Contacts of the helix formed by residues 66 - 72 (chain K) in PDB entry 1JJ2
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 VAL 66 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65K ASP* 1.3 70.4 - - - +
67K ARG* 1.3 67.2 + - - +
69K ILE* 3.0 11.6 + - - +
70K ASP* 2.8 27.7 + - + +
108K VAL* 3.8 17.2 - - + +
109K LEU 2.9 20.4 + - - +
110K GLY* 4.1 9.2 - - - -
111K ALA 3.4 21.8 - - - +
112K GLY 4.2 4.0 - - - +
113K GLN 4.1 4.0 - - - +
114K VAL* 3.8 25.8 - - + -
118K LEU* 5.5 2.0 - - + +
120K LEU* 4.6 3.4 - - + -
129K ALA* 4.3 6.3 - - + +
132K LYS* 4.5 2.2 - - + -
133K VAL* 4.2 22.0 - - + -
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Residues in contact with ARG 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6870 C 5.9 1.2 + - - -
6880 A 3.9 18.7 + - - -
6980 A 5.8 1.6 + - - -
7000 A 4.2 24.5 + - - +
7450 G 3.7 26.7 + - - +
65K ASP* 3.0 31.0 + - + +
66K VAL* 1.3 82.5 - - - +
68K GLU* 1.3 69.9 + - - +
70K ASP* 3.9 0.4 - - - +
71K GLU* 2.9 56.7 + - + +
111K ALA* 3.0 25.1 + - - +
112K GLY* 3.9 7.9 - - - +
113K GLN 4.1 11.4 - - - -
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Residues in contact with GLU 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6870 C 5.4 3.5 + - - +
7450 G 5.7 1.6 - - - +
64K ILE* 3.6 29.8 - - + +
65K ASP 2.9 13.3 + - - +
67K ARG* 1.3 89.6 + - - +
69K ILE* 1.3 66.3 + - - +
71K GLU* 4.9 3.6 - - - -
72K ASN* 3.0 37.2 + - - +
96K VAL* 5.1 6.0 - - + +
97K VAL* 6.1 0.2 - - - -
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Residues in contact with ILE 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K ILE* 3.8 37.2 - - + -
65K ASP 4.0 2.9 - - - +
66K VAL* 3.0 14.3 + - - +
68K GLU* 1.3 74.7 - - - +
70K ASP* 1.3 63.7 - - - +
72K ASN* 3.0 14.8 + - - +
73K VAL* 3.3 15.7 + - + +
76K LEU* 4.8 10.4 - - + +
91K VAL* 3.8 28.5 - - + -
93K VAL* 4.4 7.2 - - + -
96K VAL* 5.1 9.0 - - + -
108K VAL* 4.3 9.9 - - + -
118K LEU* 4.5 9.9 - - + -
120K LEU* 4.1 31.9 - - + -
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Residues in contact with ASP 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7000 A 2.7 34.6 + - - +
66K VAL 2.8 21.3 + - - +
67K ARG 3.9 0.4 - - - +
69K ILE* 1.3 74.6 - - - +
71K GLU* 1.3 61.1 + - - +
72K ASN 3.0 1.6 + - - -
73K VAL* 3.4 24.4 + - - +
113K GLN 3.9 4.3 - - - +
114K VAL* 3.6 10.5 - - + +
115K ARG* 3.3 22.6 + - - +
116K HIS* 2.9 35.2 + - - +
118K LEU* 3.8 9.0 - - + +
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Residues in contact with GLU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7000 A 3.1 46.8 - - + +
7450 G 2.8 46.3 + - - -
67K ARG* 2.9 34.6 + - - +
68K GLU* 4.2 5.7 - - - +
69K ILE 3.4 0.4 - - - -
70K ASP* 1.3 72.6 - - - +
72K ASN* 1.3 70.6 + - - +
73K VAL* 3.7 0.7 - - - -
74K THR* 5.4 0.7 + - - -
75K LEU* 4.0 7.4 - - - +
68N GLY* 3.9 15.0 + - - -
69N VAL* 3.9 22.9 - - + +
88N LYS* 5.4 1.6 + - - -
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Residues in contact with ASN 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K GLU* 3.0 32.8 + - - +
69K ILE 3.0 5.8 + - - +
70K ASP 3.0 1.2 - - - -
71K GLU* 1.3 91.6 + - - +
73K VAL* 1.3 64.1 + - - +
74K THR* 3.5 2.2 - - - -
75K LEU* 3.0 33.3 + - + +
76K LEU* 2.9 33.6 + - + +
88N LYS* 4.5 7.4 + - - -
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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