Contacts of the helix formed by residues 16 - 29 (chain A) in PDB entry 2JO0
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 PRO 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.3 22.9 - - + +
15A GLU* 1.4 106.2 - - - +
17A PHE* 1.3 66.1 + - - +
18A ARG 3.7 1.1 - - - -
19A ASP* 3.3 22.5 + - + +
20A TYR* 3.1 35.0 + - + +
46A LEU* 5.4 0.2 - - - -
59A LYS* 4.2 4.5 - - + +
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Residues in contact with PHE 17 (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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13A PRO 5.2 0.2 - - - -
14A LYS 4.1 20.2 - - - -
15A GLU* 2.9 12.5 + - - +
16A PRO* 1.3 72.3 - - - +
18A ARG* 1.3 57.9 + - - +
19A ASP* 4.4 0.4 + - - -
21A VAL* 2.8 35.8 + - - +
45A LEU 3.1 28.3 - - - -
46A LEU* 3.5 35.6 - - + +
47A VAL 4.4 0.7 - - - -
50A ALA* 4.4 9.2 - - + -
54A CYS* 3.3 34.8 - - - -
55A LYS* 4.5 19.1 - - + +
58A LEU* 3.5 39.5 - - + -
59A LYS* 5.4 2.4 - - + +
67A LEU* 3.9 4.0 - - + -
71A MET* 4.7 4.7 - - - -
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Residues in contact with ARG 18 (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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17A PHE* 1.3 77.5 - - - +
19A ASP* 1.3 102.4 + - - +
20A TYR 3.1 5.8 + - - -
21A VAL* 3.4 17.6 + - - +
22A ASP* 3.4 20.0 + - - +
49A ASN* 3.4 31.9 - - - +
55A LYS* 4.2 18.1 - - + +
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Residues in contact with ASP 19 (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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16A PRO* 3.3 25.5 + - + +
17A PHE 4.4 0.3 + - - -
18A ARG* 1.3 123.6 + - - +
20A TYR* 1.3 56.2 + - - +
23A ARG* 3.3 21.1 + - - +
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Residues in contact with TYR 20 (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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6A ILE* 3.7 5.0 - - + +
9A ILE* 2.7 55.2 + - + +
10A ARG* 3.4 10.2 - - - -
11A GLN* 5.4 6.5 - - + -
13A PRO* 3.4 37.4 - - + +
16A PRO* 3.1 27.4 + - + +
17A PHE 4.3 0.2 - - - +
19A ASP* 1.3 78.0 - - - +
21A VAL* 1.3 54.0 + - - +
22A ASP 3.3 2.0 - - - -
23A ARG* 3.2 12.5 + - + +
24A PHE* 2.8 56.2 + + + -
46A LEU* 4.4 7.0 - - + -
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Residues in contact with VAL 21 (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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17A PHE* 2.8 26.7 + - + +
18A ARG* 3.5 14.1 - - - +
20A TYR* 1.3 72.3 - - - +
22A ASP* 1.3 61.5 + - - +
24A PHE* 4.0 2.5 - - - -
25A TYR* 2.9 38.1 + - + +
46A LEU* 3.5 24.8 - - + +
47A VAL 3.3 49.4 - - - +
48A GLN* 3.5 2.7 - - - +
49A ASN* 3.4 17.5 - - - +
50A ALA* 5.5 0.2 - - + -
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Residues in contact with ASP 22 (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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18A ARG 3.4 11.3 + - - +
20A TYR 3.3 0.8 - - - -
21A VAL* 1.3 79.9 - - - +
23A ARG* 1.3 68.6 + - - +
25A TYR* 4.4 1.6 - - - +
26A LYS* 2.9 33.1 + - - +
48A GLN* 3.8 6.7 - - - +
49A ASN* 2.9 38.6 + - - +
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Residues in contact with ARG 23 (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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9A ILE* 5.1 14.6 - - + +
19A ASP 3.3 26.6 + - - +
20A TYR* 3.3 14.6 - - + +
22A ASP* 1.3 85.4 - - - +
24A PHE* 1.3 62.9 + - - +
26A LYS* 3.5 13.0 + - - +
27A THR* 3.2 22.9 + - - -
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Residues in contact with PHE 24 (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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6A ILE* 3.5 41.2 - - + +
9A ILE* 5.4 2.7 - - - -
20A TYR* 2.8 34.7 + + + +
21A VAL* 3.2 5.6 + - - +
23A ARG* 1.3 71.7 - - - +
25A TYR* 1.3 95.3 + + - +
27A THR* 3.1 9.4 + - - -
28A LEU* 2.9 55.1 + - + +
43A GLU* 3.6 18.8 - - - -
44A THR* 3.3 35.4 - - - -
45A LEU* 4.2 6.1 - - + -
46A LEU* 3.5 15.9 - - + -
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Residues in contact with TYR 25 (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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21A VAL* 2.9 21.3 + - + +
22A ASP 4.6 0.4 - - - +
24A PHE* 1.3 97.1 - + - +
26A LYS* 1.3 57.6 + - - +
28A LEU* 4.2 8.7 - - + -
29A ARG* 2.9 37.2 + - + +
32A GLN* 3.0 47.5 + - - -
33A ALA* 4.7 2.2 - - - -
35A GLN* 4.6 9.6 - - - +
39A ASN* 2.9 31.4 + - - +
44A THR* 4.2 0.2 - - - -
46A LEU 3.4 20.6 - - - -
47A VAL* 3.8 5.0 - - - +
48A GLN* 3.3 56.0 + - + +
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Residues in contact with LYS 26 (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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1A MET 5.9 2.0 - - - -
22A ASP 2.9 23.3 + - - +
23A ARG* 3.6 12.8 - - - +
25A TYR* 1.3 74.6 - - - +
27A THR* 1.3 74.1 + - + +
29A ARG* 3.5 18.4 + - - +
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Residues in contact with THR 27 (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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1A MET 5.8 1.1 - - - +
4A THR* 3.5 26.2 - - + +
5A SER* 4.4 4.6 - - - -
6A ILE* 4.0 19.0 + - - +
9A ILE* 5.3 3.5 - - - +
23A ARG 3.2 9.4 + - - +
24A PHE* 3.1 13.7 + - - -
26A LYS* 1.3 94.3 - - + +
28A LEU* 1.3 59.5 + - - +
29A ARG* 2.9 34.2 + - - +
30A ALA* 5.0 0.3 - - - +
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Residues in contact with LEU 28 (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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6A ILE* 4.0 15.7 - - + +
24A PHE* 2.9 42.5 + - + +
25A TYR* 4.1 6.5 - - + +
27A THR* 1.3 76.2 - - - +
29A ARG* 1.3 52.0 + - - +
30A ALA* 2.6 18.5 + - - +
31A GLU* 3.2 33.0 + - + +
32A GLN* 3.4 41.1 - - + +
42A THR* 4.7 4.3 - - + +
43A GLU* 3.1 25.6 - - + +
44A THR* 5.2 0.4 - - - -
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Residues in contact with ARG 29 (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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25A TYR* 2.9 25.7 + - + +
26A LYS* 3.5 17.6 + - - +
27A THR* 2.9 23.8 + - - +
28A LEU* 1.3 74.3 - - - +
30A ALA* 1.3 82.7 + - - +
31A GLU 3.3 1.1 - - - -
32A GLN 4.5 0.4 - - - -
33A ALA* 3.4 43.9 - - + +
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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