Contacts of the strand formed by residues 19 - 23 (chain O) in PDB entry 2A3W
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 HIS 19 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11O PHE* 4.1 4.0 - - - -
17O THR 2.7 23.3 + - - -
18O ASP* 1.3 74.8 - - - +
20O VAL* 1.3 68.3 + - - +
21O ASN* 3.2 31.1 + - - -
132O VAL* 3.8 7.2 - - + -
133O LEU 3.3 13.5 - - - +
135O GLN* 3.7 11.9 - - + -
141O GLY 5.0 2.8 + - - -
144O PHE* 3.5 31.8 - + - -
193O ARG* 2.9 60.9 + - + +
196O VAL* 3.9 3.9 - - - +
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Residues in contact with VAL 20 (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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9O PHE* 3.8 19.1 - - + -
11O PHE* 3.7 23.1 - - + -
19O HIS* 1.3 80.2 - - - +
21O ASN* 1.3 75.9 + - - +
22O LEU* 3.8 11.5 + - + +
132O VAL* 3.1 5.5 - - - -
133O LEU* 2.9 40.0 + - + +
190O TYR* 3.7 20.6 - - + -
191O GLU 3.4 9.0 - - - +
192O ILE* 4.3 6.7 - - + -
196O VAL* 3.7 18.4 - - + -
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Residues in contact with ASN 21 (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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19O HIS* 3.2 32.0 + - - -
20O VAL* 1.3 72.2 - - - +
22O LEU* 1.3 62.5 + - - +
23O ILE* 4.1 3.7 + - + +
130O LYS* 5.5 8.7 - - + +
131O ILE 3.4 4.9 - - - +
132O VAL* 4.0 11.6 - - - +
141O GLY* 5.3 2.9 - - - +
190O TYR* 3.1 9.5 - - - +
191O GLU* 2.9 65.9 + - + +
193O ARG* 4.2 10.7 - - - +
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Residues in contact with LEU 22 (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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9O PHE* 4.8 0.4 - - + -
20O VAL* 3.8 24.5 - - + +
21O ASN* 1.3 78.7 - - - +
23O ILE* 1.3 63.2 + - - +
24O THR* 4.1 1.6 + - - +
50O PHE* 4.2 1.1 - - + -
129O PRO 5.4 1.7 - - - +
131O ILE* 2.7 45.0 + - + +
133O LEU* 3.9 37.9 - - + -
157O LEU* 4.2 14.6 - - + -
183O LEU* 3.7 36.1 - - + -
188O LEU* 4.6 21.5 - - + -
189O ASN 3.8 2.2 - - - -
190O TYR* 4.8 0.4 - - + -
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Residues in contact with ILE 23 (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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21O ASN* 4.5 3.6 - - + +
22O LEU* 1.3 76.1 - - - +
24O THR* 1.3 69.6 + - - +
25O PRO* 5.9 0.2 - - + -
182O ILE 4.8 0.5 - - - +
183O LEU* 4.1 8.0 - - - +
189O ASN* 2.8 65.2 + - + +
190O TYR* 4.1 3.8 - - - +
191O GLU* 3.8 39.5 - - + +
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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