Contacts of the helix formed by residues 33 - 48 (chain I) in PDB entry 2J28
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 ASN 33 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31I GLY 3.9 8.4 + - - -
32I VAL* 1.3 82.0 + - - +
34I ILE* 1.3 69.1 + - - +
35I MET* 3.5 1.6 - - + -
36I GLU* 3.4 17.3 + - + +
37I PHE* 3.2 16.6 + - - +
64I ARG* 4.6 9.9 + - - +
65I SER* 5.7 1.4 - - - -
66I PHE* 3.5 18.2 - - + -
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Residues in contact with ILE 34 (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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18I ASN* 3.3 35.2 - - - +
23I VAL* 5.1 4.0 - - + -
24I GLY* 3.3 46.2 - - - +
27I LEU* 4.4 11.2 - - + -
28I GLY* 4.0 15.9 - - - +
32I VAL* 3.6 4.9 + - - +
33I ASN* 1.3 72.0 - - - +
35I MET* 1.3 64.3 + - - +
37I PHE* 3.1 6.5 + - - +
38I CYS* 2.9 21.2 + - + +
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Residues in contact with MET 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ASN* 4.3 10.3 - - - +
33I ASN* 3.5 0.8 - - + -
34I ILE* 1.3 77.5 - - - +
36I GLU* 1.3 67.6 + - - +
38I CYS* 3.1 19.0 + - - +
39I LYS* 3.1 56.5 + - + +
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Residues in contact with GLU 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ASN* 3.4 20.8 + - + +
34I ILE 3.4 0.2 - - - -
35I MET* 1.3 78.8 - - - +
37I PHE* 1.3 58.0 + - - +
39I LYS* 4.0 3.6 - - - +
40I ALA* 2.7 43.3 + - + +
65I SER* 5.5 2.6 + - - -
66I PHE* 3.1 42.2 + - - +
68I PHE* 5.1 1.9 - - - -
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Residues in contact with PHE 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LEU* 4.9 8.7 - - + -
12I VAL* 5.0 2.9 - - + -
17I ALA* 5.3 5.2 - - + -
23I VAL* 4.8 13.5 - - + -
27I LEU* 4.2 10.1 - - + -
32I VAL* 4.7 4.0 - - + -
33I ASN 3.2 4.2 + - - +
34I ILE* 3.1 9.0 + - - +
36I GLU* 1.3 77.4 - - - +
38I CYS* 1.3 63.5 + - - +
40I ALA* 3.9 3.4 - - - -
41I PHE* 2.5 69.6 + + + +
56I VAL* 3.9 14.8 - - + -
58I ILE* 3.3 40.4 - - + -
66I PHE* 3.5 19.2 - + + -
68I PHE* 3.8 32.1 - + + -
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Residues in contact with CYS 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ALA* 3.1 48.5 - - + -
18I ASN* 3.4 20.4 - - + +
34I ILE 2.9 12.5 + - - +
35I MET* 3.1 11.9 + - - +
37I PHE* 1.3 81.2 - - - +
39I LYS* 1.3 74.8 + - - +
41I PHE* 4.0 0.9 - - - +
42I ASN* 3.2 33.9 + - - +
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Residues in contact with LYS 39 (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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35I MET* 3.1 46.8 + - + +
36I GLU* 4.1 3.1 - - - +
38I CYS* 1.3 84.5 - - - +
40I ALA* 1.3 67.2 + - - +
42I ASN* 3.9 3.3 - - - +
43I ALA* 3.1 24.4 + - - +
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Residues in contact with ALA 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I GLU* 2.7 39.2 + - + +
37I PHE* 3.6 4.9 - - - +
39I LYS* 1.3 73.5 - - - +
41I PHE* 1.3 64.9 + - - +
43I ALA* 3.2 18.3 - - - +
44I LYS* 3.7 9.4 + - - +
68I PHE* 3.9 22.7 - - + -
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Residues in contact with PHE 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.1 24.5 - - + -
