Contacts of the helix formed by residues 227 - 235 (chain D) in PDB entry 3SZ9
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 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D GLU* 5.3 2.2 + - - +
54D GLY 4.3 5.5 + - - -
55D ASP* 3.9 26.5 + - - +
56D LYS* 4.7 6.2 + - - +
224D PHE* 3.3 32.2 + - + +
225D GLY 2.9 0.6 + - - -
226D PRO* 1.3 84.9 - - + +
228D ALA* 1.3 71.4 + - - +
229D GLY 3.4 0.2 - - - -
230D ALA* 3.7 1.6 + - - +
231D ALA* 3.4 21.0 + - - +
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Residues in contact with ALA 228 (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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54D GLY 4.0 19.7 - - - +
55D ASP 4.8 2.9 - - - -
59D VAL* 3.8 18.7 - - + +
192D LYS* 3.8 19.7 - - + -
221D VAL* 4.5 8.7 - - + +
222D PRO 4.6 0.4 - - - +
224D PHE 2.8 20.9 + - - +
227D THR* 1.3 76.0 + - - +
229D GLY* 1.3 62.9 + - - +
231D ALA* 3.2 13.4 + - - +
232D ILE* 3.3 16.0 + - + +
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Residues in contact with GLY 229 (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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165D ILE* 3.9 23.9 - - - +
192D LYS* 3.8 12.3 - - - +
224D PHE 3.4 2.4 + - - -
225D GLY* 3.1 14.1 + - - -
228D ALA* 1.3 78.4 - - - +
230D ALA* 1.3 62.0 + - - +
231D ALA 3.0 1.2 + - - -
232D ILE* 3.1 14.9 + - - +
233D ALA* 3.1 13.7 + - - +
253D ILE* 5.5 2.0 - - - -
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Residues in contact with ALA 230 (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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225D GLY 3.4 6.8 + - - +
226D PRO* 3.6 22.0 - - + +
227D THR 3.7 1.5 + - - +
228D ALA 3.5 0.8 - - - -
229D GLY* 1.3 74.5 - - - +
231D ALA* 1.3 57.1 + - - +
233D ALA* 3.8 7.7 - - - +
234D SER* 2.5 39.4 + - - +
252D VAL* 5.7 9.0 - - + -
253D ILE* 5.9 1.1 - - - -
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Residues in contact with ALA 231 (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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56D LYS* 3.9 41.4 - - + +
59D VAL* 4.1 11.4 - - + -
227D THR 3.4 12.6 + - - +
228D ALA 3.2 10.7 + - - +
229D GLY 3.0 0.6 - - - -
230D ALA* 1.3 76.7 - - - +
232D ILE* 1.3 60.5 + - - +
234D SER* 3.5 3.5 + - - -
235D HIS* 3.1 33.5 + - + +
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Residues in contact with ILE 232 (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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59D VAL* 3.7 24.9 - - + -
163D GLY* 3.6 30.7 - - - -
164D GLN 4.6 0.2 - - - +
165D ILE* 4.5 11.2 - - + -
190D VAL* 3.9 28.5 - - + +
191D MET 4.7 0.2 - - - -
192D LYS* 3.9 29.8 - - + +
221D VAL* 5.8 1.8 - - + -
228D ALA 3.3 9.6 + - - +
229D GLY 3.1 6.4 + - - +
231D ALA* 1.3 73.9 - - - +
233D ALA* 1.3 67.3 + - - +
234D SER 3.0 1.2 + - - -
235D HIS* 3.2 15.6 + - - +
238D VAL* 3.8 15.9 - - + +
241D VAL* 4.7 8.7 - - + -
263D LYS* 4.0 5.2 - - - -
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Residues in contact with ALA 233 (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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165D ILE* 5.3 0.4 - - + +
229D GLY 3.1 9.3 + - - +
230D ALA* 3.8 11.2 - - - +
232D ILE* 1.3 80.6 - - - +
234D SER* 1.3 57.2 + - - +
241D VAL* 4.2 13.2 - - + +
252D VAL 5.7 0.4 - - - -
253D ILE* 4.0 30.5 - - + +
256D ALA* 3.7 28.3 - - + +
257D ALA 3.9 0.7 + - - -
263D LYS* 3.1 25.3 + - - +
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Residues in contact with SER 234 (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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230D ALA* 2.5 26.6 + - - +
231D ALA* 4.3 3.4 - - - -
232D ILE 3.1 0.6 - - - -
233D ALA* 1.3 75.5 - - - +
235D HIS* 1.3 68.8 + - - +
236D GLU* 3.4 6.4 + - - +
256D ALA* 3.8 16.4 - - - +
260D SER* 3.5 19.4 - - - -
263D LYS* 4.0 1.6 - - - +
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Residues in contact with HIS 235 (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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56D LYS* 5.9 2.9 - - - -
59D VAL* 4.8 4.0 - - + -
60D ASP* 3.1 35.5 + - - +
63D VAL* 3.7 39.1 - - + +
64D LYS* 6.2 4.2 - - + +
231D ALA* 3.1 18.0 + - + +
232D ILE* 3.2 9.8 + - - +
234D SER* 1.3 76.6 - - - +
236D GLU* 1.3 73.7 + - + +
237D ASP* 3.1 27.6 + - + +
238D VAL* 3.6 11.5 + - + -
263D LYS* 2.8 28.2 + - - -
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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
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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