Contacts of the helix formed by residues 225 - 234 (chain A) in PDB entry 3UVH
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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 4.4 20.9 + - - +
21A ILE* 5.0 1.0 + - - +
223A CYS 3.6 3.1 + - - +
224A PRO* 1.3 78.0 - - - +
226A ASP* 1.3 66.2 + - - +
227A GLU* 3.7 18.2 - - + +
228A GLU* 3.2 21.9 + - + +
229A ILE* 3.3 10.4 + - - +
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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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185A HIS* 4.1 11.4 - - - -
189A VAL* 3.5 32.7 - - + +
224A PRO 3.7 0.4 + - - +
225A ASP* 1.3 71.8 - - - +
227A GLU* 1.3 71.8 + - - +
229A ILE* 2.9 5.7 + - - +
230A GLU* 2.8 47.4 + - - +
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Residues in contact with GLU 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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20A LYS* 6.0 3.6 - - - +
225A ASP* 3.2 13.5 - - + +
226A ASP* 1.3 95.4 + - - +
228A GLU* 1.3 57.2 + - - +
230A GLU* 3.7 13.7 - - - +
231A LEU* 3.0 28.9 + - - +
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Residues in contact with GLU 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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15A GLY* 3.4 6.2 - - - -
16A SER* 2.4 52.0 + - - -
20A LYS* 3.3 35.7 + - + +
21A ILE 3.6 15.9 - - - +
22A GLY* 4.7 1.8 - - - -
23A ASN* 4.6 6.6 + - - +
224A PRO* 4.5 7.6 - - + -
225A ASP* 3.2 15.9 + - + +
226A ASP 3.1 0.8 - - - -
227A GLU* 1.3 78.3 - - - +
229A ILE* 1.3 60.1 + - - +
231A LEU* 3.4 9.6 + - - +
232A ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 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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23A ASN* 3.7 21.8 - - - +
185A HIS* 3.3 40.4 - - + +
186A ILE* 4.2 17.0 - - + -
189A VAL* 3.6 20.9 - - + -
190A VAL* 3.6 25.6 - - + -
224A PRO* 3.9 24.7 - - + +
225A ASP 3.3 5.1 + - - +
226A ASP 2.9 7.2 + - - +
228A GLU* 1.3 77.6 - - - +
230A GLU* 1.3 63.0 + - - +
232A ALA* 3.2 16.7 + - - +
233A TYR* 3.3 15.3 + - + +
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Residues in contact with GLU 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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189A VAL* 3.7 20.8 - - + +
190A VAL* 5.3 0.9 - - - -
193A LYS* 3.4 47.1 + - + +
194A TYR* 2.5 35.8 + - + +
226A ASP* 2.8 30.3 + - - +
227A GLU* 3.7 14.7 - - - +
229A ILE* 1.3 75.7 - - - +
231A LEU* 1.3 61.1 + - - +
233A TYR 3.3 2.1 + - - -
234A GLU 3.3 6.1 + - - -
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Residues in contact with LEU 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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16A SER* 3.4 37.2 - - - +
227A GLU 3.0 18.1 + - - +
228A GLU* 3.5 13.7 - - - +
229A ILE 3.3 0.2 - - - -
230A GLU* 1.3 73.2 - - - +
232A ALA* 1.3 66.3 + - - +
233A TYR 3.0 1.2 + - - -
234A GLU* 3.0 43.0 + - - +
235A GLN 4.8 0.3 + - - -
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Residues in contact with ALA 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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23A ASN* 3.7 32.1 - - + +
228A GLU* 2.9 18.0 + - - +
229A ILE 3.2 6.5 + - - +
231A LEU* 1.3 76.7 - - - +
233A TYR* 1.3 63.3 + - + +
234A GLU 3.8 0.2 + - - -
235A GLN 5.0 1.7 + - - -
236A VAL* 5.0 6.2 - - - +
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Residues in contact with TYR 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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23A ASN* 3.9 20.9 + - - -
111A PHE* 3.6 27.4 - - - -
114A PHE* 3.8 16.5 - + - -
115A SER* 5.2 3.0 + - - -
118A ILE* 3.9 17.0 - - + -
119A LYS* 6.0 0.7 - - - -
186A ILE* 3.7 21.1 - - + +
190A VAL* 3.5 31.9 - - + -
194A TYR* 4.0 9.0 - - + -
229A ILE* 3.3 14.7 + - + +
230A GLU 3.3 0.9 + - - -
231A LEU 3.1 0.4 - - - -
232A ALA* 1.3 81.5 - - + +
234A GLU* 1.3 58.4 + - - +
235A GLN 3.3 2.7 - - - -
236A VAL* 2.9 26.6 + - + -
237A ALA* 2.8 32.9 + - + +
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Residues in contact with GLU 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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194A TYR* 3.4 23.8 - - + +
230A GLU 3.3 3.9 + - - +
231A LEU* 3.0 37.8 + - - +
232A ALA 3.4 0.2 - - - -
233A TYR* 1.3 77.3 - - - +
235A GLN* 1.3 83.6 + - + +
236A VAL 3.8 0.2 + - - -
237A ALA 4.2 8.7 - - - +
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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