13I ALA 3.0 23.6 - - - -
14I ALA 3.3 1.3 - - - -
16I MET 4.5 3.1 - - - -
17I ALA* 4.9 2.0 - - + -
37I PHE* 2.5 51.9 + + + +
38I CYS* 4.0 2.5 - - - +
40I ALA* 1.3 74.7 - - - +
42I ASN* 1.3 68.7 + - - +
43I ALA 3.0 6.1 + - - -
44I LYS* 3.3 4.0 + - - +
45I THR* 2.8 47.4 + - + +
54I ILE* 3.3 18.8 - - + -
56I VAL* 3.8 22.0 - - + -
68I PHE* 3.9 17.6 - + - -
70I THR* 3.9 13.0 - - - -
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Residues in contact with ASN 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA 2.8 16.8 - - - +
15I GLY* 3.6 5.3 - - - -
16I MET* 2.5 52.2 + - - +
17I ALA* 3.3 6.7 - - - +
38I CYS* 3.2 25.6 + - - +
39I LYS* 4.3 2.9 - - - +
41I PHE* 1.3 78.6 - - - +
43I ALA* 1.3 51.9 + - - +
45I THR* 2.7 21.2 + - - +
46I ASP* 2.7 29.2 - - - +
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Residues in contact with ALA 43 (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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39I LYS 3.1 14.0 + - - +
40I ALA* 3.2 15.3 - - - +
41I PHE 3.0 1.4 + - - -
42I ASN* 1.3 76.1 - - - +
44I LYS* 1.3 67.3 + - + +
46I ASP* 2.6 27.6 - - - +
47I SER* 4.4 0.7 + - - -
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Residues in contact with LYS 44 (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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40I ALA* 3.7 8.0 + - - +
41I PHE* 3.3 5.8 + - - +
43I ALA* 1.3 77.1 - - + +
45I THR* 1.3 59.9 + - + +
46I ASP 2.9 10.9 + - - -
47I SER* 3.0 19.3 + - - +
48I ILE* 3.1 10.3 + - - +
68I PHE* 5.1 18.4 - - + -
70I THR* 5.7 13.9 - - + -
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Residues in contact with THR 45 (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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14I ALA* 2.7 34.8 + - - +
15I GLY* 3.9 2.0 - - - -
41I PHE* 2.8 51.8 + - + +
42I ASN* 2.7 26.7 + - - +
44I LYS* 1.3 77.2 - - + +
46I ASP* 1.3 54.0 + - - +
48I ILE* 2.5 44.9 - - + +
49I GLU 4.0 1.9 - - - +
50I LYS* 3.9 8.4 - - - +
54I ILE* 4.7 0.7 - - + -
70I THR* 5.0 3.1 - - + +
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Residues in contact with ASP 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I GLY* 5.6 4.3 - - - -
42I ASN* 2.7 14.8 - - - +
43I ALA* 2.6 24.5 - - - +
44I LYS 2.9 0.8 + - - -
45I THR* 1.3 75.8 + - - +
47I SER* 1.3 63.9 + - - +
48I ILE 2.8 11.8 - - - +
50I LYS* 3.4 39.8 + - - +
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Residues in contact with SER 47 (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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44I LYS* 3.0 10.5 + - - -
46I ASP* 1.3 77.2 - - - +
48I ILE* 1.3 67.2 + - - +
49I GLU* 3.5 1.7 + - - -
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Residues in contact with ILE 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA* 4.8 2.0 - - + -
44I LYS 3.1 6.0 + - - +
45I THR* 2.5 61.1 - - + +
46I ASP 2.8 9.4 - - - +
47I SER* 1.3 78.3 - - - +
49I GLU* 1.3 75.1 + - + +
54I ILE* 3.5 34.3 - - + -
70I THR* 3.8 22.0 - - + +
71I LYS 3.7 11.0 - - - +
73I PRO* 5.6 2.5 - - + -
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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