Contacts of the strand formed by residues 56 - 62 (chain O) in PDB entry 2ZJR
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 VAL 56 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O LYS* 4.9 11.0 - - - +
11O GLN 4.5 12.3 - - - +
12O TYR 6.4 0.4 - - - -
13O ARG* 5.6 2.9 - - - +
32O LYS 3.6 0.2 - - - +
33O VAL* 3.0 8.7 - - - +
34O GLU* 2.8 65.4 + - + +
35O LEU 4.2 3.1 - - - +
36O LYS* 3.9 16.6 - - + +
55O THR* 1.3 83.0 + - - +
57O GLN* 1.3 63.8 + - - +
58O ALA* 4.1 1.3 - - + +
95O ILE* 5.0 16.2 - - + -
97O GLY* 3.4 9.0 - - - +
98O ILE 4.0 7.4 - - - +
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Residues in contact with GLN 57 (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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31O ASP* 6.2 3.6 - - + -
32O LYS 3.0 8.3 - - - +
33O VAL* 4.8 11.2 - - + -
55O THR* 4.7 4.5 + - - +
56O VAL* 1.3 76.0 - - - +
58O ALA* 1.3 60.8 + - - +
59O GLU* 5.9 0.4 - - - +
96O LEU* 2.9 16.7 + - + +
97O GLY* 2.6 34.6 + - - +
98O ILE* 3.2 41.6 - - - +
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Residues in contact with ALA 58 (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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31O ASP* 4.7 0.2 - - - -
32O LYS* 2.5 53.3 + - + +
34O GLU* 5.7 1.1 - - + +
56O VAL* 4.1 2.8 - - + -
57O GLN* 1.3 75.2 - - - +
59O GLU* 1.3 58.5 + - - +
93O ILE* 3.6 25.6 - - + -
94O LYS 3.1 15.7 - - - +
95O ILE* 3.6 18.6 - - + -
96O LEU* 4.8 0.4 - - - -
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Residues in contact with GLU 59 (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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29O ALA* 3.1 32.5 + - - +
30O GLY 3.8 3.4 - - - -
31O ASP* 2.3 33.5 - - + +
57O GLN 5.9 0.7 - - - +
58O ALA* 1.3 76.4 - - - +
60O VAL* 1.3 64.6 + - - +
61O VAL* 3.0 3.1 + - - +
93O ILE* 3.3 2.6 - - - -
94O LYS* 2.8 43.6 + - + +
96O LEU* 5.5 11.4 - - + -
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Residues in contact with VAL 60 (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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23O GLU* 4.8 1.1 - - + -
25O LEU 3.8 10.3 - - - +
26O GLN 4.7 0.2 - - - +
27O GLY 3.8 16.8 - - - +
28O GLU* 3.2 28.7 - - - +
29O ALA 3.3 5.0 + - - -
30O GLY* 3.5 12.1 + - - +
32O LYS* 3.2 39.5 - - + +
58O ALA 4.1 0.4 + - - -
59O GLU* 1.3 70.9 - - - +
61O VAL* 1.3 57.5 + - - +
62O GLU 4.3 4.9 - - - +
63O HIS* 4.0 10.8 - - + -
91O THR* 3.6 25.1 - - + -
92O ALA 3.4 4.9 - - - +
93O ILE* 4.0 9.2 - - + -
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Residues in contact with VAL 61 (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* 5.4 4.3 - - - -
27O GLY 5.3 0.2 - - - -
28O GLU* 4.2 14.8 - - - +
59O GLU* 3.5 2.7 - - + +
60O VAL* 1.3 75.9 - - - +
62O GLU* 1.3 66.9 + - + +
92O ALA* 2.5 28.0 + - + +
93O ILE 3.8 1.8 - - - -
94O LYS* 3.2 39.9 - - + +
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Residues in contact with GLU 62 (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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27O GLY 5.5 2.5 - - - -
60O VAL* 3.8 2.6 - - - -
61O VAL* 1.3 90.5 - - + +
63O HIS* 1.3 87.1 + - - +
64O GLY* 4.2 0.6 + - - -
90O PHE* 4.7 2.5 - - + -
91O THR* 3.2 5.0 - - - +
92O ALA* 2.5 38.7 + - + +
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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