Contacts of the helix formed by residues 227 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C GLU* 5.5 4.6 + - - +
54C GLY 4.2 4.5 + - - -
55C ASP* 3.6 36.4 + - - +
56C LYS* 5.4 0.3 - - - +
224C PHE* 3.2 24.7 + - + +
225C GLY 2.8 1.4 + - - -
226C PRO* 1.3 86.5 - - + +
228C ALA* 1.3 74.1 + - - -
229C GLY 3.3 0.4 + - - -
230C ALA* 3.4 0.9 + - - +
231C ALA* 3.0 24.7 + - - +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLY 3.7 22.6 + - - +
55C ASP* 4.6 2.4 - - - +
59C VAL* 3.7 16.9 - - + +
192C LYS* 3.8 20.6 - - + -
221C VAL* 4.6 5.8 - - + -
223C GLY* 4.4 3.6 - - - -
224C PHE 3.0 13.9 + - - +
227C THR* 1.3 81.1 + - - +
229C GLY* 1.3 62.2 + - - +
231C ALA* 3.3 3.3 + - - +
232C ILE* 3.1 25.6 + - - +
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Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 3.8 20.2 - - - +
192C LYS* 4.1 14.9 - - - +
224C PHE 3.3 3.8 + - - -
225C GLY* 3.1 14.8 + - - -
228C ALA* 1.3 78.7 - - - +
230C ALA* 1.3 62.5 + - - +
232C ILE* 3.3 5.6 + - - +
233C ALA* 3.1 22.1 + - - +
253C ILE* 5.3 2.7 - - - -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C GLY 3.0 8.4 + - - +
226C PRO* 3.5 25.4 - - + +
227C THR 3.4 0.6 + - - +
228C ALA 3.4 0.4 - - - -
229C GLY* 1.3 74.2 - - - +
231C ALA* 1.3 58.1 + - - +
233C ALA* 3.2 7.7 + - - +
234C SER* 2.8 36.6 + - - +
252C VAL* 5.9 6.7 - - + -
253C ILE* 5.7 1.6 - - - -
256C ALA* 6.0 0.7 - - - -
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 3.8 41.5 - - + +
59C VAL* 4.0 13.7 - - + +
60C ASP* 5.7 0.2 - - - +
227C THR 3.0 18.8 + - - +
228C ALA 3.5 4.9 - - - +
229C GLY 3.2 0.2 - - - -
230C ALA* 1.3 76.2 - - - +
232C ILE* 1.3 60.5 + - - +
234C SER* 3.8 5.4 - - - -
235C HIS* 3.1 26.5 + - - +
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C VAL* 3.7 24.9 - - + -
63C VAL* 5.6 0.9 - - + -
163C GLY* 3.6 32.3 - - - -
165C ILE* 4.7 8.1 - - + -
190C VAL* 4.2 28.0 - - + +
191C MET 4.6 0.4 - - - -
192C LYS* 3.7 32.5 - - + +
221C VAL* 5.6 1.8 - - + -
228C ALA 3.1 12.1 + - - +
229C GLY 3.7 5.4 - - - +
230C ALA 3.3 0.2 - - - -
231C ALA* 1.3 75.6 - - - +
233C ALA* 1.3 64.5 + - - +
234C SER 3.2 0.9 + - - -
235C HIS* 3.2 15.4 + - - +
238C VAL* 4.0 16.7 - - + +
241C VAL* 4.7 7.0 - - + -
263C LYS* 4.1 1.7 - - - -
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 5.0 0.2 - - - +
229C GLY 3.1 15.9 + - - +
230C ALA* 3.2 7.2 + - - +
232C ILE* 1.3 78.5 - - - +
234C SER* 1.3 57.9 + - - +
241C VAL* 4.6 10.3 - - + -
253C ILE* 3.8 31.9 - - + +
256C ALA* 3.8 24.9 - - + +
257C ALA* 4.0 2.3 + - - -
260C SER* 3.9 3.1 + - - -
263C LYS* 2.9 26.6 + - - +
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Residues in contact with SER 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA* 2.8 20.0 + - - +
231C ALA* 4.0 5.8 - - - -
233C ALA* 1.3 76.7 - - - +
235C HIS* 1.3 63.5 + - - +
236C GLU* 3.4 4.3 + - - +
256C ALA* 4.0 15.5 + - - +
260C SER* 3.3 20.8 - - - -
263C LYS* 3.8 1.3 - - - -
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Residues in contact with HIS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 6.2 1.1 - - - -
59C VAL* 4.4 3.6 - - + -
60C ASP* 2.8 36.9 + - - +
63C VAL* 3.5 41.6 - - + +
64C LYS* 6.3 2.5 - - + -
231C ALA* 3.1 18.1 + - + +
232C ILE 3.2 4.5 + - - +
233C ALA 3.4 0.2 - - - -
234C SER* 1.3 75.0 - - - +
236C GLU* 1.3 87.4 + - - +
237C ASP* 3.0 28.5 + - + -
238C VAL* 3.4 23.9 + - + -
261C ASN* 3.7 0.7 - - - +
263C LYS* 2.7 24.6 + - - -
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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