Contacts of the helix formed by residues 63 - 72 (chain I) in PDB entry 1NJI
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 ARG 63 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1151A G 2.4 37.5 + - - -
1152A A 4.6 15.0 + - - -
1188A A 5.8 2.4 + - - -
1209A C 5.9 0.8 + - - -
1210A G 2.8 54.8 + - - +
1211A G 3.5 23.5 + - - +
15I TRP* 3.3 31.4 - - + -
16I LYS* 3.7 10.1 - - - +
19I GLU* 5.3 5.3 + - - -
23I ILE* 5.7 0.6 - - - +
64I ASN* 1.3 69.5 + - - +
65I THR* 3.8 15.9 - - - +
66I LEU* 3.1 26.9 + - + +
67I LEU* 3.1 29.3 + - - +
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Residues in contact with ASN 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A G 4.1 3.4 + - - -
1211A G 2.9 47.2 + - - +
1212A C 4.5 6.5 + - - +
63I ARG* 1.3 73.2 - - - +
65I THR* 1.3 53.8 + - + +
67I LEU* 2.8 21.3 + - - +
68I GLU* 2.7 50.5 + - + +
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Residues in contact with THR 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A A 4.1 20.5 + - - +
1151A G 2.7 45.3 + - + +
1211A G 4.7 0.8 + - - +
63I ARG* 3.8 11.4 - - - +
64I ASN* 1.3 76.1 - - + +
66I LEU* 1.3 62.6 + - - +
68I GLU* 3.5 16.8 + - - +
69I ARG* 3.1 26.7 + - - +
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Residues in contact with LEU 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A A 4.0 32.5 - - - +
15I TRP* 4.4 19.7 - - + -
16I LYS* 4.4 11.4 - - + +
19I GLU* 3.5 30.5 - - + +
20I VAL* 4.1 13.0 - - + +
23I ILE* 3.6 22.1 - - + +
63I ARG* 3.1 33.1 + - + +
64I ASN 3.1 0.8 - - - -
65I THR* 1.3 82.6 - - - +
67I LEU* 1.3 61.4 + - - +
69I ARG* 3.0 6.7 - - + +
70I ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ILE* 3.6 33.0 - - + -
27I ILE* 6.3 0.2 - - + -
63I ARG 3.1 19.0 + - - +
64I ASN* 2.8 20.0 + - + +
66I LEU* 1.3 74.1 - - - +
68I GLU* 1.3 58.3 - - + +
69I ARG 2.9 4.6 + - - -
70I ALA* 3.0 3.6 + - - +
71I LEU* 2.8 39.2 + - + +
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Residues in contact with GLU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I ASN* 2.7 40.7 + - + +
65I THR* 3.5 16.1 + - - +
67I LEU* 1.3 72.9 - - + +
69I ARG* 1.3 61.4 + - - +
71I LEU* 3.7 14.9 + - + +
72I ASP* 2.8 32.4 + - - +
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Residues in contact with ARG 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A A 3.2 62.9 + - + +
20I VAL* 3.6 29.1 - - + +
65I THR 3.1 16.5 + - - +
66I LEU* 3.0 15.7 - - + +
67I LEU 2.9 0.2 - - - -
68I GLU* 1.3 75.7 - - - +
70I ALA* 1.3 61.7 + - - +
72I ASP* 2.9 23.0 + - - +
73I ASP* 2.8 20.2 - - - +
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Residues in contact with ALA 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I VAL* 4.1 4.0 - - - +
23I ILE* 3.1 38.4 - - + -
24I VAL* 3.4 22.7 - - + +
27I ILE* 3.4 12.1 - - + +
66I LEU 3.0 4.1 + - - +
67I LEU 3.6 2.2 - - - +
69I ARG* 1.3 75.8 - - - +
71I LEU* 1.3 58.0 + - - +
73I ASP* 2.6 42.3 + - - +
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ILE* 3.7 25.6 - - + -
67I LEU* 2.8 24.4 + - + +
68I GLU* 3.7 16.2 - - + +
70I ALA* 1.3 76.4 - - - +
72I ASP* 1.3 55.5 + - - +
73I ASP 2.7 18.9 + - - +
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Residues in contact with ASP 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I GLU* 2.8 19.8 + - - +
69I ARG* 2.9 20.0 + - - +
71I LEU* 1.3 76.5 - - - +
73I ASP* 1.3 65.4 + - - +
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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