Contacts of the helix formed by residues 15 - 31 (chain A) in PDB entry 1J3C
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 ALA 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 1.3 74.2 - - - +
16A PHE* 1.3 65.8 + - - +
17A PHE 3.2 0.7 - - - -
18A LEU* 2.8 18.6 + - - +
19A PHE* 2.9 13.2 + - - +
47A TRP* 4.5 7.2 - - + -
55A LYS* 3.9 30.7 - - + +
58A TYR* 3.4 26.7 - - - +
59A GLU* 3.8 14.1 - - + -
62A ALA* 3.6 11.9 - - - +
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Residues in contact with PHE 16 (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 SER* 2.6 12.5 + - - +
15A ALA* 1.3 74.0 - - - +
17A PHE* 1.3 70.8 + + + +
19A PHE* 3.0 5.9 + + + +
20A CYS* 2.7 54.3 + - + +
43A LEU* 5.1 2.2 - - + -
44A GLY* 4.6 16.8 - - - -
47A TRP* 3.5 59.2 - + + +
55A LYS* 6.2 1.1 - - - -
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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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12A PRO 5.6 0.4 - - - -
13A PRO* 3.5 28.5 - - + -
14A SER* 3.9 14.0 + - - +
15A ALA 3.2 0.4 - - - -
16A PHE* 1.3 90.6 - + + +
18A LEU* 1.3 54.5 + - - +
20A CYS* 4.6 5.2 - - + -
21A SER* 2.5 44.6 + - - -
24A ARG* 5.9 6.3 - - - -
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Residues in contact with LEU 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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13A PRO* 3.1 33.7 - - + -
15A ALA 2.8 19.7 + - - +
17A PHE* 1.3 75.9 - - - +
19A PHE* 1.3 59.1 + - - +
21A SER* 3.2 5.2 + - - +
22A GLU* 3.0 32.0 - - - +
58A TYR* 3.4 33.0 - - + +
61A LYS* 3.4 51.6 - - + +
62A ALA* 3.6 13.0 - - + +
65A LEU* 5.0 0.9 - - + -
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Residues in contact with PHE 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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15A ALA 2.9 8.4 + - - +
16A PHE* 3.5 7.6 - + - +
18A LEU* 1.3 76.8 - - - +
20A CYS* 1.3 59.8 + - + +
22A GLU* 3.0 1.8 + - - -
23A TYR* 2.6 106.9 + + + -
43A LEU* 4.7 17.5 - - + -
46A MET* 5.4 10.1 - - + -
47A TRP* 3.4 46.2 - + + -
50A GLN* 5.5 8.7 - - + -
54A ASP* 5.1 10.3 - - + -
58A TYR* 4.4 16.6 - + + -
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Residues in contact with CYS 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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16A PHE* 2.7 40.2 + - + +
17A PHE* 4.3 3.8 - - + +
19A PHE* 1.3 76.3 - - + +
21A SER* 1.3 58.9 + - - +
24A ARG* 2.8 83.5 + - - +
39A THR 5.3 0.7 - - - -
40A ALA* 5.9 2.2 - - - -
43A LEU* 3.6 25.6 - - + -
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Residues in contact with SER 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* 2.5 30.3 + - - -
18A LEU* 3.2 10.0 + - - +
20A CYS* 1.3 77.3 - - - +
22A GLU* 1.3 68.4 + - - +
24A ARG* 4.2 10.9 - - - +
25A PRO* 3.3 18.5 - - - +
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Residues in contact with GLU 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 LEU* 3.0 22.9 - - - +
19A PHE 3.0 3.0 + - - +
20A CYS 3.0 0.6 - - - -
21A SER* 1.3 90.6 + - - +
23A TYR* 1.3 67.2 + - + +
24A ARG 3.6 0.2 - - - -
25A PRO* 3.3 16.9 - - - +
26A LYS* 4.3 5.5 + - - +
58A TYR* 4.1 20.9 + - + +
61A LYS* 5.4 7.6 - - - +
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Residues in contact with TYR 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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19A PHE* 2.6 79.6 + + + +
