Contacts of the strand formed by residues 83 - 89 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I ARG* 3.1 32.3 + - - +
63I HIS* 3.5 13.8 + - - -
79I ARG* 3.0 36.7 + - + +
80I HIS* 3.1 39.4 + - - +
81I VAL 3.3 0.2 - - - -
82I GLY* 1.3 74.4 - - - +
84I LEU* 1.3 58.0 + - - +
85I GLY* 3.3 7.3 + - - +
124I ASP* 4.8 7.4 - - - +
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Residues in contact with LEU 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I PHE* 5.0 7.2 - - + -
31I VAL* 5.2 5.2 - - + -
45I PHE* 3.0 42.9 + - + +
47I VAL* 4.0 21.8 - - + -
79I ARG* 4.1 1.6 - - - +
82I GLY 3.1 8.7 + - - +
83I ASP* 1.3 75.5 - - - +
85I GLY* 1.3 59.6 + - - +
86I ASN 3.8 2.1 + - - +
99I ILE* 3.9 24.6 - - + +
101I ASP* 3.6 34.1 - - + +
104I ILE* 3.9 28.9 - - + -
117I LEU* 4.4 7.6 - - + -
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Residues in contact with GLY 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLY* 3.6 4.9 - - - -
45I PHE* 2.9 23.0 + - - +
46I ARG* 5.1 1.4 - - - +
83I ASP* 3.3 7.2 + - - +
84I LEU* 1.3 78.4 - - - +
86I ASN* 1.3 66.0 + - - -
124I ASP* 4.0 8.1 + - - +
126I LEU* 3.7 24.7 - - - -
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Residues in contact with ASN 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I LEU* 3.9 32.8 - - + +
43I HIS 3.0 8.4 - - - +
44I GLY 3.3 12.5 + - - -
45I PHE* 4.2 1.3 - - - +
84I LEU 3.8 4.6 + - - +
85I GLY* 1.3 77.4 - - - -
87I VAL* 1.3 67.8 + - - +
88I THR* 5.3 1.1 + - - -
99I ILE* 4.7 7.1 - - - +
123I ALA* 3.3 2.8 - - - -
124I ASP* 2.6 49.7 + - - +
126I LEU* 3.9 13.9 - - - +
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Residues in contact with VAL 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ILE* 4.4 5.4 - - + -
38I LEU* 4.8 2.5 - - + -
41I GLY 3.5 1.4 - - - +
42I LEU* 3.5 2.1 - - - -
43I HIS* 2.8 50.7 + - + +
45I PHE* 3.5 35.2 - - + -
86I ASN* 1.3 76.2 - - - +
88I THR* 1.3 62.6 + - - +
89I ALA 4.1 0.2 + - - -
95I ALA* 4.4 12.3 - - + -
96I ASP 6.0 0.2 - - - -
97I VAL* 3.6 33.9 - - + -
99I ILE* 4.9 1.6 - - + -
119I VAL* 4.2 15.0 - - + -
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Residues in contact with THR 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I GLY* 3.3 12.1 - - - +
42I LEU* 3.1 24.9 - - + +
86I ASN* 5.3 1.0 + - - +
87I VAL* 1.3 75.6 - - - +
89I ALA* 1.3 69.9 + - - +
90I ASP* 3.9 1.0 + - - -
94I VAL 3.8 0.9 - - - +
95I ALA* 3.2 21.1 - - - +
96I ASP 4.1 7.7 + - - +
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Residues in contact with ALA 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I LEU* 3.6 27.4 - - + -
39I THR 3.3 24.2 - - - +
40I GLU* 3.4 2.9 - - - +
41I GLY* 2.7 36.0 + - - +
43I HIS* 4.3 1.1 - - + -
87I VAL 4.1 0.6 + - - -
88I THR* 1.3 77.9 - - - +
90I ASP* 1.3 64.3 + - - +
93I GLY 4.1 8.3 - - - -
94I VAL 3.3 10.8 - - - +
95I ALA* 4.0 0.4 - - - +
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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