Contacts of the helix formed by residues 64 - 76 (chain D) 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 ARG 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ASN* 1.3 79.4 + - - +
65D HIS* 1.3 92.6 + - - +
66D HIS 3.2 0.4 - - - -
67D ASP* 3.5 12.3 + - + +
68D GLU* 3.0 49.8 + - + +
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 3.4 41.9 + + + -
44D PRO* 4.2 12.8 - - + -
45D PRO* 3.5 15.4 - - + +
61D PHE* 4.3 4.5 - + + -
63D ASN* 2.7 39.2 + - - +
64D ARG* 1.3 104.3 + - - +
66D HIS* 1.3 57.0 + - - +
68D GLU* 2.6 28.4 + - - +
69D ILE* 2.7 44.4 + - + +
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Residues in contact with HIS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER 5.6 0.6 + - - -
60D ILE* 4.8 2.6 - - + +
61D PHE* 3.2 29.9 + - - +
63D ASN* 3.2 9.3 + - - +
64D ARG 3.2 0.2 - - - -
65D HIS* 1.3 79.6 - - - +
67D ASP* 1.3 62.6 + - - +
69D ILE* 3.7 7.8 - - - +
70D ALA* 2.8 39.2 + - + +
96D GLN* 3.1 41.9 + - + +
99D GLU* 5.1 8.7 + - - +
100D LEU* 3.5 45.2 - - + +
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Residues in contact with ASP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ASN 4.4 0.6 + - - -
64D ARG* 3.5 13.5 + - + +
65D HIS 3.4 0.2 - - - -
66D HIS* 1.3 85.9 - - - +
68D GLU* 1.3 60.6 + - + +
70D ALA* 3.5 7.4 - - - +
71D ALA* 2.8 33.7 + - - +
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PRO* 5.4 0.5 - - - +
45D PRO* 3.4 23.5 - - + +
46D PRO 4.8 3.5 - - - +
64D ARG* 3.0 41.2 + - + +
65D HIS* 2.6 33.7 + - - +
67D ASP* 1.3 76.4 - - + +
69D ILE* 1.3 52.8 + - - +
71D ALA* 3.3 4.7 + - - +
72D LEU* 2.7 38.5 + - - +
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.5 29.2 - - + -
43D TRP* 4.1 10.3 - - + -
45D PRO* 3.9 8.7 - - + -
58D THR* 3.6 30.5 - - + +
59D SER 4.7 1.6 - - - +
61D PHE* 3.7 27.4 - - + -
65D HIS* 2.7 31.6 + - + +
66D HIS* 3.7 5.4 - - - +
68D GLU* 1.3 72.4 - - - +
70D ALA* 1.3 57.6 + - - +
72D LEU* 3.2 8.3 + - - +
73D LEU* 2.9 47.5 + - + +
100D LEU* 4.8 8.7 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D HIS* 2.8 23.3 + - + +
67D ASP* 3.5 11.2 - - - +
69D ILE* 1.3 77.4 - - - +
71D ALA* 1.3 57.6 + - - +
73D LEU* 3.3 3.6 + - - +
74D ALA* 2.8 30.4 + - - +
100D LEU* 3.9 22.6 - - + +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ASP 2.8 20.1 + - - +
68D GLU* 3.7 4.5 - - - +
70D ALA* 1.3 69.6 - - - +
72D LEU* 1.3 66.7 + - - +
74D ALA* 3.0 17.5 + - - +
75D ALA* 3.1 17.0 + - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.8 19.7 - - + -
45D PRO* 4.4 4.0 - - + -
46D PRO* 3.8 28.3 - - + +
47D GLU 3.9 10.4 - - - +
48D ALA* 3.9 29.4 - - - +
49D PHE* 3.3 51.2 - - + -
68D GLU 2.7 20.2 + - - +
69D ILE* 3.4 4.7 - - - +
71D ALA* 1.3 74.6 - - - +
73D LEU* 1.3 61.9 + - + +
75D ALA* 3.7 3.5 + - - +
76D GLY* 3.4 15.6 + - - -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PHE* 3.9 19.1 - - + -
56D VAL* 3.8 29.2 - - + -
69D ILE* 2.9 37.7 + - + +
70D ALA* 4.2 2.7 - - - +
72D LEU* 1.3 73.8 - - + +
74D ALA* 1.3 64.2 + - - +
75D ALA 3.2 0.2 - - - -
76D GLY* 3.4 15.8 + - - +
77D THR 5.5 0.7 - - - +
78D PRO* 6.1 0.2 - - - +
80D THR* 4.6 11.2 - - + -
82D LEU* 3.4 45.3 - - + -
100D LEU* 5.4 3.8 - - + -
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ALA 2.8 17.8 + - - +
71D ALA* 3.0 10.7 + - - +
73D LEU* 1.3 78.9 - - - +
75D ALA* 1.3 61.6 + - - +
76D GLY 3.6 4.0 + - - +
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLU 5.6 5.4 - - - +
71D ALA 3.1 11.8 + - - +
72D LEU* 4.1 4.3 - - - +
74D ALA* 1.3 80.2 - - - +
76D GLY* 1.3 61.4 + - - +
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PHE* 6.0 5.8 - - - -
72D LEU 3.4 13.0 + - - -
73D LEU* 3.4 13.2 + - - +
74D ALA 3.3 5.6 - - - +
75D ALA* 1.3 82.4 - - - +
77D THR* 1.3 68.8 + - - -
78D PRO* 3.1 9.4 - - - +
80D THR* 6.2 0.2 - - - -
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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