Contacts of the strand formed by residues 228 - 233 (chain O) in PDB entry 3HOU
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 PHE 228 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21O ILE* 3.6 4.1 - - - +
22O LEU* 2.7 43.4 + - + +
25O VAL* 3.7 19.3 - - + -
27O LEU* 3.5 35.9 - - + -
30O ALA* 3.7 19.1 - - + -
178O PHE* 4.0 16.4 - + + -
179O GLU 3.6 5.8 - - - +
180O TYR* 3.5 28.9 - + + -
225O ALA* 3.2 26.0 - - + -
226O ASP* 3.6 17.7 - - - -
227O THR* 1.3 75.6 - - - +
229O TYR* 1.3 61.4 + - - +
230O MET* 3.3 23.8 + - + -
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Residues in contact with TYR 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ARG* 3.7 7.9 - - - +
20O PHE 3.9 5.6 - - - -
21O ILE* 3.6 31.4 - - + -
177O GLU* 4.2 2.6 - - - +
178O PHE* 3.7 4.2 + - - -
179O GLU* 3.3 37.3 + - + +
180O TYR* 4.4 2.2 - - - -
182O PRO* 4.1 10.5 - - + -
206O ASN* 2.8 48.4 + - + +
209O TYR* 3.9 20.2 + - + -
210O GLU* 3.0 37.6 + - - +
227O THR* 3.3 33.6 - - + +
228O PHE* 1.3 69.1 - - - +
230O MET* 1.3 63.1 + - - +
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Residues in contact with MET 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O ASP* 3.6 5.4 - - - +
20O PHE* 3.1 57.7 + - + +
22O LEU* 3.3 46.2 - - + -
30O ALA* 4.4 15.0 - - + +
33O LEU* 4.7 5.4 - - + -
34O ARG* 5.1 1.3 - - - -
37O MET* 4.3 20.6 - - - -
176O ILE* 5.1 1.1 - - - -
177O GLU* 3.3 15.3 - - - +
178O PHE* 3.7 24.7 - - + -
228O PHE* 3.3 10.5 + - + +
229O TYR* 1.3 77.8 - - - +
231O ASN* 1.3 64.5 + - - +
232O VAL* 5.2 0.7 - - + -
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Residues in contact with ASN 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ASN* 3.5 34.1 + - - +
18O VAL 3.5 4.7 + - - -
19O ASP* 3.4 29.8 + - + +
175O ALA 4.8 0.2 - - - -
176O ILE* 3.5 5.6 - - - -
177O GLU* 3.0 58.1 + - + +
230O MET* 1.3 78.3 - - - +
232O VAL* 1.3 60.2 + - - +
233O GLU* 3.6 7.6 + - - +
43V ARG* 5.7 1.4 - - - +
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Residues in contact with VAL 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O ASP 3.7 0.5 - - - +
17O ASN* 3.4 3.8 - - - -
18O VAL* 3.2 27.9 + - + +
20O PHE* 3.8 23.3 - - + -
37O MET* 3.4 36.6 - - + -
173O ALA* 5.2 0.4 - - + -
176O ILE* 4.3 13.2 - - + -
230O MET* 5.2 0.9 - - + -
231O ASN* 1.3 75.7 + - - +
233O GLU* 1.3 64.5 + - - +
240O VAL* 4.0 6.7 - - - +
243O VAL* 3.5 34.8 - - + -
244O VAL* 3.9 13.0 - - + -
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Residues in contact with GLU 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O ASP* 3.2 10.0 - - + +
17O ASN* 3.3 25.4 - - - +
173O ALA* 2.8 18.7 - - - +
174O ALA* 4.0 15.6 - - + +
175O ALA* 3.9 8.4 + - + +
231O ASN* 3.6 9.2 + - - +
232O VAL* 1.3 84.5 - - - +
234O SER* 1.3 73.4 + - - +
240O VAL* 4.4 0.2 - - - -
243O VAL* 4.7 0.3 - - - +
12V LYS* 3.0 39.9 + - - +
43V ARG* 2.6 33.8 + - - +
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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