Contacts of the helix formed by residues 66 - 74 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LYS* 4.3 1.2 + - - -
83A GLU* 4.0 23.6 - - - +
64B LEU 4.4 2.2 - - - +
65B LEU* 1.3 76.3 - - - +
67B LYS* 1.3 65.4 + - - +
68B GLU* 3.7 13.6 + - - +
69B ASP* 3.1 25.6 + - - -
70B PHE* 3.1 27.0 + - - -
82B TYR* 3.9 6.7 - - - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 1.3 73.3 - - - +
68B GLU* 1.3 64.6 + - - +
70B PHE* 3.2 5.0 + - - +
71B ARG* 3.0 49.6 + - - +
79B ASP* 3.7 30.3 - - + -
82B TYR* 3.6 48.5 - - + -
83B GLU* 3.0 28.2 + - - +
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Residues in contact with GLU 68 (chain B).
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* 3.5 29.5 + - - +
71A ARG* 5.6 0.3 + - - -
66B THR* 3.8 9.4 + - - +
67B LYS* 1.3 79.1 - - - +
69B ASP* 1.3 59.5 + - - +
71B ARG* 3.3 14.6 + - + +
72B TYR* 2.9 36.6 + - + +
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Residues in contact with ASP 69 (chain B).
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* 2.5 41.8 + - - -
71A ARG* 3.6 10.6 + - - -
79A ASP* 4.2 6.0 - - - +
83A GLU* 3.3 14.6 - - - +
65B LEU* 3.8 21.7 - - + +
66B THR* 3.1 30.4 + - - +
68B GLU* 1.3 77.3 - - - +
70B PHE* 1.3 61.4 + - - +
72B TYR* 2.8 22.2 + - - +
73B ARG* 3.1 19.3 + - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TRP* 4.3 8.7 - + - -
55B PHE* 3.6 33.6 - + - -
62B LEU* 4.0 22.0 - - + -
65B LEU* 3.8 21.7 - - + +
66B THR 3.1 23.5 + - - -
67B LYS 3.5 7.9 - - - +
69B ASP* 1.3 74.4 - - - +
71B ARG* 1.3 56.4 + - - +
73B ARG* 3.4 2.8 + - - +
74B SER* 2.9 28.6 + - - +
78B GLY* 3.5 26.7 - - - +
81B LEU* 4.0 22.2 - - + -
82B TYR* 3.5 30.7 - + + -
85B LEU* 3.9 23.3 - - + -
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 3.0 40.5 + - - +
68B GLU* 3.4 15.4 - - + +
69B ASP 3.2 0.2 - - - -
70B PHE* 1.3 73.0 - - - +
72B TYR* 1.3 63.3 + - - +
74B SER 3.3 21.3 - - - +
75B PRO* 3.6 14.0 - - + +
78B GLY* 4.0 1.3 - - - -
79B ASP* 3.1 49.4 + - + +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 3.2 55.8 + - - +
79A ASP* 5.3 0.2 - - - -
68B GLU* 2.9 23.1 + - + +
69B ASP* 2.8 12.2 + - - +
71B ARG* 1.3 77.5 - - - +
73B ARG* 1.3 64.0 + - + +
74B SER* 4.7 0.2 - - - -
75B PRO* 4.7 5.7 - - - +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO 5.4 1.6 + - - -
76A HIS* 3.3 24.9 + - - +
79A ASP* 3.1 40.8 + - - +
80A VAL* 3.7 9.5 - - - +
54B THR* 2.5 56.6 + - + +
55B PHE* 3.6 32.7 - - + +
56B GLU 4.5 2.6 - - - +
57B MET* 3.7 17.0 - - - +
65B LEU* 4.3 7.2 - - - +
69B ASP 3.1 13.1 + - - +
70B PHE 3.9 0.2 - - - +
72B TYR* 1.3 81.4 - - + +
74B SER* 1.3 63.6 + - - +
75B PRO* 4.1 4.1 - - - +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 3.5 28.3 - - - +
54B THR* 4.4 2.1 - - - +
55B PHE* 4.7 3.0 - - - -
70B PHE 2.9 9.0 + - - -
71B ARG* 3.3 10.0 - - - +
73B ARG* 1.3 80.7 + - - +
75B PRO* 1.3 65.7 - - - +
76B HIS* 4.6 0.4 - - - -
77B SER* 4.1 12.8 - - - -
78B GLY* 3.0 39.0 + - - -
81B LEU* 4.8 4.7 - - - +
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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