Contacts of the helix formed by residues 69 - 78 (chain C) in PDB entry 5U03
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 LEU 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C GLY* 6.1 0.2 - - - -
57C GLU* 3.4 53.6 + - + +
59C PHE* 3.9 27.6 - - + -
67C VAL 3.8 1.6 + - - -
68C ASP* 1.3 71.8 + - - +
70C ASP* 1.3 58.6 + - - +
71C LEU 3.0 3.6 - - - -
72C GLY* 2.7 22.1 + - - -
73C ASN* 2.8 26.6 + - - +
76C ARG* 5.3 2.2 - - - +
315C ALA* 4.3 10.3 - - + -
316C SER* 3.9 27.8 - - - +
529C PHE* 4.7 1.3 - - + -
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Residues in contact with ASP 70 (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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17C GLY* 4.6 4.7 - - - -
38C LYS* 3.6 12.8 - - + -
68C ASP* 2.9 16.3 + - - +
69C LEU* 1.3 77.6 - - - +
71C LEU* 1.3 57.7 + - - +
73C ASN* 3.1 23.2 + - + +
74C TYR* 2.9 36.7 + - + -
146C GLU* 3.3 21.3 - - - +
601C ATP 2.8 47.3 + - - -
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Residues in contact with LEU 71 (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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36C SER* 4.6 3.4 - - - +
38C LYS* 3.8 28.9 - - + +
59C PHE* 4.6 1.3 - - - -
61C LEU* 4.8 8.7 - - + -
67C VAL* 3.6 35.2 - - + -
68C ASP 3.1 8.0 + - - +
69C LEU 3.0 0.4 - - - -
70C ASP* 1.3 76.7 - - - +
72C GLY* 1.3 58.9 + - - +
74C TYR* 3.2 27.3 + - + +
75C GLU* 3.0 29.8 + - - +
82C LEU* 3.7 20.0 - - + +
86C ASN* 4.5 11.7 - - + +
87C ASN* 3.8 25.1 - - + +
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Residues in contact with GLY 72 (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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59C PHE* 3.6 41.3 - - - -
69C LEU* 2.7 12.0 + - - -
71C LEU* 1.3 76.5 - - - +
73C ASN* 1.3 58.4 + - - +
75C GLU* 3.0 4.3 + - - +
76C ARG* 2.8 32.2 + - - +
532C ARG* 4.6 3.1 + - - -
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Residues in contact with ASN 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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17C GLY 5.7 2.7 - - - +
18C ILE* 5.2 12.6 - - + +
21C SER* 5.0 4.7 - - - +
69C LEU* 2.8 26.3 + - - +
70C ASP* 3.1 33.4 + - - +
72C GLY* 1.3 75.2 - - - +
74C TYR* 1.3 68.7 + - + +
76C ARG* 2.7 47.4 + - - +
77C PHE* 2.9 28.1 + - + -
601C ATP 5.5 0.2 + - - -
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Residues in contact with TYR 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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17C GLY* 3.5 24.8 - - - -
20C ALA* 3.3 21.0 - - + +
21C SER* 3.6 24.0 - - - -
36C SER* 3.6 24.0 - - - +
37C ILE 5.9 0.4 - - - -
38C LYS* 5.2 1.6 - - + -
70C ASP* 2.9 22.4 + - + -
71C LEU* 3.4 33.9 - - + +
72C GLY 3.1 0.2 - - - -
73C ASN* 1.3 77.7 - - + +
75C GLU* 1.3 52.4 + - - +
77C PHE* 3.3 1.6 + - - +
78C LEU* 2.7 48.2 + - + +
80C ILE* 4.7 7.4 - - + -
82C LEU* 4.2 8.3 - - + -
146C GLU* 2.4 39.0 + - + +
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Residues in contact with GLU 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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59C PHE* 3.3 26.2 - - - -
61C LEU* 4.0 4.9 - - - +
62C ASP* 5.4 0.3 - - - +
71C LEU 3.0 14.2 + - - +
72C GLY* 3.0 7.9 + - - +
74C TYR* 1.3 74.5 - - - +
76C ARG* 1.3 57.6 + - - +
78C LEU 2.7 21.7 - - - +
79C ASP* 4.6 3.5 - - - +
80C ILE* 3.4 15.3 - - + +
81C ARG* 3.2 34.9 + - - +
82C LEU* 2.8 42.3 + - + +
477C ARG* 4.4 0.9 + - - -
532C ARG* 3.0 25.3 + - - +
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Residues in contact with ARG 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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59C PHE* 6.4 0.2 - - - -
69C LEU* 5.3 2.4 - - - +
72C GLY 2.8 12.1 + - - +
73C ASN* 2.7 44.6 + - - +
75C GLU* 1.3 81.3 - - - +
77C PHE* 1.3 74.7 + - + +
78C LEU* 3.6 1.0 + - - +
79C ASP* 5.4 2.1 - - - +
284C LYS* 5.9 0.3 + - - -
316C SER* 4.2 21.6 + - - +
319C LYS* 3.6 35.0 - - - +
323C HIS* 3.7 21.9 + - - -
528C GLU 5.3 4.0 + - - -
531C SER 4.8 3.2 + - - -
532C ARG* 3.5 19.2 - - - +
533C PRO* 3.8 25.9 - - + +
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Residues in contact with PHE 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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18C ILE* 6.5 0.2 - - + -
21C SER* 3.2 44.4 - - - +
22C SER* 4.1 11.0 - - - -
25C THR* 2.7 28.8 + - + -
28C LYS* 5.8 0.5 - - - +
73C ASN* 2.9 23.7 + - + +
74C TYR 3.8 0.2 - - - +
76C ARG* 1.3 96.5 - - + +
78C LEU* 1.4 71.7 + - + +
79C ASP* 5.7 0.2 - - - -
250C ILE* 4.0 23.8 - - + -
251C TYR* 5.7 0.2 - - - -
254C PRO* 4.4 3.8 - - + -
284C LYS* 4.3 8.5 + - - +
285C TRP* 3.5 39.5 - + - -
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Residues in contact with LEU 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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21C SER* 4.3 3.6 - - - +
24C GLY* 3.6 17.3 - - - +
25C THR* 3.8 16.6 - - - +
28C LYS* 3.9 15.9 - - + -
34C VAL* 3.5 36.3 - - + -
74C TYR* 2.7 25.6 + - + +
75C GLU* 2.7 33.3 - - - +
76C ARG 4.7 0.7 - - - -
77C PHE* 1.4 89.6 - - + +
79C ASP* 1.3 61.8 + - - +
80C ILE* 3.1 28.8 + - + -
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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