Contacts of the helix formed by residues 45 - 52 (chain N) 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 LEU 45 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N ASN* 1.3 69.4 - - - +
46N GLY* 1.3 65.5 + - - +
47N ARG 3.1 0.2 + - - -
48N ILE* 3.1 9.9 + - + +
49N GLU* 3.0 26.1 + - - +
64N VAL* 3.9 9.2 - - + -
65N LEU 3.7 14.6 - - - +
66N GLY* 4.3 4.0 - - - +
67N SER 2.9 14.7 + - - +
68N GLY 4.1 11.4 - - - +
69N VAL 4.5 1.1 - - - -
70N LEU* 4.2 24.0 - - + +
85N ALA* 4.6 3.8 - - + +
88N LYS* 3.4 45.5 - - + -
89N ILE* 3.6 33.2 - - + -
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Residues in contact with GLY 46 (chain N).
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 3.7 14.0 + - - +
7450 G 3.3 23.4 + - - -
44N ASN* 3.3 2.0 - - - +
45N LEU* 1.3 78.2 - - - +
47N ARG* 1.3 59.9 + - - +
49N GLU* 3.8 7.0 + - - +
50N ARG* 3.3 30.7 + - - +
67N SER 3.4 7.3 + - - -
68N GLY* 4.2 1.5 - - - -
69N VAL 4.5 5.8 - - - -
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Residues in contact with ARG 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7010 U 4.8 4.9 + - - -
7210 A 3.7 16.2 - - - -
7220 G 3.4 20.8 + - - -
7450 G 3.4 30.7 + - - -
7460 A 4.7 5.1 + - - -
43N VAL* 3.6 15.2 - - + +
44N ASN 3.4 2.7 + - - +
45N LEU 3.1 0.8 - - - -
46N GLY* 1.3 74.5 - - - +
48N ILE* 1.3 66.1 + - - +
49N GLU 3.2 0.2 - - - -
50N ARG* 3.2 24.1 + - - +
51N TYR* 3.2 37.8 + - + +
114N ILE* 4.0 8.5 - - + +
115N ARG 3.0 30.2 + - - -
8508N CL 3.5 23.6 - - + +
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Residues in contact with ILE 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N VAL* 4.1 9.9 - - + -
44N ASN 3.9 9.4 - - - +
45N LEU* 3.1 17.2 + - + +
47N ARG* 1.3 76.2 - - - +
49N GLU* 1.3 58.2 + - - +
52N ALA* 2.9 48.4 + - + +
58N VAL* 4.2 13.0 - - + -
60N VAL* 4.7 3.8 - - + -
64N VAL* 3.8 33.2 - - + -
70N LEU* 4.1 16.8 - - + -
74N VAL* 4.4 1.3 - - + -
76N VAL* 4.1 37.5 - - + -
89N ILE* 4.6 0.9 - - + -
114N ILE* 4.8 9.6 - - + -
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Residues in contact with GLU 49 (chain N).
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 6.1 0.7 - - - +
115K ARG* 6.1 3.1 - - - +
45N LEU 3.0 12.7 + - - +
46N GLY 3.9 5.4 - - - +
48N ILE* 1.3 78.9 - - - +
50N ARG* 1.3 57.6 + - - +
69N VAL 3.4 23.8 - - - +
70N LEU* 3.4 9.9 - - + +
71N GLN* 2.7 42.1 + - - +
72N LYS* 3.1 57.6 + - - +
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Residues in contact with ARG 50 (chain N).
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 38.0 + - - -
7010 U 3.0 55.9 + - - +
7440 G 3.8 9.7 + - - -
7450 G 4.9 4.9 + - - -
46N GLY 3.3 12.6 + - - +
47N ARG* 3.2 39.9 + - - +
48N ILE 3.2 0.6 - - - -
49N GLU* 1.3 83.1 - - + +
51N TYR* 1.3 93.4 + - + +
52N ALA 3.7 0.2 - - - -
72N LYS* 4.2 6.9 + - - -
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Residues in contact with TYR 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7010 U 3.9 21.1 + - - -
7200 G 6.0 2.0 - - - -
7210 A 3.5 55.2 - - - -
7220 G 4.1 8.7 + - - -
47N ARG* 3.2 31.5 + - + +
48N ILE 3.9 0.4 - - - -
50N ARG* 1.3 121.5 - - + +
52N ALA* 1.3 63.3 + - - +
53N GLN* 4.2 3.3 + - - -
56N GLU* 5.0 0.2 - - - +
72N LYS* 4.8 0.2 - - - -
112N ARG* 4.3 20.5 + - - -
114N ILE* 4.2 17.3 - - + -
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Residues in contact with ALA 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N ILE* 2.9 24.0 + - + +
49N GLU* 5.2 0.2 - - - -
50N ARG 3.7 0.4 - - - -
51N TYR* 1.3 80.1 - - - +
53N GLN* 1.3 62.0 + - - +
56N GLU* 5.2 1.8 - - - -
58N VAL* 3.5 31.9 - - + -
72N LYS* 2.6 38.7 + - + +
74N VAL* 4.0 13.2 - - + -
112N ARG* 5.3 2.2 - - - -
114N ILE* 5.8 0.9 - - + -
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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