1.3 57.4 + - - +
195D VAL* 3.7 14.1 - - + -
196D ARG* 2.9 69.3 + - + +
220D HIS* 4.8 10.1 - - + -
267D ALA* 4.1 6.1 - - + -
270D SER* 3.7 39.9 - - - +
271D MET* 3.7 30.7 - - - -
274D ALA* 3.7 14.9 - - + +
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Residues in contact with ASP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D THR* 2.8 15.0 + - - +
192D LEU* 1.3 76.9 - - - +
194D VAL* 1.3 58.6 + - - +
196D ARG* 3.9 17.5 + - - +
197D ALA* 2.9 30.1 + - - +
216D VAL* 3.8 22.0 - - + +
219D GLY 4.1 2.4 - - - +
220D HIS* 2.6 43.9 + - - -
225D ILE* 3.5 29.1 - - + +
250D ILE* 4.3 8.9 - - + +
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D THR* 3.6 4.9 + - - +
191D MET* 2.8 27.3 + - + +
193D ASP* 1.3 76.0 - - - +
195D VAL* 1.3 60.2 + - + +
197D ALA* 3.4 1.2 + - - +
198D ASN* 2.9 50.0 + - - +
213D ASP* 4.4 9.0 - - - +
214D VAL 3.7 12.6 - - - +
216D VAL* 3.8 23.1 - - + -
295D CYS* 3.6 36.6 - - + -
311D LYS* 6.2 0.4 - - - +
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C HIS 3.1 22.7 - - - +
91C MET* 3.8 6.1 - - - -
92C ASP* 3.2 35.7 - - - +
191D MET* 2.8 24.6 + - + +
192D LEU* 3.7 17.7 - - + +
194D VAL* 1.3 73.4 - - + +
196D ARG* 1.3 67.9 + - - +
198D ASN* 3.0 6.2 + - - +
199D THR* 2.9 21.7 + - - -
273D TYR* 3.7 16.2 - - + +
274D ALA* 4.2 12.8 - - + -
277D LYS* 5.2 5.4 - - + -
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Residues in contact with ARG 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C HIS* 2.9 46.5 + - + +
192D LEU* 2.9 42.9 + - + +
193D ASP* 3.9 17.2 + - - +
195D VAL* 1.3 75.0 - - - +
197D ALA* 1.3 64.2 + - - +
199D THR* 3.0 2.9 + - - -
200D PHE* 2.8 43.8 + - + -
220D HIS* 5.8 2.4 - - - -
250D ILE* 4.8 9.3 + - - -
253D GLY* 3.5 15.0 + - - -
254D GLY* 3.2 37.2 - - - +
257D VAL* 4.4 1.4 - - - +
267D ALA* 3.5 28.5 - - - +
270D SER* 4.8 0.2 + - - -
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ASP 2.9 20.5 + - - +
194D VAL 3.5 5.4 - - - +
195D VAL 3.2 0.2 - - - -
196D ARG* 1.3 75.8 - - - +
198D ASN* 1.3 57.0 + - - +
200D PHE* 4.0 0.5 - - - +
201D VAL* 2.9 35.7 + - - +
214D VAL* 3.7 29.2 - - + -
216D VAL* 3.8 11.0 - - + -
250D ILE* 3.8 23.0 - - + +
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Residues in contact with ASN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASP* 3.6 25.2 + - + -
194D VAL* 2.9 38.0 + - - +
195D VAL* 3.0 6.4 + - - +
197D ALA* 1.3 76.0 - - - +
199D THR* 1.3 57.3 + - - +
202D ALA* 2.9 33.1 + - - +
209D PRO* 4.1 6.0 - - - +
212D VAL* 3.0 33.3 + - - +
213D ASP* 3.1 3.5 + - - -
214D VAL 2.8 30.1 + - - -
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Residues in contact with THR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER 3.4 22.7 - - - +
90C HIS 2.8 24.1 + - - +
91C MET 3.3 2.9 - - - +
92C ASP* 3.1 20.8 + - - +
195D VAL 2.9 5.0 + - - -
