Contacts of the helix formed by residues 225 - 234 (chain A) in PDB entry 5TDE
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 ALA 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A TYR* 3.6 41.5 - - + -
222A ASP* 3.0 16.0 + - + +
224A THR* 1.3 76.5 + - - +
226A ASP* 1.3 63.7 + - - +
227A TYR* 3.2 5.4 - - - -
228A ILE* 2.9 15.5 + - + +
229A CYS* 2.9 13.8 + - - +
233A TRP* 3.9 6.3 - - + -
602B PRO* 4.0 12.8 - - + -
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA 3.4 13.8 + - - +
224A THR 3.2 3.2 - - - -
225A ALA* 1.3 76.3 - - - +
227A TYR* 1.3 59.2 + - - +
230A LYS* 2.9 53.7 + - - +
233A TRP* 3.5 27.5 - - + -
234A GLY 4.8 6.6 - - - +
236A ILE* 4.8 3.8 - - - +
238A PHE* 6.1 1.1 - - + -
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Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A THR 3.2 27.6 - - - -
225A ALA 4.3 0.2 - - - -
226A ASP* 1.3 78.9 - - - +
228A ILE* 1.3 81.4 + - + +
230A LYS* 3.9 23.9 - - - +
575B LEU* 3.6 36.0 + - + -
576B ARG* 4.0 53.4 + - + +
579B TYR* 5.9 0.2 - - - +
602B PRO* 3.4 28.1 - - + +
605B LEU* 3.7 9.0 - - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASP 5.9 0.4 - - - +
196A TYR* 3.8 43.1 - - + +
225A ALA* 2.9 7.7 + - + +
227A TYR* 1.3 117.7 - - + +
229A CYS* 1.3 62.9 + - - +
230A LYS* 3.6 2.1 + - - +
231A VAL* 5.1 3.1 + - - +
602B PRO* 4.0 13.2 - - + -
605B LEU* 4.2 8.5 - - + -
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Residues in contact with CYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ASP 3.9 12.3 - - - -
195A LEU* 4.0 2.7 - - - -
196A TYR* 3.4 34.8 - - - -
225A ALA 2.9 13.1 + - - +
226A ASP 3.8 0.2 - - - -
228A ILE* 1.3 79.3 - - - +
230A LYS* 1.3 61.4 + - - +
231A VAL* 3.2 3.4 - - - -
232A LYS* 2.9 11.2 + - + -
233A TRP* 2.8 66.7 + - + +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP* 2.9 39.8 + - - +
227A TYR* 3.9 22.2 + - - +
228A ILE 3.6 1.3 - - - +
229A CYS* 1.3 76.8 - - - +
231A VAL* 1.3 73.4 + - + +
233A TRP* 4.4 4.3 - - - +
234A GLY* 2.9 26.3 + - - +
576B ARG* 5.1 8.5 - - - +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 5.2 0.9 - - - -
228A ILE 5.8 2.7 - - - +
229A CYS 3.1 1.6 + - - -
230A LYS* 1.3 87.9 - - + +
232A LYS* 1.3 67.0 + - + +
234A GLY* 4.2 3.3 + - - -
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.7 5.2 - - - +
17A LYS* 5.7 1.9 + - - -
18A PHE* 3.4 52.1 - - + -
194A ASP* 4.3 28.3 + - - +
195A LEU* 3.8 28.0 - - + +
229A CYS* 2.9 10.2 + - + +
231A VAL* 1.3 86.0 - - + +
233A TRP* 1.3 65.9 + - + +
234A GLY* 3.5 0.3 + - - -
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Residues in contact with TRP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.3 16.6 - - + +
195A LEU* 3.0 49.7 + - + +
196A TYR* 4.3 2.9 - - + -
221A VAL* 4.1 15.4 - - + +
222A ASP 3.2 28.9 - - - -
223A ALA* 4.1 5.4 - - - -
225A ALA 3.9 1.8 - - - -
226A ASP* 3.5 46.9 - - + -
229A CYS* 2.8 39.3 + - + +
230A LYS* 4.4 1.8 - - - +
232A LYS* 1.3 73.5 - - - +
234A GLY* 1.3 69.9 + - - +
235A ASP 3.7 0.7 + - - -
236A ILE* 3.9 39.8 + - + +
238A PHE* 4.4 12.6 - + - -
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Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP* 4.8 5.7 - - - +
230A LYS* 2.9 19.4 + - - +
231A VAL 4.2 3.1 + - - -
232A LYS 3.3 3.0 + - - -
233A TRP* 1.3 84.9 - - - +
235A ASP* 1.3 58.7 + - - -
236A ILE* 2.8 11.1 + - - +
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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