Contacts of the helix formed by residues 70 - 78 (chain D) in PDB entry 1JI5
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 70 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C THR* 4.0 2.4 - - - +
82C GLU* 3.3 35.4 - - + -
83C ALA 3.6 17.7 - - - +
85C TYR* 3.9 7.4 - - + +
68D VAL 4.0 0.8 - - - -
69D ALA* 1.3 83.7 - - - +
71D MET* 1.3 63.7 - - - +
72D LYS* 3.8 5.5 + - + +
73D GLU* 2.8 45.7 + - - +
74D TYR* 3.1 25.8 + - - -
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Residues in contact with MET 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C SER* 4.0 16.2 - - - +
18C VAL* 4.1 16.2 - - - -
21C THR* 3.5 22.9 - - + +
71C MET* 3.1 71.5 - - + +
74C TYR* 3.7 19.3 - - + -
75C LEU* 3.9 21.5 - - + -
82C GLU* 2.8 18.3 + - - +
21D THR* 5.2 0.7 - - - +
70D THR* 1.3 71.4 - - - +
72D LYS* 1.3 62.8 + - - +
74D TYR* 3.2 4.3 + - - +
75D LEU* 2.9 27.5 + - - +
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.9 14.9 - - + +
82C GLU* 3.2 17.0 + - - +
70D THR* 3.8 7.0 - - + +
71D MET* 1.3 79.7 - - - +
73D GLU* 1.3 66.3 + - + +
75D LEU* 3.3 5.5 + - - +
76D GLU* 3.2 45.7 + - - +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 2.4 39.8 + - - -
68D VAL* 3.9 27.7 - - + +
69D ALA 4.0 0.3 + - - -
70D THR* 2.8 25.0 + - - +
72D LYS* 1.3 79.0 - - + +
74D TYR* 1.3 61.2 + - - +
76D GLU* 2.9 27.0 + - + +
77D ILE* 2.5 32.1 + - + +
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Residues in contact with TYR 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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21C THR* 3.5 27.2 - - + +
28C TRP* 3.8 12.0 - - - -
71C MET* 3.7 20.2 - - + -
13D VAL* 3.5 17.9 - - + +
14D ALA* 3.4 29.8 - - + +
17D SER* 3.4 22.4 + - - -
18D VAL* 5.0 0.4 - - + -
53D ILE* 5.1 0.3 - - - +
68D VAL* 3.0 45.4 + - + -
69D ALA* 3.6 8.1 - - - -
70D THR 3.1 15.4 + - - -
71D MET* 3.2 15.7 + - - +
73D GLU* 1.3 76.1 - - - +
75D LEU* 1.3 56.0 + - - +
78D SER* 2.7 39.7 + - - -
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Residues in contact with LEU 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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71C MET* 3.9 35.4 - - + -
72C LYS* 3.9 15.0 - - + +
75C LEU* 3.4 34.3 - - + -
18D VAL* 4.9 5.8 - - + -
71D MET 2.9 11.7 + - - +
72D LYS* 3.6 5.4 - - - +
73D GLU 3.1 0.2 - - - -
74D TYR* 1.3 78.7 - - - +
76D GLU* 1.3 61.0 + - - +
77D ILE 3.3 0.9 + - - -
78D SER* 4.2 10.5 + - - +
82D GLU* 4.1 20.0 - - + +
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Residues in contact with GLU 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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72D LYS* 3.2 41.7 + - - +
73D GLU* 3.1 27.7 - - - +
75D LEU* 1.3 78.3 - - - +
77D ILE* 1.3 60.1 + - + +
78D SER 5.1 0.4 - - - -
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Residues in contact with ILE 77 (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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7D GLU* 4.3 15.7 - - - +
10D ASN* 3.6 15.3 - - + +
11D LYS* 2.9 45.5 + - + +
14D ALA* 3.9 7.0 - - + -
68D VAL* 5.0 10.1 - - + -
73D GLU* 2.5 42.1 + - + +
74D TYR* 3.7 6.7 - - + +
76D GLU* 1.3 81.0 - - + +
78D SER* 1.3 67.6 + - - +
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Residues in contact with SER 78 (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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11D LYS* 3.8 1.1 - - - +
14D ALA* 3.9 11.0 - - - +
15D ASP* 3.1 15.0 + - - -
18D VAL* 3.1 31.4 - - - +
74D TYR 2.7 22.5 + - - -
75D LEU* 4.2 10.1 - - - +
76D GLU 5.1 0.3 - - - -
77D ILE* 1.3 76.7 - - - +
79D SER* 1.3 60.7 + - - +
80D ILE* 3.0 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