Contacts of the strand formed by residues 83 - 89 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46M ARG* 3.3 23.1 - - - -
63M HIS* 3.5 6.6 + - - -
71M HIS* 2.9 35.6 + - + -
72M GLY 3.2 17.9 + - - +
73M GLY 4.8 1.6 - - - -
74M PRO* 3.7 6.6 - - - +
79M ARG* 3.4 23.9 + - - +
80M HIS* 3.0 38.0 + - - +
81M VAL 3.3 0.4 - - - -
82M GLY* 1.3 72.3 - - - +
84M LEU* 1.3 60.8 + - - +
85M GLY 3.3 6.5 + - - +
124M ASP* 4.9 2.2 - - - +
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Residues in contact with LEU 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M PHE* 5.0 7.2 - - + -
31M VAL* 5.1 6.3 - - + -
45M PHE* 3.1 45.0 + - + +
47M VAL* 4.1 21.1 - - + -
74M PRO* 3.2 12.8 - - - +
79M ARG* 4.3 0.2 - - - +
82M GLY 3.2 8.9 + - - +
83M ASP* 1.3 76.1 - - - +
85M GLY* 1.3 61.9 + - - +
86M ASN 3.7 1.9 + - - +
99M ILE* 4.0 23.9 - - + +
101M ASP* 3.7 28.3 - - + +
104M ILE* 3.9 33.0 - - + -
117M LEU* 4.4 6.7 - - + -
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Residues in contact with GLY 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M GLY* 3.6 5.2 - - - -
45M PHE* 2.9 23.7 + - - +
74M PRO* 3.0 25.6 - - - +
83M ASP* 3.3 2.4 - - - +
84M LEU* 1.3 79.7 - - - +
86M ASN* 1.3 67.1 + - - -
124M ASP* 3.9 15.6 + - - +
126M LEU* 4.7 2.5 - - - -
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Residues in contact with ASN 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LEU* 3.8 34.0 - - + +
43M HIS 3.1 14.2 - - - +
44M GLY 3.4 0.5 + - - -
45M PHE* 4.3 1.3 - - - +
84M LEU 3.7 4.2 + - - +
85M GLY* 1.3 74.3 - - - -
87M VAL* 1.3 67.0 + - - +
88M THR* 5.2 0.7 - - - +
99M ILE* 4.7 7.1 - - - +
123M ALA* 3.3 8.6 - - - +
124M ASP* 2.6 32.8 + - - +
126M LEU* 3.7 28.1 - - - +
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Residues in contact with VAL 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M ILE* 4.4 5.6 - - + -
38M LEU* 4.8 2.9 - - + -
41M GLY 3.6 0.9 - - - +
42M LEU* 3.5 2.6 - - - -
43M HIS* 2.9 50.4 + - + +
45M PHE* 3.5 35.0 - - + -
86M ASN* 1.3 76.9 - - - +
88M THR* 1.3 62.7 + - - +
95M ALA* 4.4 13.7 - - + -
96M ASP 5.8 0.4 - - - +
97M VAL* 3.6 33.9 - - + -
99M ILE* 4.9 1.3 - - + -
119M VAL* 4.2 15.0 - - + -
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Residues in contact with THR 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M GLY* 3.3 12.1 - - - +
42M LEU* 3.1 26.3 - - + +
86M ASN* 5.2 0.9 - - - +
87M VAL* 1.3 76.0 - - - +
89M ALA* 1.3 72.4 + - - +
90M ASP 3.9 0.7 + - - -
94M VAL 3.8 0.5 - - - +
95M ALA* 3.2 20.3 - - - +
96M ASP 4.1 7.1 + - - +
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Residues in contact with ALA 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M LEU* 3.6 26.2 - - + -
39M THR 3.4 24.2 - - - +
40M GLU* 3.6 4.5 - - - +
41M GLY* 2.7 36.1 + - - +
43M HIS* 4.2 1.1 - - + -
87M VAL 4.2 0.6 + - - -
88M THR* 1.3 80.2 - - - +
90M ASP* 1.3 62.3 + - - +
93M GLY 4.1 7.2 - - - -
94M VAL 3.3 10.3 - - - +
95M ALA* 3.9 1.8 - - + -
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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