Contacts of the helix formed by residues 66 - 74 (chain A) in PDB entry 2QB1
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU 4.4 6.7 - - - +
65A LEU* 1.3 75.2 - - - +
67A LYS* 1.3 64.2 + - - +
68A GLU* 3.7 13.3 + - - +
69A ASP* 3.1 29.4 + - - +
70A PHE* 3.1 26.0 + - - -
82A TYR* 3.9 6.7 - - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 1.3 74.8 - - - +
68A GLU* 1.3 63.4 + - - +
69A ASP 3.3 0.2 + - - -
70A PHE* 3.3 4.6 + - - +
71A ARG* 3.0 44.1 + - - +
79A ASP* 3.7 21.3 - - + -
82A TYR* 3.6 47.6 + - + -
83A GLU* 3.1 16.7 + - - -
66B THR* 4.3 1.4 + - - -
68B GLU* 3.5 17.4 + - - +
69B ASP* 2.5 42.4 + - - -
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 3.7 11.1 + - - +
67A LYS* 1.3 79.1 - - - +
69A ASP* 1.3 72.5 + - - +
71A ARG* 3.3 15.5 + - + +
72A TYR* 2.9 37.2 + - + +
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU 4.9 0.3 - - - +
65A LEU* 3.8 26.2 - - + +
66A THR* 3.1 36.9 + - - +
68A GLU* 1.3 86.8 - - - +
70A PHE* 1.3 58.3 + - - +
72A TYR* 2.8 29.9 + - - +
73A ARG* 3.0 20.2 + - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TRP* 4.3 7.9 - + - -
55A PHE* 3.6 35.2 - + - -
62A LEU* 4.0 22.0 - - + -
65A LEU* 3.9 22.8 - - + +
66A THR 3.1 21.3 + - - -
67A LYS 3.5 7.9 - - - +
69A ASP* 1.3 77.5 - - - +
71A ARG* 1.3 57.1 + - - +
73A ARG* 3.4 2.6 + - - +
74A SER* 2.9 28.4 + - - +
78A GLY* 3.5 26.6 - - - +
81A LEU* 4.0 23.3 - - + -
82A TYR* 3.4 31.6 - + + -
85A LEU* 3.9 23.6 - - + -
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS* 3.0 35.3 + - - +
68A GLU* 3.4 15.4 - - + +
70A PHE* 1.3 73.8 - - - +
72A TYR* 1.3 63.2 + - - +
74A SER 3.3 21.3 - - - +
75A PRO* 3.5 13.7 - - + +
78A GLY* 4.0 1.1 - - - -
79A ASP* 3.1 49.8 + - + +
68B GLU* 5.6 0.6 + - - -
69B ASP* 3.6 12.7 + - - -
72B TYR* 3.2 62.0 + - - +
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 2.9 24.2 + - + +
69A ASP* 2.8 21.4 + - - +
71A ARG* 1.3 78.1 - - - +
73A ARG* 1.3 64.2 + - + +
74A SER* 4.7 0.3 - - - -
75A PRO* 4.7 5.5 - - - +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 2.4 56.7 + - + +
55A PHE* 3.6 34.9 - - + +
56A GLU 4.6 2.0 - - - +
57A MET* 3.7 24.9 - - - +
65A LEU* 4.3 16.1 - - - +
69A ASP* 3.0 12.4 + - - +
70A PHE 3.9 2.0 - - - +
72A TYR* 1.3 82.5 - - + +
74A SER* 1.3 62.7 + - - +
75A PRO* 4.1 3.7 - - - +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.5 28.6 - - - +
54A THR* 4.4 2.4 - - - +
55A PHE* 4.7 3.0 - - - -
70A PHE 2.9 7.8 + - - -
71A ARG* 3.3 8.8 - - - +
73A ARG* 1.3 81.2 + - - +
75A PRO* 1.3 65.6 - - - +
76A HIS* 3.3 0.7 - - - -
77A SER* 4.2 13.2 - - - -
78A GLY* 3.0 40.0 + - - -
81A LEU* 4.8 4.6 - - - +
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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