Contacts of the helix formed by residues 47 - 69 (chain A) in PDB entry 1J46
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 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET 4.6 5.2 - - - +
46A LEU* 1.3 75.5 - - - +
48A GLU* 1.3 59.2 + - - +
49A ALA* 3.6 7.2 + - - +
50A GLU* 3.2 37.2 + - - +
51A LYS* 2.8 31.0 + - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 1.3 74.5 - - - +
49A ALA* 1.3 53.6 + - - +
51A LYS* 4.2 10.1 - - + +
52A TRP* 2.5 44.0 + - + +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.2 8.1 + - - +
48A GLU* 1.3 78.3 - - - +
50A GLU* 1.3 61.5 + - + +
52A TRP* 3.4 7.4 - - - +
53A PRO* 2.8 25.6 - - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.9 25.3 - - + +
47A THR* 3.2 33.5 + - - +
49A ALA* 1.3 79.6 - - + +
51A LYS* 1.3 58.0 + - - +
53A PRO* 3.0 21.6 - - - +
54A PHE* 3.5 14.0 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TRP* 3.6 37.6 + - + +
44A LYS* 5.5 2.6 + - - +
46A LEU* 3.5 35.8 + - + +
47A THR 2.8 26.8 + - - +
48A GLU* 3.8 8.3 - - + +
50A GLU* 1.3 71.4 - - - +
52A TRP* 1.3 68.3 + - - +
54A PHE* 2.8 20.6 + - - +
55A PHE* 3.0 33.2 + - + -
122C G 3.3 19.4 + - - -
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Residues in contact with TRP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 2.5 28.9 + - + +
49A ALA* 3.4 8.3 - - - +
51A LYS* 1.3 72.4 - - - +
53A PRO* 1.3 77.1 - - + +
55A PHE* 2.8 26.5 + - + +
56A GLN* 2.9 59.6 + - + +
59A GLN* 5.2 11.2 - - - -
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Residues in contact with PRO 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 2.8 27.8 - - - +
50A GLU* 3.0 18.2 - - - +
52A TRP* 1.3 93.3 - - + +
54A PHE* 1.3 66.9 + - + +
56A GLN* 4.2 5.4 - - + +
57A GLU* 3.4 22.5 + - - +
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.6 22.5 - - - +
14A VAL* 5.4 7.8 - - + +
15A TRP* 3.6 47.3 - + + -
18A ASP* 6.5 0.9 - - + -
43A TRP* 4.3 11.4 - + + -
46A LEU* 5.7 2.9 - - + -
50A GLU 3.5 22.0 - - - -
51A LYS* 2.8 14.5 + - - +
53A PRO* 1.3 80.2 - - + +
55A PHE* 1.3 65.6 + - - +
57A GLU* 3.5 11.7 + - - +
58A ALA* 3.1 18.0 + - - +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.6 23.8 - - + -
43A TRP* 3.9 5.8 - + - -
51A LYS* 3.0 52.2 + - + +
52A TRP* 2.8 21.4 + - + +
54A PHE* 1.3 75.6 - - - +
56A GLN* 1.3 66.8 + - - +
58A ALA* 3.1 4.0 + - + +
59A GLN* 2.8 23.8 + - - +
122C G 4.3 24.0 - - - -
123C T 4.0 23.1 - - - -
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TRP* 2.9 58.9 + - + +
53A PRO* 4.2 5.5 - - + +
55A PHE* 1.3 78.8 - - - +
57A GLU* 1.3 58.6 + - - +
59A GLN* 3.1 18.1 + - - +
60A LYS* 2.7 29.8 + - + +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.6 15.9 - - + +
53A PRO 3.4 16.1 + - - +
54A PHE* 3.8 12.8 - - - +
55A PHE 3.2 0.6 - - - -
56A GLN* 1.3 80.0 - - - +
58A ALA* 1.3 57.9 + - - +
60A LYS* 3.0 9.9 + - + +
61A LEU* 2.7 53.6 + - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO* 5.4 0.7 - - - +
9A MET 3.8 12.3 - - - +
10A ASN* 3.8 2.2 - - - -
11A ALA* 3.3 33.4 - - + +