196D ARG 3.5 6.1 - - - -
198D ASN* 1.3 75.3 - - - +
200D PHE* 1.3 70.1 + - + +
202D ALA* 3.1 4.9 + - - +
203D GLU* 2.9 32.4 + - + +
209D PRO* 3.9 13.4 - - + +
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER 5.1 0.7 - - - -
90C HIS* 3.4 44.2 - + - -
196D ARG* 2.8 40.0 + - + +
197D ALA 4.1 2.2 - - - +
199D THR* 1.3 85.7 - - + +
201D VAL* 1.3 62.0 + - - +
203D GLU* 3.2 17.0 + - - +
204D VAL* 3.2 10.7 + - - +
245D TYR* 4.8 1.5 + - - +
246D LEU* 3.4 23.6 - - + +
249D ARG* 3.4 69.5 - - + +
250D ILE* 4.0 17.5 - - + -
253D GLY* 4.8 0.4 - - - -
256D GLU* 4.2 0.9 - - - -
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Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA 2.9 24.2 + - - +
198D ASN 4.1 0.9 - - - +
200D PHE* 1.3 73.1 - - - +
202D ALA* 1.3 64.5 + - - +
204D VAL* 3.1 4.2 + - - +
205D LEU* 3.0 32.9 + - + +
212D VAL* 4.0 13.7 - - + -
214D VAL* 3.7 16.6 - - + -
229D LEU* 3.8 25.8 - - + -
232D VAL* 4.0 7.6 - - + -
238D PHE* 3.6 23.3 - - + -
246D LEU* 3.9 19.3 - - + -
250D ILE* 4.9 2.5 - - + -
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ASN 2.9 20.4 + - - +
199D THR 3.1 4.7 + - - +
201D VAL* 1.3 79.5 - - - +
203D GLU* 1.3 56.1 + - - +
205D LEU* 3.2 2.8 + - - +
206D GLY* 2.7 26.5 + - - -
207D LEU 2.9 30.7 + - - +
209D PRO* 3.4 23.1 - - + -
212D VAL* 3.9 16.2 - - + -
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Residues in contact with GLU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D THR* 2.9 17.2 + - + +
200D PHE* 3.4 11.6 - - - +
201D VAL 3.2 0.2 - - - -
202D ALA* 1.3 78.5 - - - +
204D VAL* 1.3 62.9 + - - +
206D GLY* 3.3 10.9 + - - -
207D LEU 5.2 0.2 - - - -
245D TYR* 3.6 19.8 + - - -
249D ARG* 3.9 13.8 + - - -
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D PHE 3.5 2.5 - - - +
201D VAL 3.1 7.3 + - - +
203D GLU* 1.3 79.2 - - + +
205D LEU* 1.3 62.4 + - + +
206D GLY 3.6 0.3 + - - -
238D PHE* 4.3 11.9 - - + -
242D GLU* 3.5 41.8 - - + +
245D TYR* 3.7 17.7 - - + +
246D LEU* 3.4 36.8 - - + -
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D VAL* 3.0 36.4 + - + +
202D ALA 3.9 1.8 - - - +
204D VAL* 1.3 78.8 - - + +
206D GLY* 1.3 63.6 + - - +
207D LEU* 3.7 34.7 - - + +
212D VAL* 5.0 2.5 - - + -
232D VAL* 4.9 5.8 - - + -
234D PRO* 4.9 1.3 - - + +
236D SER* 3.9 29.4 - - - +
237D SER 5.5 2.2 - - - +
238D PHE* 3.8 26.2 - - + -
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Residues in contact with GLY 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ALA 2.7 8.6 + - - -
203D GLU* 3.3 7.0 + - - -
204D VAL 3.3 3.4 + - - -
205D LEU* 1.3 79.8 - - - +
207D LEU* 1.3 60.4 + - - +
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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
------------------------------------------------------------
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