Contacts of the helix formed by residues 68 - 76 (chain L) in PDB entry 1JI4
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 68 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I MET* 3.6 13.4 - - - +
80I GLU* 3.4 29.2 - - + -
81I GLU 3.3 22.4 - - - +
82I THR* 4.1 14.1 - - + +
66L LEU* 3.7 1.4 - - - +
67L VAL* 1.3 88.6 + - + +
69L LEU* 1.3 63.8 + - - +
70L SER* 3.7 5.2 + - - -
71L GLU* 3.0 40.0 + - - +
72L ALA* 3.2 15.1 + - - +
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Residues in contact with LEU 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE* 4.0 17.9 - - + +
16I VAL* 3.7 38.8 - - + +
19I MET* 3.3 39.9 - - + -
69I LEU* 3.9 21.8 - - + +
72I ALA* 5.0 3.8 - - + -
73I ILE* 4.3 15.9 - - + -
80I GLU* 2.9 16.3 + - - +
15L ILE* 4.3 15.5 - - + -
68L THR* 1.3 71.2 - - - +
70L SER* 1.3 56.3 + - - +
72L ALA* 3.2 7.3 + - - +
73L ILE* 3.0 34.2 + - - +
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Residues in contact with SER 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I ILE* 4.0 15.2 - - - +
80I GLU* 3.5 12.7 + - - -
68L THR* 3.1 7.8 - - - -
69L LEU* 1.3 77.5 - - - +
71L GLU* 1.3 64.2 + - - +
73L ILE* 3.6 5.9 + - - +
74L LYS* 3.3 20.8 + - - +
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Residues in contact with GLU 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I THR* 5.1 2.3 - - - +
8L LYS* 4.6 5.7 + - - -
65L PRO 4.5 2.1 - - - +
66L LEU* 3.8 28.5 - - + +
67L VAL* 3.2 38.2 + - - +
68L THR* 3.0 27.7 + - + +
70L SER* 1.3 76.3 - - - +
72L ALA* 1.3 64.2 + - - +
74L LYS* 3.1 11.1 + - - +
75L LEU* 3.0 29.6 + - + +
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Residues in contact with ALA 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I MET* 4.7 2.5 - - + -
69I LEU* 5.0 2.0 - - + -
12L ALA* 3.6 5.9 - - - +
15L ILE* 3.6 31.0 - - + -
16L VAL* 4.8 3.4 - - + -
66L LEU* 3.8 19.0 - - + +
68L THR 3.2 9.6 + - - +
69L LEU* 3.2 14.5 + - - +
71L GLU* 1.3 79.2 - - - +
73L ILE* 1.3 59.6 + - - +
75L LEU 3.1 1.4 + - - -
76L THR* 3.0 28.9 + - - -
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Residues in contact with ILE 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I LEU* 4.3 9.9 - - + -
70I SER* 4.0 24.9 - - - +
73I ILE* 3.7 26.0 - - + -
16L VAL* 4.3 12.3 - - + -
69L LEU 3.0 14.7 + - - +
70L SER* 3.8 8.5 - - - +
71L GLU 3.5 0.2 - - - -
72L ALA* 1.3 74.5 - - - +
74L LYS* 1.3 59.7 + - - +
76L THR* 3.5 13.7 + - - +
79L LYS* 6.0 2.0 - - - +
80L GLU* 3.7 27.8 - - - +
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Residues in contact with LYS 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L SER 3.3 12.9 + - - +
71L GLU* 3.1 13.4 + - - +
72L ALA 3.0 0.8 - - - -
73L ILE* 1.3 81.6 - - - +
75L LEU* 1.3 69.4 + - + +
76L THR 3.7 1.8 - - - +
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Residues in contact with LEU 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LYS* 4.0 33.0 - - + +
9L HIS* 3.0 43.7 + - + +
12L ALA* 3.8 13.5 - - + +
66L LEU* 3.5 27.4 - - + -
71L GLU* 3.0 22.1 + - + +
72L ALA 3.1 0.2 + - - -
74L LYS* 1.3 91.5 - - + +
76L THR* 1.3 67.4 + - - +
77L ARG* 4.1 2.9 + - - +
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Residues in contact with THR 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ALA* 3.4 14.8 - - + +
13L ASP* 2.9 25.6 - - - +
16L VAL* 3.2 34.1 - - + +
72L ALA 3.0 13.9 + - - -
73L ILE* 3.5 19.1 + - - +
74L LYS 3.7 2.5 - - - +
75L LEU* 1.3 79.7 - - - +
77L ARG* 1.3 60.7 + - - +
78L VAL* 3.3 18.8 + - + +
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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