Contacts of the strand formed by residues 83 - 89 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46L ARG* 3.3 29.8 + - - -
63L HIS* 3.5 11.8 + - - -
79L ARG* 3.1 32.4 + - + +
80L HIS* 3.1 38.6 + - - +
81L VAL 3.3 0.4 - - - -
82L GLY* 1.3 74.2 - - - +
84L LEU* 1.3 59.8 + - - +
85L GLY* 3.3 6.6 + - - +
124L ASP* 4.7 6.1 - - - +
126L LEU 4.0 17.2 - - - +
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Residues in contact with LEU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L PHE* 5.0 7.4 - - + -
31L VAL* 5.1 5.6 - - + -
45L PHE* 3.1 44.4 + - + +
47L VAL* 4.1 20.9 - - + +
79L ARG* 4.3 2.0 - - - +
81L VAL 4.7 0.2 - - - +
82L GLY 3.2 8.0 + - - +
83L ASP* 1.3 76.6 - - - +
85L GLY* 1.3 60.5 + - - +
86L ASN 3.7 2.3 + - - +
99L ILE* 3.9 24.5 - - + +
101L ASP* 3.7 32.5 - - + +
104L ILE* 3.9 28.0 - - + -
117L LEU* 4.5 7.0 - - + -
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Residues in contact with GLY 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L GLY* 3.6 0.2 - - - -
45L PHE* 2.9 21.4 + - - +
83L ASP* 3.3 5.8 + - - +
84L LEU* 1.3 77.1 - - - +
86L ASN* 1.3 70.2 + - - -
124L ASP* 3.1 20.1 + - - +
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Residues in contact with ASN 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L LEU* 3.9 34.9 - - + +
43L HIS 3.1 7.6 - - - +
44L GLY 3.4 6.1 + - - -
45L PHE* 4.2 2.5 - - - +
84L LEU 3.7 4.9 + - - +
85L GLY* 1.3 75.6 - - - -
87L VAL* 1.3 68.9 + - - +
88L THR* 5.3 0.7 - - - -
99L ILE* 4.6 6.9 - - - +
123L ALA* 3.4 7.2 - - - +
124L ASP* 2.5 42.8 + - - +
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Residues in contact with VAL 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L ILE* 4.3 8.5 - - + -
38L LEU* 4.7 2.7 - - + -
41L GLY 3.6 1.2 - - - +
42L LEU* 3.5 2.3 - - - -
43L HIS* 2.8 50.2 + - + +
45L PHE* 3.5 35.0 - - + -
86L ASN* 1.3 76.3 - - - +
88L THR* 1.3 61.7 + - - +
89L ALA 4.1 0.2 + - - -
95L ALA* 4.3 9.4 - - + -
97L VAL* 3.5 35.0 - - + -
99L ILE* 4.9 0.9 - - + -
119L VAL* 4.1 15.0 - - + -
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Residues in contact with THR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L GLY* 3.3 9.0 - - - +
42L LEU* 3.1 27.7 - - + +
86L ASN 5.3 0.7 - - - -
87L VAL* 1.3 75.2 - - - +
89L ALA* 1.3 70.9 + - - +
90L ASP* 3.9 0.9 + - - -
94L VAL 3.8 0.7 - - - +
95L ALA* 3.2 19.9 - - - +
96L ASP 4.2 7.0 + - - +
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Residues in contact with ALA 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L LEU* 3.6 25.1 - - + -
39L THR 3.3 24.5 - - - +
40L GLU* 3.5 2.8 - - - +
41L GLY* 2.7 35.8 + - - +
43L HIS* 4.7 0.4 - - - -
87L VAL 4.1 0.6 + - - -
88L THR* 1.3 78.6 - - - +
90L ASP* 1.3 67.3 + - - +
93L GLY 4.1 6.1 - - - -
94L VAL 3.3 11.0 - - - +
95L ALA* 3.9 2.2 - - + -
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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