Contacts of the helix formed by residues 227 - 232 (chain A) in PDB entry 3N4U
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 ASP 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASP* 3.1 14.6 + - - +
226A PRO* 1.3 81.1 - - - +
228A ASN* 1.3 62.1 + - - +
229A ASP 3.2 0.4 - - - -
230A PHE* 3.2 13.3 + - - +
231A ILE* 3.2 27.7 + - + +
254A HIS* 2.6 30.8 + - - -
259A THR* 4.3 5.4 - - - +
260A VAL* 3.5 21.8 - - + +
263A LYS* 2.8 38.8 + - + +
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Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 4.0 11.9 - - + +
196A ASN* 4.8 9.2 + - - +
224A SER* 3.9 16.6 + - - -
225A ASP* 3.4 30.4 + - - +
226A PRO 3.0 1.2 - - - -
227A ASP* 1.3 79.3 - - - +
229A ASP* 1.3 58.4 + - - +
231A ILE* 3.9 15.3 - - - +
232A SER* 2.8 28.1 + - - -
263A LYS* 5.1 2.6 - - - +
267A LYS* 4.0 24.2 + - - +
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.8 19.8 - - + +
130A LEU* 3.9 0.5 - - - +
131A HIS* 3.0 26.9 + - + +
194A ILE* 3.4 7.8 - - - +
195A HIS* 3.0 21.2 + - - -
196A ASN* 2.9 28.9 + - - -
198A PHE* 3.2 34.2 - - + +
226A PRO 3.1 11.5 + - - +
228A ASN* 1.3 77.7 - - - +
230A PHE* 1.3 59.7 + - - +
232A SER* 3.4 8.7 + - - -
233A LEU* 3.3 8.5 - - - +
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Residues in contact with PHE 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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127A LEU* 3.8 12.3 - - + -
131A HIS* 4.3 4.5 - + - -
226A PRO* 3.6 21.8 - - + -
227A ASP* 3.2 13.6 + - - +
229A ASP* 1.3 78.6 - - - +
231A ILE* 1.3 60.1 + - - +
232A SER 3.2 2.2 - - - -
233A LEU* 3.0 28.0 + - + +
234A MET* 3.6 22.2 - - + +
245A VAL* 4.0 5.5 - - + +
248A ILE* 3.7 32.1 - - + -
249A LEU* 3.4 31.9 - - + -
252A TYR* 3.4 55.9 - + + -
254A HIS* 4.2 7.6 - + - -
260A VAL* 4.4 3.8 - - + -
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Residues in contact with ILE 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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227A ASP* 3.2 27.1 + - + +
228A ASN* 4.1 14.8 - - - +
230A PHE* 1.3 73.5 - - - +
232A SER* 1.3 57.2 + - - +
233A LEU 3.0 9.7 + - - -
234A MET* 3.3 20.6 + - - +
235A GLU* 4.5 1.4 + - - +
260A VAL* 3.9 20.6 - - + +
263A LYS* 3.5 33.0 - - + -
264A TYR* 3.6 35.2 - - + +
267A LYS* 4.2 20.0 - - + -
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Residues in contact with SER 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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196A ASN 5.8 1.1 - - - -
197A ASP* 4.7 4.9 - - - -
198A PHE 2.8 40.8 + - - +
199A SER* 3.6 15.7 - - - -
228A ASN 2.8 19.0 + - - -
229A ASP* 3.4 8.8 + - - -
231A ILE* 1.3 77.3 - - - +
233A LEU* 1.3 57.2 + - - +
235A GLU 5.4 0.2 - - - -
239A GLU* 3.6 12.0 - - - +
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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