14A VAL* 4.7 2.0 - - + +
54A PHE 3.1 12.0 + - - +
55A PHE* 3.6 7.6 - - + +
57A GLU* 1.3 76.7 - - - +
59A GLN* 1.3 57.6 + - - +
61A LEU* 3.6 12.6 - - - +
62A GLN* 2.8 30.5 + - - +
123C T 6.5 0.4 - - - -
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TRP* 5.2 10.8 - - - -
55A PHE 2.8 13.9 + - - +
56A GLN* 3.1 22.9 + - - +
58A ALA* 1.3 78.8 - - - +
60A LYS* 1.3 57.5 + - - +
62A GLN* 3.2 15.0 + - - +
63A ALA* 2.9 28.9 + - + +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 2.7 20.1 + - + +
57A GLU* 3.5 12.6 - - + +
59A GLN* 1.3 71.1 - - - +
61A LEU* 1.3 62.4 + - + +
63A ALA* 3.2 5.6 + - + +
64A MET* 2.8 52.2 + - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO* 4.7 4.9 - - + -
9A MET* 4.6 19.7 - - + +
14A VAL* 3.6 35.0 - - + -
57A GLU* 2.7 46.2 + - + +
58A ALA* 3.6 5.4 - - - +
60A LYS* 1.3 73.8 - - + +
62A GLN* 1.3 58.0 + - - +
64A MET* 4.0 18.1 - - + +
65A HIS* 2.7 32.5 + - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO* 4.0 31.2 - - + +
58A ALA 2.8 17.4 + - - +
59A GLN* 3.5 14.8 - - - +
60A LYS 3.1 0.2 - - - -
61A LEU* 1.3 77.8 - - - +
63A ALA* 1.3 58.4 + - - +
65A HIS* 3.6 1.7 - - - +
66A ARG* 2.9 29.0 + - + +
123C T 3.3 13.1 + - - -
124C G 2.4 33.2 + - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 2.9 17.3 + - + +
60A LYS* 3.8 6.1 - - + +
62A GLN* 1.3 77.1 + - - +
64A MET* 1.3 63.3 + - - +
66A ARG* 3.1 11.0 + - - +
67A GLU* 3.0 21.2 + - - +
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 2.8 45.5 + - + +
61A LEU* 4.0 18.4 - - + +
63A ALA* 1.3 73.1 - - - +
65A HIS* 1.3 64.3 + - - +
67A GLU* 3.0 25.2 + - + +
68A LYS* 3.2 12.0 + - - +
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Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.4 31.0 - - + +
6A LYS 3.3 21.0 + - - -
7A ARG 5.1 0.2 - - - -
8A PRO* 3.8 29.3 - - + +
61A LEU 2.7 24.2 + - - +
62A GLN* 3.6 7.4 - - - +
64A MET* 1.3 73.0 - - - +
66A ARG* 1.3 64.7 + - - +
68A LYS* 3.2 9.3 + - - +
69A TYR* 3.2 32.7 + + - +
72A TYR* 4.7 15.5 - + + -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 2.9 16.7 + - + +
63A ALA* 3.1 12.3 + - - +
65A HIS* 1.3 79.4 - - - +
67A GLU* 1.3 58.2 + - - +
69A TYR 4.1 6.1 - - - +
70A PRO* 2.9 49.2 + - + +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA 3.0 12.2 + - - +
64A MET* 3.0 21.5 + - + +
66A ARG* 1.3 79.5 - - - +
68A LYS* 1.3 62.8 + - - +
70A PRO* 3.5 14.3 - - + +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET 3.2 7.9 + - - +
65A HIS* 3.2 12.3 + - - +
67A GLU* 1.3 80.3 - - - +
69A TYR* 1.3 106.6 + - + +
70A PRO* 3.4 6.6 - - - +
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.4 45.1 - - + +
65A HIS* 3.2 22.1 + + - +
66A ARG* 3.2 12.3 - - - +
68A LYS* 1.3 128.3 - - + +
70A PRO* 1.3 63.4 - - - +
71A ASN 3.0 5.2 - - - +
72A TYR* 3.0 32.2 + - + +
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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
------------------------------------------------------------
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