Contacts of the strand formed by residues 83 - 89 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H ARG* 3.2 30.3 + - - -
63H HIS* 4.0 10.0 - - - -
79H ARG* 2.5 36.1 + - + +
80H HIS* 2.8 50.8 + - - +
81H VAL 3.3 0.2 - - - -
82H GLY* 1.3 71.2 - - - +
84H LEU* 1.3 56.9 + - - +
85H GLY 3.3 6.5 + - - +
124H ASP* 4.6 8.7 - - - +
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Residues in contact with LEU 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H PHE* 5.0 7.2 - - + -
31H VAL* 5.1 5.6 - - + -
45H PHE* 3.1 44.5 + - + +
47H VAL* 4.1 21.8 - - + -
79H ARG* 4.1 0.7 - - - +
82H GLY 3.1 7.8 + - - +
83H ASP* 1.3 75.8 - - - +
85H GLY* 1.3 59.6 + - - +
86H ASN 3.8 1.9 + - - +
99H ILE* 4.0 24.2 - - + +
101H ASP* 3.6 34.5 - - + +
104H ILE* 3.9 28.0 - - + -
117H LEU* 4.4 7.0 - - + -
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Residues in contact with GLY 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H GLY* 3.6 5.4 - - - -
45H PHE* 2.9 22.6 + - - +
83H ASP* 3.3 6.8 - - - +
84H LEU* 1.3 79.8 - - - +
86H ASN* 1.3 66.9 + - - +
124H ASP* 3.8 13.8 + - - +
126H LEU* 4.6 17.3 - - - -
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Residues in contact with ASN 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LEU* 4.0 31.4 - - + +
43H HIS 3.1 7.4 - - - +
44H GLY 3.3 10.4 + - - -
45H PHE* 4.3 2.2 - - - +
84H LEU 3.8 3.8 + - - +
85H GLY* 1.3 76.9 - - - -
87H VAL* 1.3 67.0 + - - +
88H THR* 5.3 0.8 + - - -
99H ILE* 4.7 7.1 - - - +
123H ALA* 3.3 2.9 - - - -
124H ASP* 2.5 52.6 + - - +
126H LEU* 3.8 18.8 - - - +
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Residues in contact with VAL 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ILE* 4.4 8.1 - - + -
38H LEU* 4.8 2.5 - - + -
41H GLY 3.5 1.2 - - - +
42H LEU* 3.5 2.6 - - - -
43H HIS* 2.8 51.3 + - + +
45H PHE* 3.6 34.5 - - + -
86H ASN* 1.3 76.7 - - - +
88H THR* 1.3 61.9 + - - +
95H ALA* 4.4 10.1 - - + -
96H ASP 5.8 0.4 - - - +
97H VAL* 3.5 35.0 - - + -
99H ILE* 4.9 1.6 - - + -
119H VAL* 4.2 15.5 - - + -
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Residues in contact with THR 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H GLY* 3.3 12.1 - - - +
42H LEU* 3.2 26.0 - - + +
86H ASN* 5.3 1.0 - - - +
87H VAL* 1.3 75.9 - - - +
89H ALA* 1.3 70.0 + - - +
90H ASP 3.9 0.9 + - - -
94H VAL 3.8 0.7 - - - +
95H ALA* 3.2 21.1 - - - +
96H ASP 4.1 7.1 + - - +
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H LEU* 3.6 25.6 - - + -
39H THR 3.3 24.9 - - - +
40H GLU* 3.3 3.1 - - - +
41H GLY* 2.8 35.4 + - - +
43H HIS* 4.3 0.9 - - + -
87H VAL 4.1 0.6 + - - -
88H THR* 1.3 77.3 - - - +
90H ASP* 1.3 64.8 + - - +
93H GLY 4.1 8.1 - - - -
94H VAL 3.3 11.2 - - - +
95H ALA* 4.0 1.6 - - + -
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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