Contacts of the strand formed by residues 89 - 95 (chain O) in PDB entry 2ZJP
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 ASN 89 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21O ARG* 4.5 4.5 - - - -
22O VAL* 3.9 21.1 + - + +
64O GLY 3.1 13.9 - - - +
65O ARG* 2.9 42.0 + - - +
87O ARG 4.0 2.0 + - - +
88O GLN* 1.3 93.2 - - - +
90O PHE* 1.3 67.5 + - - +
1173X G 4.7 4.0 + - - +
1174X G 4.1 29.3 + - - -
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Residues in contact with PHE 90 (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 VAL* 3.2 37.9 - - + -
20O ILE 2.9 17.9 - - - +
22O VAL* 3.7 12.4 - - - +
62O GLU* 4.6 6.7 - - - -
63O HIS* 3.5 7.0 + - - +
64O GLY* 2.9 45.7 + - - +
65O ARG 3.7 20.9 - - - -
66O GLY* 4.2 9.9 - - - -
88O GLN 4.6 0.9 - - - -
89O ASN* 1.3 79.6 - - - +
91O THR* 1.3 85.6 + - - +
92O ALA* 4.0 8.1 - - + -
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Residues in contact with THR 91 (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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20O ILE* 3.0 19.2 + - - +
21O ARG 3.7 11.9 - - - -
22O VAL* 3.3 14.0 - - - -
23O GLU* 3.3 14.1 + - + -
60O VAL* 3.8 16.6 - - + -
62O GLU 3.4 5.6 - - - -
63O HIS* 2.7 36.8 + - + -
90O PHE* 1.3 83.1 + - - +
92O ALA* 1.3 63.9 + - - +
93O ILE* 3.1 24.3 + - + +
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Residues in contact with ALA 92 (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 GLY 5.1 2.5 - - - +
18O ASP 3.5 13.7 - - - +
19O VAL* 4.3 11.2 - - + -
60O VAL* 3.3 2.4 - - - +
61O VAL* 2.4 50.8 + - + -
62O GLU* 2.6 24.1 + - + +
90O PHE* 4.0 7.8 - - + -
91O THR* 1.3 72.7 - - - +
93O ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 93 (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 GLU 3.8 3.6 - - - +
17O GLY* 3.8 6.3 - - - -
18O ASP* 3.3 26.4 + - - +
20O ILE* 4.1 12.1 - - + -
23O GLU* 4.9 9.6 - - + -
32O LYS* 5.1 5.8 - - + -
58O ALA* 3.3 13.0 - - + +
59O GLU 3.5 10.3 - - - +
60O VAL* 3.9 12.1 - - + +
61O VAL* 3.6 1.1 - - - +
91O THR* 3.1 24.7 - - + +
92O ALA* 1.3 82.8 - - - +
94O LYS* 1.3 63.8 + - - +
95O ILE* 3.1 32.2 + - + +
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Residues in contact with LYS 94 (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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15O SER* 4.2 15.3 - - - +
16O GLU 3.4 11.2 - - - +
17O GLY* 3.6 7.4 - - - -
58O ALA* 2.9 3.9 - - - -
59O GLU* 2.8 35.4 + - + +
61O VAL* 2.8 23.7 - - + +
93O ILE* 1.3 68.5 - - - +
95O ILE* 1.3 70.4 + - - +
96O LEU* 4.6 11.0 - - + +
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Residues in contact with ILE 95 (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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13O ARG* 3.3 38.4 - - + +
15O SER* 2.9 34.0 - - - +
16O GLU 2.5 21.4 + - - +
18O ASP* 4.0 10.8 - - - +
56O VAL* 5.4 14.1 - - + -
57O GLN 4.8 0.2 - - - +
58O ALA* 3.3 9.2 - - + -
93O ILE* 3.1 34.3 - - + +
94O LYS* 1.3 79.4 - - - +
96O LEU* 1.3 73.8 + - - +
97O GLY 4.2 6.7 - - - +
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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