Contacts of the strand formed by residues 81 - 86 (chain D) in PDB entry 1QO0
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 THR 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ASP 2.8 7.7 + - - -
55D VAL* 3.4 23.7 - - + -
56D VAL* 2.9 26.7 + - - +
79D ARG 3.2 0.6 + - - -
80D THR* 1.3 75.9 - - - +
82D LEU* 1.3 64.0 + - - +
83D VAL* 4.7 1.3 - - + -
103D HIS* 3.6 7.6 - - + -
119D LEU* 5.1 1.8 - - + +
122D ALA* 3.5 42.8 - - + +
123D ARG* 3.0 23.4 + - + +
126D SER* 2.5 19.9 + - - +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 3.7 13.7 - - + +
58D THR* 3.9 22.7 - - + -
73D LEU* 3.4 36.3 - - + -
80D THR* 4.6 2.9 - - + +
81D THR* 1.3 74.4 - - - +
83D VAL* 1.3 69.2 + - - +
84D ALA 4.3 0.2 - - - -
100D LEU* 3.5 40.8 - - + +
101D GLU 4.5 0.9 - - - +
102D CYS* 3.6 17.0 - - - -
103D HIS* 2.7 48.4 + - + +
104D GLY 3.2 5.9 + - - +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 4.9 3.6 - - + -
56D VAL 2.9 11.9 + - - +
57D PHE* 3.3 44.4 - - + +
58D THR* 3.0 26.7 + - - +
81D THR* 4.7 4.9 - - + -
82D LEU* 1.3 81.7 - - - +
84D ALA* 1.3 68.2 + - - +
85D LEU* 4.9 0.2 - - + -
104D GLY 3.3 10.5 - - - +
106D ILE* 4.1 9.6 - - + -
118D VAL* 3.8 21.5 - - + +
119D LEU* 5.2 2.0 - - - -
122D ALA* 3.9 24.7 - - + -
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D THR* 3.4 10.3 - - + +
60D ILE* 4.2 24.0 - - + -
82D LEU 4.3 0.2 - - - -
83D VAL* 1.3 74.4 - - - +
85D LEU* 1.3 64.1 + - - +
86D VAL* 3.7 1.1 + - + -
97D ILE* 4.5 7.2 - - + -
102D CYS* 3.6 26.4 - - - -
104D GLY 3.0 9.2 + - - +
105D VAL* 3.2 8.3 - - + +
106D ILE 2.9 25.1 + - - -
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASN* 4.6 7.9 - - + +
24D VAL* 3.8 29.2 - - + -
28D LEU* 3.8 27.6 - - + -
57D PHE* 4.4 9.0 - - + -
58D THR* 2.8 19.8 + - - +
59D SER* 3.6 29.8 - - - +
60D ILE* 3.8 10.4 + - - +
84D ALA* 1.3 74.4 - - - +
86D VAL* 1.3 59.2 - - - +
106D ILE* 3.4 36.3 - - + +
108D GLN* 3.7 21.1 - - - +
110D LEU* 5.0 5.2 - - + -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 5.1 3.1 - - + -
84D ALA* 3.9 4.0 - - + +
85D LEU* 1.3 77.8 - - - +
87D GLU* 1.3 61.9 + - - +
88D TYR 3.1 27.1 - - - +
93D VAL* 3.8 8.5 - - + -
97D ILE* 3.6 31.6 - - + -
105D VAL* 3.8 30.7 - - + -
106D ILE 2.9 8.5 + - - +
107D THR* 3.2 12.0 - - + -
108D GLN* 2.8 28.6 + - - -
117E PRO* 4.3 13.2 - - + -
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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