Contacts of the helix formed by residues 59 - 74 (chain B) 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 ASP 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B PRO 3.1 10.6 + - - +
57B GLY 3.1 5.3 + - - +
58B GLY* 1.3 76.9 - - - +
60B PRO* 1.3 73.0 - - - +
61B ASP* 2.9 24.1 + - - +
62B ARG* 3.0 31.5 + - + +
63B TYR* 2.9 25.8 + - - -
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Residues in contact with PRO 60 (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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58B GLY 3.4 9.2 - - - +
59B ASP* 1.3 89.1 - - - +
61B ASP* 1.3 68.5 + - - +
63B TYR* 3.2 10.0 + - + +
64B ARG* 3.0 18.4 + - - +
86B HIS* 3.8 47.8 - - + +
87B THR* 4.3 3.8 - - + -
90B ALA* 3.4 17.3 - - + +
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Residues in contact with ASP 61 (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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59B ASP* 2.9 14.7 + - - +
60B PRO* 1.3 82.7 - - - +
62B ARG* 1.3 63.3 + - + +
64B ARG* 3.3 25.9 + - - +
65B LEU* 3.0 31.6 + - + +
90B ALA* 5.5 0.9 - - - +
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Residues in contact with ARG 62 (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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17B THR* 4.5 4.6 + - - -
55B ASP* 3.0 29.9 + - - -
56B PRO* 3.4 31.9 + - + +
57B GLY* 3.9 18.4 + - - +
59B ASP* 3.0 24.1 + - - +
61B ASP* 1.3 73.0 - - + +
63B TYR* 1.3 60.9 + - - +
65B LEU* 3.4 12.4 + - + +
66B CYS* 2.8 37.0 + - - -
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Residues in contact with TYR 63 (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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13B LEU* 3.6 31.7 - - + +
15B SER* 3.0 12.9 + - - -
20B THR* 4.8 0.2 + - - -
24B GLU* 2.5 29.0 + - - -
56B PRO* 3.6 22.2 - - + -
58B GLY* 3.8 17.0 - - - -
59B ASP 2.9 32.1 + - - -
60B PRO* 3.2 5.8 + - + +
62B ARG* 1.3 75.7 - - - +
64B ARG* 1.3 65.1 + - - +
66B CYS* 3.3 1.9 + - - -
67B ALA* 2.9 25.5 + - - +
82B CYS* 3.9 25.4 - - - -
83B TYR* 4.5 1.0 + - - +
84B MET* 5.5 0.7 + - - +
87B THR* 3.3 39.4 + - + +
91B VAL* 3.6 13.8 - - + +
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Residues in contact with ARG 64 (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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60B PRO 3.0 10.4 + - - +
61B ASP* 3.6 35.1 + - - +
63B TYR* 1.3 80.7 - - - +
65B LEU* 1.3 71.3 + - - +
67B ALA* 3.3 3.6 + - - +
68B GLU* 2.9 66.0 + - - +
90B ALA* 3.6 30.5 - - + +
91B VAL* 4.2 4.2 - - - +
94B VAL* 4.0 8.2 - - + +
97B ARG* 6.0 1.6 - - - +
23E GLU* 5.2 13.4 + - - -
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Residues in contact with LEU 65 (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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54B GLN* 5.0 0.4 - - - -
61B ASP* 3.0 25.8 + - + +
62B ARG* 3.7 11.9 - - + +
64B ARG* 1.3 90.0 - - - +
66B CYS* 1.3 60.5 + - - +
68B GLU* 3.2 18.0 + - + +
69B ASP* 2.9 30.2 + - - +
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Residues in contact with CYS 66 (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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13B LEU* 3.7 20.0 - - + -
54B GLN* 2.9 45.5 - - + +
55B ASP 4.8 2.5 - - - -
56B PRO* 4.3 16.6 - - + -
62B ARG* 2.8 34.6 + - - +
63B TYR* 4.6 0.7 - - - -
65B LEU* 1.3 72.8 - - - +
67B ALA* 1.3 62.9 + - - +
69B ASP* 3.3 2.1 + - - +
70B PHE* 3.0 28.0 + - + -
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Residues in contact with ALA 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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13B LEU* 3.6 12.8 - - + +
63B TYR 2.9 17.0 + - - +
64B ARG* 3.6 5.2 - - - +
66B CYS* 1.3 76.2 - - - +
68B GLU* 1.3 56.3 + - - +
70B PHE* 3.5 6.2 + - - +
71B ILE* 3.0 37.0 + - + +
79B LEU* 4.6 4.9 - - + -
91B VAL* 4.0 27.4 - - + -
94B VAL* 4.4 13.5 - - + -
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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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64B ARG* 2.9 59.5 + - - +
65B LEU* 3.5 16.0 - - + +
67B ALA* 1.3 72.9 - - - +
69B ASP* 1.3 59.6 + - - +
71B ILE 4.7 0.2 - - - +
72B ARG* 2.8 73.3 + - - +
94B VAL* 3.9 22.6 - - + +
97B ARG* 4.7 6.1 + - - -
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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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54B GLN* 3.0 28.0 - - - +
65B LEU 2.9 19.8 + - - +
66B CYS 3.3 5.8 + - - +
68B GLU* 1.3 70.6 - - - +
70B PHE* 1.3 57.8 + - - +
73B ASN* 2.7 63.9 + - - +
74B ARG* 3.3 13.0 + - - +
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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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11B GLY* 3.8 18.6 - - - -
12B LEU 3.9 9.0 - - - -
13B LEU* 3.8 26.0 - - + -
52B LEU* 3.5 50.5 - - + -
54B GLN* 3.6 37.2 - - + -
66B CYS 3.0 17.6 + - - +
67B ALA 3.8 2.7 - - - +
69B ASP* 1.3 77.4 - - - +
71B ILE* 1.3 57.4 + - - +
74B ARG* 2.9 28.1 + - + +
76B VAL* 3.1 32.4 + - + -
79B LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 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 ALA* 3.0 16.7 + - + +
68B GLU 4.3 1.1 - - - +
70B PHE* 1.3 82.1 - - + +
72B ARG* 1.3 67.6 + - - +
75B GLY* 4.0 5.5 + - - -
76B VAL 3.5 19.3 - - - +
77B ARG* 3.0 29.6 + - - +
79B LEU* 4.5 14.8 - - + -
94B VAL* 3.4 42.6 - - + +
95B VAL* 4.0 9.9 - - + -
98B ALA* 3.3 27.1 - - + -
100B ALA* 4.5 6.1 - - + -
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Residues in contact with ARG 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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99A ASP* 3.2 26.3 + - - -
68B GLU* 2.8 65.4 + - - +
71B ILE* 1.3 82.5 - - - +
73B ASN* 1.3 75.8 + - - +
75B GLY* 4.7 1.1 + - - -
94B VAL* 4.5 11.5 - - - +
97B ARG* 5.3 8.9 - - - +
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Residues in contact with ASN 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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69B ASP* 2.7 46.1 + - - +
72B ARG* 1.3 89.2 - - - +
74B ARG* 1.3 69.9 + - - +
75B GLY 3.6 0.7 - - - -
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Residues in contact with ARG 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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9B LEU* 3.7 18.3 - - + +
52B LEU* 3.4 46.5 - - + +
69B ASP* 4.0 19.4 + - - +
70B PHE* 2.9 18.3 + - + +
73B ASN* 1.3 91.9 + - + +
75B GLY* 1.3 64.0 + - - +
76B VAL* 3.2 5.5 + - + -
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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