Contacts of the strand formed by residues 83 - 89 (chain N) 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 ASP 83 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46N ARG* 3.3 12.1 - - - -
63N HIS* 3.2 22.0 + - - -
71N HIS* 2.9 32.9 + - + -
72N GLY 3.4 15.9 + - - +
73N GLY* 5.1 2.2 - - - -
74N PRO* 4.0 4.0 - - - +
79N ARG* 3.3 28.5 + - + -
80N HIS* 3.1 38.1 + - - +
81N VAL 3.3 0.2 + - - -
82N GLY* 1.3 75.2 - - - +
84N LEU* 1.3 58.1 + - - +
85N GLY* 3.3 6.4 + - - +
124N ASP* 5.0 2.0 - - - +
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Residues in contact with LEU 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N PHE* 5.0 6.5 - - + -
31N VAL* 5.1 5.4 - - + -
45N PHE* 3.1 44.7 + - + +
47N VAL* 4.1 22.0 - - + +
74N PRO* 3.3 13.5 - - - +
79N ARG* 4.3 0.4 - - - +
82N GLY 3.2 7.8 + - - +
83N ASP* 1.3 75.0 - - - +
85N GLY* 1.3 60.0 + - - +
86N ASN 3.6 2.8 + - - +
99N ILE* 4.0 25.7 - - + +
101N ASP* 3.7 33.0 - - + +
104N ILE* 4.0 28.5 - - + -
117N LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N GLY* 3.6 3.1 - - - -
45N PHE* 3.0 21.8 + - - +
74N PRO* 3.0 29.3 - - - +
83N ASP* 3.3 4.0 - - - +
84N LEU* 1.3 77.1 - - - +
86N ASN* 1.3 67.0 + - - +
124N ASP* 3.7 10.8 + - - +
126N LEU* 4.3 7.6 - - - -
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Residues in contact with ASN 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N LEU* 3.9 31.2 - - + +
43N HIS 3.1 8.7 - - - +
44N GLY 3.3 10.0 + - - -
45N PHE* 4.3 1.6 - - - -
84N LEU 3.6 4.4 + - - +
85N GLY* 1.3 73.7 - - - -
87N VAL* 1.3 67.9 + - - +
88N THR* 5.3 0.4 - - - -
99N ILE* 4.6 6.8 - - - +
123N ALA* 3.4 1.9 - - - -
124N ASP* 2.5 50.7 + - - +
126N LEU* 3.7 17.6 - - - +
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Residues in contact with VAL 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N ILE* 4.4 5.8 - - + -
38N LEU* 4.7 2.5 - - + -
41N GLY 3.6 0.9 - - - +
42N LEU* 3.5 2.1 - - - -
43N HIS* 2.9 50.0 + - + +
45N PHE* 3.5 35.7 - - + -
86N ASN* 1.3 75.5 - - - +
88N THR* 1.3 62.0 + - - +
95N ALA* 4.4 13.2 - - + -
96N ASP 6.0 0.4 - - - -
97N VAL* 3.6 33.7 - - + -
99N ILE* 4.8 2.0 - - + -
119N VAL* 4.0 16.2 - - + -
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Residues in contact with THR 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N GLY* 3.3 11.9 - - - +
42N LEU* 3.1 27.1 - - + +
86N ASN 5.3 0.9 + - - -
87N VAL* 1.3 74.6 - - - +
89N ALA* 1.3 70.1 + - - +
90N ASP* 3.9 1.0 + - - -
94N VAL 3.9 0.5 - - - +
95N ALA* 3.2 20.5 - - - +
96N ASP 4.1 7.1 + - - +
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Residues in contact with ALA 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N LEU* 3.7 23.1 - - + -
39N THR 3.4 23.8 - - - +
40N GLU* 3.3 2.4 - - - +
41N GLY* 2.7 35.6 + - - +
43N HIS* 4.3 0.6 - - + -
87N VAL 4.2 0.4 + - - -
88N THR* 1.3 76.9 - - - +
90N ASP* 1.3 65.2 + - - +
93N GLY 4.1 8.7 - - - -
94N VAL 3.3 11.0 - - - +
95N ALA* 3.9 4.2 - - + +
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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