Contacts of the helix formed by residues 59 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO 3.1 11.6 + - - +
57A GLY 3.1 4.5 - - - +
58A GLY* 1.3 75.8 - - - +
60A PRO* 1.3 68.8 - - - +
61A ASP* 3.2 22.8 + - - +
62A ARG* 2.9 47.2 + - - +
63A TYR* 3.0 16.0 + - - -
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Residues in contact with PRO 60 (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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58A GLY 3.3 11.0 - - - +
59A ASP* 1.3 89.1 - - - +
61A ASP* 1.3 67.5 + - - +
63A TYR* 3.2 10.7 + - + +
64A ARG 3.1 18.2 + - - -
86A HIS* 3.9 46.4 - - + +
87A THR* 4.4 4.5 - - + -
90A ALA* 3.3 17.5 - - + +
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Residues in contact with ASP 61 (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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59A ASP* 3.2 13.3 + - - +
60A PRO* 1.3 80.9 - - - +
62A ARG* 1.3 59.5 + - + +
64A ARG* 3.3 25.3 + - - +
65A LEU* 3.0 35.6 + - + +
90A ALA* 5.4 0.4 - - - -
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Residues in contact with ARG 62 (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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17A THR* 4.8 2.0 + - - -
55A ASP* 3.0 28.5 + - - -
56A PRO* 3.3 29.2 + - + +
57A GLY* 3.7 11.3 + - - +
59A ASP* 2.9 33.3 + - - +
61A ASP* 1.3 78.2 - - + +
63A TYR* 1.3 57.4 + - - +
65A LEU* 4.3 13.7 - - + +
66A CYS* 2.8 39.7 + - - -
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Residues in contact with TYR 63 (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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13A LEU* 3.7 28.7 - - + +
15A SER* 2.9 10.0 + - - -
20A THR* 4.7 0.2 + - - -
24A GLU* 2.6 29.8 + - - -
56A PRO* 3.4 30.1 - - + -
58A GLY* 3.8 3.5 - - - -
59A ASP 3.0 41.9 + - - -
60A PRO* 3.2 6.0 + - + +
62A ARG* 1.3 72.2 - - - +
64A ARG* 1.3 62.8 + - - +
67A ALA* 2.8 33.1 + - - +
82A CYS* 3.9 19.1 - - - -
83A TYR* 4.6 1.0 + - - +
84A MET* 5.5 0.7 + - - +
87A THR* 3.5 45.7 + - + +
91A VAL* 3.5 14.6 - - + +
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Residues in contact with ARG 64 (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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60A PRO 3.1 10.1 + - - +
61A ASP* 3.3 33.2 + - - +
63A TYR* 1.3 81.1 - - - +
65A LEU* 1.3 91.6 + - - +
67A ALA* 3.2 6.4 + - - +
68A GLU* 3.0 44.4 + - - +
90A ALA* 3.6 28.0 - - + +
91A VAL* 4.0 1.4 - - - +
94A VAL* 3.9 8.0 - - + +
97A ARG* 6.2 1.1 - - - +
23D GLU* 4.8 14.5 + - - -
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Residues in contact with LEU 65 (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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61A ASP* 3.0 27.9 + - + +
62A ARG* 4.0 14.1 - - + +
63A TYR 3.4 0.2 - - - -
64A ARG* 1.3 101.3 - - - +
66A CYS* 1.3 65.7 + - - +
68A GLU* 3.2 17.3 + - - +
69A ASP* 2.9 22.5 + - - +
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Residues in contact with CYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.0 16.4 - - + -
54A GLN* 3.4 39.4 - - + +
55A ASP 4.6 4.3 - - - -
56A PRO* 4.6 15.9 - - - -
62A ARG* 2.8 31.4 + - - +
65A LEU* 1.3 74.3 - - - +
67A ALA* 1.3 63.0 + - - +
69A ASP* 3.1 4.7 + - - +
70A PHE* 2.8 27.9 + - + -
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Residues in contact with ALA 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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13A LEU* 4.1 5.5 - - + +
63A TYR 2.8 23.4 + - - +
64A ARG 3.5 4.9 - - - +
66A CYS* 1.3 71.3 - - - +
68A GLU* 1.3 57.9 + - - +
70A PHE* 3.2 14.7 + - - +
71A ILE* 3.0 31.2 + - - +
79A LEU* 4.5 7.2 - - + -
91A VAL* 4.0 27.8 - - + -
94A VAL* 4.1 16.6 - - + -
95A VAL* 5.2 0.2 - - + -
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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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64A ARG* 3.0 44.1 + - - +
65A LEU* 3.4 23.6 - - - +
67A ALA* 1.3 72.3 - - - +
69A ASP* 1.3 58.6 + - - +
71A ILE* 4.5 1.1 - - - +
72A ARG* 2.6 83.1 + - - +
94A VAL* 3.8 21.8 - - + +
97A ARG* 5.2 3.3 + - - +
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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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54A GLN* 2.9 28.1 + - - +
65A LEU 2.9 13.6 + - - +
66A CYS* 3.4 11.0 - - - +
68A GLU* 1.3 75.8 - - - +
70A PHE* 1.3 57.8 + - - +
73A ASN* 2.8 43.5 + - - +
74A ARG* 2.8 46.2 + - - +
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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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11A GLY* 3.7 8.3 - - - -
12A LEU 3.6 17.5 - - - -
13A LEU* 4.0 14.4 - - + -
52A LEU* 3.0 48.7 - - + -
54A GLN* 3.6 32.5 - - + -
66A CYS 2.8 26.4 + - - -
67A ALA* 3.2 9.8 + - - +
69A ASP* 1.3 72.6 - - - +
71A ILE* 1.3 59.2 + - + +
74A ARG* 3.1 20.3 + - - +
76A VAL* 3.1 41.0 + - + -
79A LEU* 3.5 30.5 - - + -
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Residues in contact with ILE 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 ALA 3.0 19.3 + - - +
68A GLU* 4.1 4.3 - - - +
70A PHE* 1.3 77.4 - - + +
72A ARG* 1.3 71.3 + - + +
75A GLY* 4.1 5.9 + - - -
76A VAL 3.4 16.4 - - - +
77A ARG* 3.3 31.7 + - - +
79A LEU* 4.4 8.3 - - + -
94A VAL* 3.7 24.0 - - + +
95A VAL* 4.4 10.5 - - + -
98A ALA* 3.7 30.5 - - + -
100A ALA* 4.4 14.6 - - + -
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Residues in contact with ARG 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* 2.6 61.6 + - - +
71A ILE* 1.3 80.0 - - + +
73A ASN* 1.3 75.3 + - - +
75A GLY 4.9 1.0 + - - -
94A VAL* 5.9 1.2 - - - +
97A ARG* 5.7 5.7 - - - +
99B ASP* 2.6 34.8 + - - +
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Residues in contact with ASN 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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69A ASP* 2.8 38.0 + - - +
72A ARG* 1.3 91.9 - - - +
74A ARG* 1.3 89.7 + - - +
75A GLY 3.6 1.3 - - - -
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Residues in contact with ARG 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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9A LEU* 3.9 12.9 - - + +
52A LEU* 3.5 33.0 - - + -
69A ASP* 2.8 46.5 + - - +
70A PHE* 3.1 14.4 + - - +
73A ASN* 1.3 97.6 + - - +
75A GLY* 1.3 65.0 + - - +
76A VAL* 3.1 13.3 + - + +
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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