Contacts of the helix formed by residues 72 - 80 (chain C) in PDB entry 1JIG
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 THR 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU 3.9 0.2 - - - -
71C ALA* 1.3 84.6 - - - +
73C MET* 1.3 64.4 + - - +
74C LYS* 3.8 4.1 + - - +
75C GLU* 3.1 32.5 + - + +
76C TYR* 3.1 29.5 + - - -
23D VAL* 3.9 1.3 - - - -
27D ASN* 4.7 0.9 - - - +
84D GLU* 3.4 23.8 - - + -
85D GLY 3.3 24.9 - - - +
87D SER* 5.7 2.9 - - - +
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Residues in contact with MET 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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23C VAL* 5.2 1.8 - - + -
72C THR* 1.3 69.8 - - - +
74C LYS* 1.3 64.7 + - - +
76C TYR* 3.2 8.7 + - - +
77C LEU* 3.0 28.2 + - - +
19D ASN* 3.7 45.1 - - + +
20D VAL* 3.9 11.9 - - - +
23D VAL* 4.1 14.3 - - + +
73D MET* 2.9 44.6 - - + -
76D TYR* 3.9 18.8 - - + -
77D LEU* 3.9 22.0 - - + -
84D GLU* 2.4 28.8 + - - +
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Residues in contact with LYS 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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72C THR* 3.2 4.9 - - - +
73C MET* 1.3 77.5 - - - +
75C GLU* 1.3 65.7 + - + +
77C LEU* 3.7 4.4 + - - +
78C ALA* 3.2 25.0 + - + +
77D LEU* 3.9 15.3 - - + +
84D GLU* 3.1 15.4 + - - +
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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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70C LEU* 4.3 29.2 - - + +
71C ALA 5.6 0.9 - - - +
72C THR* 3.1 30.7 + - + +
74C LYS* 1.3 82.0 - - + +
76C TYR* 1.3 58.4 + - - +
78C ALA* 3.3 8.0 + - - +
79C THR* 2.6 49.0 + - - +
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Residues in contact with TYR 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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15C VAL* 3.7 12.1 - - + +
16C ALA* 3.5 25.4 - - + +
19C ASN* 3.1 42.7 + - + -
20C VAL* 4.4 1.6 - - + -
70C LEU* 2.8 45.0 + - + -
71C ALA* 3.5 7.9 - - - -
72C THR 3.1 16.4 + - - -
73C MET* 3.2 13.7 + - - +
75C GLU* 1.3 75.2 - - - +
77C LEU* 1.3 56.2 + - - +
79C THR* 3.4 3.8 - - - -
80C SER* 2.7 38.9 + - - -
23D VAL* 3.7 19.8 - - + +
26D HIS* 5.6 0.3 - - - +
30D TRP* 3.7 13.5 - - - -
73D MET* 3.9 16.2 - - + -
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Residues in contact with LEU 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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20C VAL* 5.1 3.6 - - + -
73C MET 3.0 12.8 + - - +
74C LYS* 3.9 4.3 - - - +
76C TYR* 1.3 78.6 - - - +
78C ALA* 1.3 60.6 + - - +
79C THR 3.5 0.5 + - - -
80C SER* 4.3 12.6 + - - +
84C GLU* 3.5 31.0 - - + +
73D MET* 3.9 23.6 - - + -
74D LYS* 4.0 16.2 - - + +
77D LEU* 3.4 33.9 - - + -
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Residues in contact with ALA 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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74C LYS* 3.2 19.0 + - + +
75C GLU* 3.9 15.0 - - - +
76C TYR 3.2 0.6 - - - -
77C LEU* 1.3 79.7 - - - +
79C THR* 1.3 61.7 + - + +
80C SER 5.1 0.7 - - - -
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Residues in contact with THR 79 (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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12C ASN 5.4 0.4 - - - -
13C LYS* 3.2 23.8 + - - +
16C ALA* 2.8 30.8 - - - +
70C LEU* 3.5 22.7 - - + +
75C GLU* 2.6 35.3 + - - +
76C TYR* 3.4 0.3 - - - -
78C ALA* 1.3 84.6 - - + +
80C SER* 1.3 64.9 + - - +
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Residues in contact with SER 80 (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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16C ALA* 3.9 11.0 - - - -
17C ASN* 3.3 15.9 - - - -
20C VAL* 3.0 32.0 - - - +
76C TYR 2.7 20.4 + - - -
77C LEU* 4.3 11.8 + - - +
78C ALA 5.1 0.5 - - - -
79C THR* 1.3 77.6 + - - +
81C SER* 1.3 59.5 + - - +
82C VAL* 3.3 16.3 + - - +
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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