Contacts of the helix formed by residues 239 - 252 (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 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D SER 5.7 0.9 - - - +
238D PHE* 1.3 75.3 - - - +
240D GLN* 1.3 66.3 + - - +
241D GLU* 3.6 8.8 + - - +
242D GLU* 2.9 54.6 + - - +
243D ILE* 3.0 11.3 + - - +
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Residues in contact with GLN 240 (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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238D PHE 3.8 1.4 + - - -
239D THR* 1.3 72.7 - - - +
241D GLU* 1.3 56.0 + - - +
243D ILE* 3.6 12.4 + - + +
244D SER* 3.2 26.7 + - - -
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Residues in contact with GLU 241 (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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239D THR* 3.0 9.1 + - - +
240D GLN* 1.3 78.2 - - - +
242D GLU* 1.3 60.9 + - + +
244D SER* 3.4 6.3 + - - -
245D TYR* 3.0 28.6 + - + +
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Residues in contact with GLU 242 (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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204D VAL* 3.5 31.8 - - + +
237D SER 4.6 1.2 - - - +
238D PHE* 3.4 20.6 - - + +
239D THR* 2.9 48.0 + - - +
241D GLU* 1.3 74.3 - - + +
243D ILE* 1.3 60.5 + - - +
245D TYR* 4.4 7.9 - - + -
246D LEU* 2.8 39.5 + - + +
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Residues in contact with ILE 243 (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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229D LEU* 3.8 23.3 - - + +
238D PHE* 3.6 32.8 - - + +
239D THR 3.0 13.3 + - - +
240D GLN* 3.7 14.8 - - + +
242D GLU* 1.3 77.4 - - - +
244D SER* 1.3 62.8 + - - +
246D LEU* 5.1 0.2 - - - -
247D THR* 2.8 30.5 + - - -
329D ASN* 5.3 10.8 - - - +
331D TYR* 3.6 42.0 - - + -
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Residues in contact with SER 244 (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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240D GLN 3.2 14.2 + - - -
241D GLU* 3.7 7.4 - - - -
243D ILE* 1.3 81.1 - - - +
245D TYR* 1.3 62.1 - - - +
247D THR* 3.8 1.4 - - - -
248D ASP* 3.0 25.5 + - - +
331D TYR* 4.0 17.1 + - - -
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Residues in contact with TYR 245 (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* 4.8 2.1 + - - +
203D GLU* 3.6 12.4 + - - -
204D VAL* 3.7 15.0 - - + -
241D GLU* 3.0 18.2 + - + +
242D GLU* 3.9 7.0 - - + -
244D SER* 1.3 74.2 - - - +
246D LEU* 1.3 96.4 + - + +
248D ASP* 3.2 5.1 + - - +
249D ARG* 2.8 73.9 + - + +
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Residues in contact with LEU 246 (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* 3.4 40.2 - - + +
201D VAL* 3.8 19.3 - - + +
204D VAL* 3.4 22.0 - - + -
229D LEU* 4.3 12.3 - - + -
238D PHE* 4.1 25.8 - - + -
242D GLU 2.8 25.6 + - - +
243D ILE 4.2 1.6 - - - +
245D TYR* 1.3 86.3 - - + +
247D THR* 1.3 65.2 + - - +
249D ARG* 3.2 3.4 + - - +
250D ILE* 2.8 37.9 + - + +
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Residues in contact with THR 247 (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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226D LEU* 5.8 3.8 - - + -
227D PRO* 4.0 22.1 + - + +
229D LEU* 3.4 15.6 - - - +
243D ILE 2.8 24.5 + - - -
244D SER 3.8 1.6 - - - -
246D LEU* 1.3 76.8 - - - +
248D ASP* 1.3 61.1 + - - +
250D ILE* 3.9 1.4 - - - +
251D GLN* 2.9 53.1 + - - +
331D TYR* 3.6 31.9 - - + +
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Residues in contact with ASP 248 (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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244D SER* 3.0 19.4 + - - +
245D TYR* 3.7 4.9 - - - +
247D THR* 1.3 76.7 - - - +
249D ARG* 1.3 70.0 + - - +
251D GLN* 3.3 10.0 + - - +
252D ASN* 2.7 51.0 + - - +
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Residues in contact with ARG 249 (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* 5.0 3.6 + - - -
90C HIS* 4.2 2.4 + - - -
200D PHE* 3.4 47.4 - - + -
203D GLU* 3.9 17.4 + - - -
245D TYR* 2.8 59.6 + - + +
246D LEU* 3.8 3.8 - - - +
248D ASP* 1.3 76.3 + - - +
250D ILE* 1.3 57.9 + - - +
252D ASN* 3.0 5.2 + - - -
253D GLY* 2.8 29.1 + - - -
256D GLU* 2.6 44.2 + - - +
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Residues in contact with ILE 250 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D ASP* 4.3 22.5 - - + +
196D ARG* 4.8 6.2 + - + -
197D ALA* 3.8 30.5 - - + +
200D PHE* 4.0 17.5 - - + -
201D VAL* 4.9 1.3 - - + -
216D VAL* 5.1 1.1 - - + -
225D ILE* 4.0 26.3 - - + +
227D PRO* 3.5 35.0 - - + -
229D LEU* 4.5 11.2 - - + -
246D LEU* 2.8 29.4 + - + +
247D THR 3.9 3.4 - - - +
249D ARG* 1.3 76.7 - - - +
251D GLN* 1.3 63.5 + - - +
252D ASN 3.2 0.2 + - - -
253D GLY* 3.3 9.0 + - - -
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Residues in contact with GLN 251 (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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222D GLY* 3.3 27.1 + - - +
223D VAL* 3.6 28.5 + - - +
225D ILE* 2.9 49.1 + - + +
226D LEU* 5.0 4.6 - - - +
227D PRO* 4.7 3.7 - - + +
247D THR* 2.9 40.8 + - + +
248D ASP* 3.6 12.8 - - - +
249D ARG 3.2 0.4 - - - -
250D ILE* 1.3 75.8 - - - +
252D ASN* 1.3 65.0 + - - +
253D GLY 3.5 0.4 + - - -
254D GLY 5.3 0.5 + - - -
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Residues in contact with ASN 252 (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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222D GLY* 5.3 4.5 - - - -
248D ASP* 2.7 47.2 + - - +
249D ARG* 3.0 8.2 + - - +
251D GLN* 1.3 87.5 + - - +
253D GLY* 1.3 65.5 + - - +
254D GLY 3.2 3.1 - - - -
255D THR* 3.0 20.5 + - + +
256D GLU* 3.0 21.1 + - - +
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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