Contacts of the helix formed by residues 7 - 30 (chain A) in PDB entry 4JR8
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 GLU 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 3.6 2.6 - - + +
5A GLU* 2.5 38.3 + - - +
6A GLY* 1.3 71.2 - - - -
8A ALA* 1.3 66.1 + - - +
9A ILE 3.3 1.6 - - - -
10A TRP* 3.2 25.7 + - - +
11A LEU* 3.4 15.2 + - + +
64A LEU* 5.2 0.7 - - - +
75A PRO* 6.0 1.0 - - - +
77A TYR* 2.6 34.8 + - + +
205A ILE* 3.2 30.5 - - + +
206A GLY* 4.0 3.8 - - - -
209A THR* 3.5 27.8 - - - +
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Residues in contact with ALA 8 (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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4A PRO* 4.4 21.3 - - + +
5A GLU 4.7 0.2 - - - -
6A GLY 3.3 6.8 - - - +
7A GLU* 1.3 83.2 - - - +
9A ILE* 1.3 62.1 + - - +
11A LEU* 2.9 13.5 + - - +
12A TRP* 2.9 41.1 + - + +
59A ALA* 5.8 1.1 - - - +
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 4.6 8.9 + - - +
8A ALA* 1.3 77.3 - - - +
10A TRP* 1.3 94.6 + - + +
12A TRP* 3.3 9.0 + - + +
13A LEU* 2.9 47.8 + - + +
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Residues in contact with TRP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 4.7 3.6 + - - -
7A GLU* 3.2 17.8 + - - +
9A ILE* 1.3 97.1 - - + +
11A LEU* 1.3 58.4 + - - +
13A LEU* 3.4 17.6 + - + -
14A GLY* 2.9 25.1 + - - -
55A TYR* 4.4 0.9 - - - -
206A GLY* 3.2 30.6 + - - -
207A ILE* 5.3 0.2 - - - +
209A THR* 3.7 17.5 - - + +
210A ALA* 3.6 26.6 - - + +
213A MET* 3.6 35.5 - - + +
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Residues in contact with LEU 11 (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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4A PRO* 4.6 2.9 - - + -
7A GLU* 3.8 12.8 - - + +
8A ALA* 2.9 12.8 + - - +
10A TRP* 1.3 78.5 - - - +
12A TRP* 1.3 53.3 + - - +
14A GLY 3.4 0.5 + - - -
15A THR* 2.7 36.1 + - - -
55A TYR* 3.4 22.0 - - + +
58A MET* 3.8 38.8 - - + +
59A ALA* 3.9 16.2 - - + +
77A TYR* 3.7 36.6 - - + +
80A ARG* 4.3 3.4 - - - +
209A THR* 3.6 24.5 - - + -
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Residues in contact with TRP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 2.9 39.5 + - + +
9A ILE* 3.8 9.0 - - + +
11A LEU* 1.3 74.4 - - - +
13A LEU* 1.3 66.1 + - + +
15A THR* 3.2 11.2 + - + -
16A ALA* 3.0 24.3 + - - +
56A LEU* 3.6 21.1 - - + -
59A ALA* 3.7 28.1 + - + +
60A LEU* 3.3 27.4 - - + -
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Residues in contact with LEU 13 (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* 2.9 37.5 + - + +
10A TRP* 4.2 23.3 - - + -
12A TRP* 1.3 78.6 - - + +
14A GLY* 1.3 57.1 + - - +
16A ALA* 3.5 7.0 + - + +
17A GLY* 2.8 25.5 + - - -
213A MET* 3.7 19.3 - - + -
217A LEU* 5.0 2.6 - - - +
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Residues in contact with GLY 14 (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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10A TRP 2.9 16.8 + - - -
13A LEU* 1.3 75.1 - - - +
15A THR* 1.3 65.4 + - - +
17A GLY* 3.3 1.4 + - - -
18A MET* 2.9 29.8 + - - +
55A TYR* 3.8 23.6 - - - -
213A MET* 4.0 11.8 - - - -
217A LEU* 4.6 6.2 - - - +
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Residues in contact with THR 15 (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 LEU 2.7 22.1 + - - -
12A TRP* 3.4 16.6 - - + -
14A GLY* 1.3 76.4 - - - +
16A ALA* 1.3 63.1 + - - +
18A MET* 3.3 1.4 + - - +
19A PHE* 3.0 22.8 + - - +
52A PHE* 3.4 34.6 - - + -
55A TYR* 3.4 25.4 + - - +
56A LEU* 3.8 26.4 - - + +
59A ALA* 4.1 2.6 - - - +
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Residues in contact with ALA 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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12A TRP 3.0 15.9 + - - +
13A LEU* 3.9 9.2 - - + +
15A THR* 1.3 76.8 - - - +
17A GLY* 1.3 59.0 + - - +
19A PHE* 3.3 5.0 + - - +
20A LEU* 2.8 45.9 + - + +
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Residues in contact with GLY 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 LEU 2.8 21.4 + - - -
