Contacts of the helix formed by residues 66 - 78 (chain C) in PDB entry 1DXO
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 GLN 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLY* 6.3 0.4 - - - -
301A FAD 3.3 42.1 + - - +
61C ASP* 5.2 2.4 - - - +
64C ASN* 3.3 37.2 + - - +
65C PHE* 1.3 77.0 - - - +
67C TYR* 1.3 65.9 + - - +
68C PRO* 3.4 8.0 - - + -
69C ALA* 3.6 11.7 + - + +
70C GLU* 3.1 28.1 + - - +
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Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A FAD 3.7 25.1 - - + -
50C ILE* 3.7 32.5 - - + +
51C SER 3.5 15.9 - - - -
54C ASP* 2.4 37.6 + - + +
55C ILE* 4.7 2.2 - - + -
65C PHE* 3.8 33.0 + + + -
66C GLN* 1.3 70.9 - - - +
68C PRO* 1.3 72.4 - - + +
70C GLU 3.3 0.2 + - - -
71C SER* 2.9 49.3 + - - -
117C GLU 4.1 15.3 + - - -
118C ARG* 4.1 3.8 + - - -
121C ILE* 4.0 15.3 - - + +
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Residues in contact with PRO 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A FAD 3.7 40.6 - - + +
302A DQN 3.9 25.8 - - + +
66C GLN* 3.5 9.4 - - + -
67C TYR* 1.3 95.6 - - + +
69C ALA* 1.3 62.3 + - - +
71C SER* 2.9 19.8 + - - +
72C VAL* 3.0 19.8 - - + +
126C TYR* 5.2 2.7 - - - +
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLN* 3.6 13.7 + - + +
67C TYR 3.4 0.4 - - - -
68C PRO* 1.3 80.0 - - - +
70C GLU* 1.3 63.8 + - + +
72C VAL* 3.4 6.4 + - - +
73C LEU* 3.1 23.4 + - - +
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 3.9 10.6 - - + +
58C LYS 4.8 0.7 - - - +
59C LEU* 3.4 19.7 - - + +
60C LYS* 3.1 21.1 + - - +
61C ASP* 3.0 35.5 + - - +
65C PHE* 3.4 29.6 - - + -
66C GLN* 3.1 24.5 + - + +
67C TYR 3.9 1.6 - - - +
69C ALA* 1.3 77.0 - - + +
71C SER* 1.3 53.0 + - - +
73C LEU* 3.3 13.6 + - - +
74C ALA* 2.8 34.1 + - - +
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Residues in contact with SER 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 6.0 0.4 - - - -
55C ILE* 4.2 7.5 - - - +
67C TYR* 2.9 34.5 + - - -
68C PRO* 2.9 16.1 + - - +
70C GLU* 1.3 73.5 - - - +
72C VAL* 1.3 60.8 + - - +
74C ALA* 3.6 8.2 - - - +
75C TYR* 2.8 23.9 + - - -
80C LEU* 3.8 5.4 - - - +
121C ILE* 3.4 37.8 - - - +
122C GLY 4.9 1.0 + - - -
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PRO* 3.0 25.7 + - + +
69C ALA* 3.8 6.7 - - - +
71C SER* 1.3 75.2 + - - +
73C LEU* 1.3 60.6 + - - +
75C TYR* 3.4 2.4 + - - +
76C LYS* 3.0 61.4 + - - +
121C ILE* 4.0 5.4 - - - -
122C GLY* 3.6 30.5 - - - +
123C GLU* 3.3 18.6 - - + +
126C TYR* 5.3 2.5 - - - +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LYS 5.7 2.7 - - - +
60C LYS* 3.4 56.8 - - + +
69C ALA 3.1 14.0 + - - +
70C GLU* 3.4 16.8 - - - +
72C VAL* 1.3 75.9 - - - +
74C ALA* 1.3 56.9 + - - +
76C LYS* 2.9 16.2 + - + +
77C GLU* 2.6 73.0 + - + +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ILE* 3.4 29.4 - - + -
70C GLU 2.8 16.8 + - - +
71C SER 3.6 5.4 - - - +
73C LEU* 1.3 77.3 - - - +
75C TYR* 1.3 56.8 + - - +
77C GLU* 4.6 1.8 - - - +
78C GLY* 2.8 10.4 + - - -
79C HIS* 2.7 49.8 + - - +
80C LEU* 3.7 10.6 + - + -
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C SER 2.8 17.3 + - - +
72C VAL 3.5 4.5 - - - +
74C ALA* 1.3 78.9 - - - +
76C LYS* 1.3 70.1 + - + +
78C GLY* 3.3 9.3 + - - -
80C LEU* 3.8 15.7 - - + +
88C GLN* 3.7 24.5 - - - -
92C GLU* 4.0 10.7 + - - -
121C ILE* 4.0 8.5 - - + -
122C GLY 4.1 1.6 - - - -
123C GLU* 3.8 24.8 + - + -
124C PHE* 3.8 43.9 - + + -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C VAL* 3.0 45.8 + - + +
73C LEU* 2.9 17.7 + - + +
75C TYR* 1.3 90.1 - - + +
77C GLU* 1.3 62.6 + - + +
78C GLY 3.6 0.3 + - - -
123C GLU* 3.6 20.1 - - + +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LYS 5.4 2.9 - - - +
60C LYS* 5.4 0.7 - - - -
73C LEU* 2.6 56.0 + - + +
74C ALA* 5.4 0.2 - - - -
76C LYS* 1.3 74.0 - - + +
78C GLY* 1.3 59.5 - - - +
79C HIS* 3.3 36.7 + - + +
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C THR* 4.9 0.9 + - - -
74C ALA 2.8 7.1 + - - -
75C TYR* 3.3 9.4 + - - -
76C LYS 3.3 0.6 + - - -
77C GLU* 1.3 80.5 - - - +
79C HIS* 1.3 64.9 + - - +
80C LEU* 3.5 6.0 + - - +
85C VAL* 6.4 0.4 - - - -
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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