22A GLU* 1.3 81.9 - - + +
24A ARG* 1.3 66.8 + - - +
25A PRO 3.3 0.4 - - - -
26A LYS* 2.8 33.3 + - + +
27A ILE* 3.0 14.8 + - + +
43A LEU* 3.4 18.4 - - + -
46A MET* 6.3 3.8 - - + -
58A TYR* 5.3 10.4 - + - -
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Residues in contact with ARG 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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17A PHE* 5.9 6.5 - - - -
20A CYS* 2.8 51.8 + - - +
21A SER* 4.1 7.9 - - - +
23A TYR* 1.3 71.0 - - - +
25A PRO* 1.3 68.6 - - + +
27A ILE* 3.0 12.7 + - - +
28A LYS* 2.8 28.7 - - + +
36A ILE* 4.8 22.4 - - - +
39A THR* 4.1 17.7 + - + +
40A ALA* 5.0 12.5 - - - +
43A LEU* 3.3 24.5 - - + +
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Residues in contact with PRO 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 SER 3.3 20.4 - - - +
22A GLU* 3.3 18.2 - - - +
23A TYR 3.4 0.9 - - - -
24A ARG* 1.3 97.9 - - + +
26A LYS* 1.3 60.6 + - - +
28A LYS* 3.4 19.2 + - + +
29A SER* 3.4 11.1 + - - -
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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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22A GLU 4.3 3.4 - - - +
23A TYR* 2.8 30.0 + - + +
25A PRO* 1.3 78.9 - - - +
27A ILE* 1.3 72.4 + - + +
28A LYS 3.1 0.7 + - - -
29A SER* 3.1 21.3 + - - -
30A GLU* 3.6 22.2 + - + +
31A HIS* 5.3 5.5 - - - -
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Residues in contact with ILE 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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23A TYR* 3.3 20.6 - - + +
24A ARG* 3.0 8.5 + - - +
26A LYS* 1.3 86.9 - - + +
28A LYS* 1.3 55.2 + - + +
31A HIS* 2.6 66.1 + - + +
34A LEU* 3.5 33.7 - - + -
39A THR* 5.0 0.4 - - - +
42A LYS* 4.9 12.1 - - + -
43A LEU* 4.0 26.7 - - + -
46A MET* 6.2 6.5 - - + -
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Residues in contact with LYS 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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24A ARG* 2.8 28.7 - - + +
25A PRO* 3.5 15.7 - - + +
26A LYS 3.1 0.4 - - - -
27A ILE* 1.3 83.2 - - + +
29A SER* 1.3 64.9 + - - +
30A GLU 3.1 0.5 + - - -
31A HIS 3.5 22.0 + - - +
32A PRO* 4.1 7.3 - - - +
34A LEU* 3.3 28.8 + - - -
35A SER* 5.3 1.8 - - - +
36A ILE* 5.4 7.1 - - - +
39A THR* 4.1 13.3 + - + +
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Residues in contact with SER 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 PRO 3.4 7.6 + - - -
26A LYS* 3.1 14.0 + - - -
28A LYS* 1.3 78.8 - - - +
30A GLU* 1.3 65.6 + - - +
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Residues in contact with GLU 30 (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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26A LYS* 3.6 19.7 + - + +
27A ILE 3.4 1.6 + - - +
29A SER* 1.3 84.5 - - - +
31A HIS* 1.3 88.4 + - + +
32A PRO* 3.5 10.6 - - - +
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 5.3 5.2 - - - -
27A ILE* 2.6 57.8 + - + +
28A LYS* 3.6 13.3 - - - +
30A GLU* 1.3 96.3 + - + +
32A PRO* 1.3 67.7 - - - +
33A GLY 3.4 1.1 - - - +
34A LEU* 3.2 41.8 - - + +
42A LYS* 5.2 11.9 + - - -
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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