Contacts of the strand formed by residues 81 - 86 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E ASP 2.8 14.1 + - - -
55E VAL* 3.2 21.2 - - + +
56E VAL 2.7 31.7 + - - -
79E ARG 3.1 0.6 + - - -
80E THR* 1.3 75.6 - - - +
82E LEU* 1.3 56.6 + - - +
83E VAL* 4.7 0.9 - - + -
103E HIS* 3.7 5.6 - - - +
119E LEU* 4.9 1.6 - - + +
122E ALA* 3.7 42.0 - - + +
123E ARG* 3.0 25.5 + - + +
126E SER* 2.6 18.5 + - - -
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E VAL* 3.5 18.6 - - + +
58E THR* 3.7 25.1 - - + -
73E LEU* 3.8 29.8 - - + -
80E THR* 3.6 2.4 + - + +
81E THR* 1.3 74.4 - - - +
83E VAL* 1.3 69.1 + - - +
100E LEU* 3.7 26.0 - - + +
101E GLU 4.5 0.7 - - - +
102E CYS* 3.5 30.8 - - - -
103E HIS* 2.7 47.6 + - + +
104E GLY 3.4 3.1 + - - -
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Residues in contact with VAL 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E VAL* 5.1 2.5 - - + -
56E VAL 2.8 11.5 + - - +
57E PHE* 3.4 43.1 - - + +
58E THR* 3.1 25.3 + - - +
81E THR* 4.7 5.4 - - + -
82E LEU* 1.3 80.1 - - - +
84E ALA* 1.3 71.4 + - - +
85E LEU 4.0 0.2 + - - -
104E GLY 3.4 7.2 - - - +
106E ILE* 4.2 7.6 - - + -
118E VAL* 4.0 24.5 - - + +
119E LEU* 5.2 1.3 - - - -
122E ALA* 3.8 26.9 - - + -
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Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E THR* 3.5 5.8 - - + +
60E ILE* 4.0 13.9 - - + -
83E VAL* 1.3 73.5 - - - +
85E LEU* 1.3 58.4 + - - +
86E VAL* 3.6 6.4 + - + +
97E ILE* 4.0 19.3 - - + -
102E CYS* 3.6 25.9 - - + -
104E GLY 3.1 11.6 + - - +
105E VAL* 3.3 4.6 - - + -
106E ILE 2.6 33.8 + - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 5.5 0.2 - - + -
19E ASN* 4.3 14.8 - - + +
24E VAL* 4.6 4.3 - - + -
28E LEU* 3.8 31.4 - - + -
57E PHE* 4.3 15.5 - - + -
58E THR 2.9 24.5 + - - +
59E SER* 3.8 17.4 + - - +
60E ILE* 3.8 25.8 + - - +
83E VAL 4.9 0.2 - - - +
84E ALA* 1.3 72.7 - - - +
86E VAL* 1.3 59.7 + - - +
87E GLU* 4.2 3.8 + - - +
106E ILE* 3.5 26.5 - - + +
108E GLN* 3.7 24.0 - - - +
110E LEU* 4.3 12.3 - - + -
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D PRO* 4.1 20.4 - - + -
60E ILE* 5.1 2.0 - - - -
84E ALA 3.7 13.7 - - - +
85E LEU* 1.3 75.6 - - - +
87E GLU* 1.3 61.6 + - - +
88E TYR 3.0 28.3 - - - +
93E VAL* 4.4 2.5 - - + -
94E LEU* 4.6 1.1 - - + -
97E ILE* 3.5 33.0 - - + -
105E VAL* 3.9 19.3 - - + -
106E ILE 3.0 8.8 + - - +
107E THR* 3.5 9.0 - - + -
108E GLN* 2.8 30.9 + - - +
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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