Contacts of the strand formed by residues 29 - 36 (chain J) in PDB entry 1OZT
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 29 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J PHE* 4.1 20.9 - - + -
21J GLU 3.3 10.8 - - - +
22J GLN* 3.7 25.4 - - + +
27J GLY 4.5 0.2 - - - +
28J PRO* 1.3 76.8 - - - +
30J LYS* 1.3 72.0 + - - +
31J VAL* 3.8 3.3 + - + +
100J GLU* 3.5 2.8 - - - -
101J ASP 2.8 35.3 + - - +
104J ILE* 3.5 43.5 - - + +
105J SER* 3.9 7.4 - - - -
106J LEU* 4.4 7.4 - - + +
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Residues in contact with LYS 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ASN 3.5 0.3 - - - +
20J PHE* 3.1 5.5 - - - -
21J GLU* 2.7 54.4 + - + +
23J LYS* 6.2 3.4 - - + -
28J PRO 4.1 2.7 - - - +
29J VAL* 1.3 75.0 - - - +
31J VAL* 1.3 60.0 + - - +
32J TRP* 3.8 18.1 - - + -
99J ILE 3.6 7.6 - - - +
100J GLU* 3.9 26.0 - - + +
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Residues in contact with VAL 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ILE* 3.8 18.4 - - + -
19J ASN 3.0 7.6 - - - +
20J PHE* 3.9 21.5 - - + -
29J VAL 3.9 10.8 - - - +
30J LYS* 1.3 77.7 - - - +
32J TRP* 1.3 62.7 + - - +
45J PHE* 4.1 14.4 - - + -
84J LEU* 5.2 4.5 - - + -
97J VAL* 4.1 13.7 - - + -
98J SER* 3.5 0.9 + - - -
99J ILE* 2.8 50.0 + - + +
101J ASP* 5.0 1.6 - - + +
104J ILE* 4.5 13.0 - - + -
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Residues in contact with TRP 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LYS* 5.0 9.6 - - - -
18J ILE* 4.4 5.6 - - - -
19J ASN* 2.7 80.2 + - + +
20J PHE 4.6 2.2 - - - -
21J GLU* 3.6 43.3 - - + -
30J LYS* 3.8 23.6 - - + -
31J VAL* 1.3 78.2 - - - +
33J GLY* 1.3 61.7 + - - +
97J VAL* 3.1 17.9 - - - +
98J SER* 4.1 9.0 - - - +
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Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ILE 3.3 12.3 - - - -
18J ILE* 4.2 2.0 - - - -
19J ASN* 4.2 4.7 - - - -
32J TRP* 1.3 84.2 - - - +
34J SER* 1.3 62.4 + - - -
96J ASP* 3.8 3.1 - - - +
97J VAL* 2.7 32.4 + - - +
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Residues in contact with SER 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLY* 3.2 3.1 - - - -
17J ILE 3.2 28.0 + - - +
18J ILE* 4.1 0.2 - - - +
33J GLY* 1.3 76.6 - - - -
35J ILE* 1.3 68.1 + - - +
36J LYS* 6.1 0.3 - - - +
94J VAL* 4.8 8.4 - - - +
95J ALA 3.1 14.8 - - - -
96J ASP* 3.9 15.7 - - - -
97J VAL* 4.3 1.3 - - - +
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Residues in contact with ILE 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LEU* 4.9 7.4 - - + -
14J VAL* 3.7 22.4 - - + -
15J GLN 3.5 10.5 - - - +
16J GLY* 4.0 4.9 - - - +
18J ILE* 4.2 12.6 - - + -
34J SER* 1.3 81.3 - - - +
36J LYS* 1.3 62.1 + - - +
38J LEU* 3.4 22.1 - - + +
45J PHE* 4.1 24.5 - - + -
87J VAL* 4.4 7.9 - - + -
93J GLY 3.8 1.2 - - - +
94J VAL* 3.4 4.1 - - - +
95J ALA* 2.7 37.6 + - + +
97J VAL* 4.4 13.7 - - + -
119J VAL* 4.4 20.9 - - + -
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Residues in contact with LYS 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J PRO 3.6 1.1 - - - +
14J VAL* 3.2 6.6 - - - +
15J GLN* 2.8 68.3 + - + +
34J SER* 6.1 0.4 - - - +
35J ILE* 1.3 75.5 - - - +
37J GLY* 1.3 64.4 + - - +
38J LEU 3.2 3.7 + - - -
93J GLY 3.4 5.4 - - - -
94J VAL* 4.0 19.1 - - + +
92K ASP* 4.1 25.9 + - - +
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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