14A GLY 3.3 2.0 + - - -
16A ALA* 1.3 74.8 - - - +
18A MET* 1.3 56.4 + - - +
20A LEU* 3.5 9.1 + - - +
21A GLY* 2.9 24.3 + - - -
217A LEU* 4.1 18.2 - - - -
221A VAL* 4.0 6.6 - - - +
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Residues in contact with MET 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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14A GLY 2.9 21.1 + - - +
15A THR 3.8 0.2 - - - +
17A GLY* 1.3 73.2 - - - +
19A PHE* 1.3 62.1 + - - +
21A GLY 3.2 0.5 + - - -
22A MET* 2.9 29.6 + - - +
48A THR* 3.5 15.9 - - - +
51A ALA* 3.4 25.1 - - + -
52A PHE* 3.7 24.5 - - - +
55A TYR* 4.3 10.3 - - + -
216A ASP* 3.7 24.5 - - + +
217A LEU* 3.7 24.2 - - + -
220A LYS* 3.4 35.7 - - + -
221A VAL* 4.4 6.3 - - - -
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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 THR 3.0 17.9 + - - +
16A ALA* 3.8 6.5 - - - +
18A MET* 1.3 76.7 - - - +
20A LEU* 1.3 66.4 + - + +
22A MET* 3.4 26.4 + - + +
23A LEU* 3.1 56.7 + - + +
52A PHE* 3.8 41.4 - + + +
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Residues in contact with LEU 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 ALA* 2.8 31.6 + - + +
17A GLY* 3.7 7.9 - - - +
19A PHE* 1.3 87.6 - - + +
21A GLY* 1.3 61.2 + - - +
23A LEU* 3.3 14.0 + - + +
24A TYR* 2.9 28.1 + - - +
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Residues in contact with GLY 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 GLY 2.9 16.6 + - - -
18A MET 3.2 3.1 + - - -
20A LEU* 1.3 77.9 - - - +
22A MET* 1.3 56.2 + - - +
24A TYR* 3.3 7.5 + - - +
25A PHE* 2.8 49.6 + - - -
48A THR* 4.2 0.2 - - - -
221A VAL* 4.4 17.0 - - - -
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Residues in contact with MET 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 MET 2.9 14.8 + - - +
19A PHE* 3.6 26.9 - - + +
21A GLY* 1.3 74.3 - - - +
23A LEU* 1.3 86.6 + - + +
25A PHE* 3.4 3.2 + - - +
26A ILE* 2.9 45.8 + - + +
45A ILE* 3.9 19.9 - - + +
48A THR* 3.2 25.9 + - - +
49A ALA* 3.8 26.9 - - - +
52A PHE* 5.5 3.6 - - - -
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Residues in contact with LEU 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* 3.1 46.4 + - + +
20A LEU* 3.5 18.6 - - + +
21A GLY 3.3 0.2 - - - -
22A MET* 1.3 96.4 - - + +
24A TYR* 1.3 61.8 + - - +
26A ILE* 3.2 11.7 + - + +
27A ALA* 3.0 22.5 + - - +
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Residues in contact with TYR 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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20A LEU 2.9 14.9 + - - +
21A GLY* 3.4 10.1 - - - +
23A LEU* 1.3 76.5 - - - +
25A PHE* 1.3 81.2 + + - +
27A ALA* 3.0 11.3 + - + +
28A ARG* 2.8 66.4 + - + +
221A VAL* 6.0 1.3 - - + -
225A ILE* 4.5 22.0 - - + +
229A ARG* 4.0 15.4 + - - -
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Residues in contact with PHE 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 GLY 2.8 29.0 + - - +
22A MET 3.9 1.3 - - - +
24A TYR* 1.3 93.1 - + - +
26A ILE* 1.3 62.0 + - - +
28A ARG* 3.3 7.8 + - + +
29A GLY 3.1 17.5 + - - -
41A TYR* 3.9 8.4 - - + -
44A THR* 3.8 17.3 - - + -
45A ILE* 3.7 21.9 - - + +
48A THR* 3.5 32.3 - - + -
220A LYS 4.3 1.1 - - - -
221A VAL* 3.5 35.4 - - + -
224A GLY* 3.5 28.7 - - - -
225A ILE* 3.6 4.5 - - + -
228A LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 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 MET* 2.9 52.2 + - + +
23A LEU* 3.5 10.5 - - + +
25A PHE* 1.3 76.2 - - - +
27A ALA* 1.3 58.1 + - - +
29A GLY 3.4 1.6 + - - -
30A TRP* 2.9 53.7 + - + +
45A ILE* 3.7 31.4 - - + -
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Residues in contact with ALA 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 LEU 3.0 13.2 + - - +
24A TYR* 3.4 14.1 - - + +
26A ILE* 1.3 80.2 - - - +
28A ARG* 1.3 61.6 + - - +
29A GLY 3.2 0.9 + - - -
30A TRP* 3.3 23.0 + - - +
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Residues in contact with ARG 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 TYR* 2.8 48.0 + - + +
25A PHE* 3.4 14.6 - - - +
27A ALA* 1.3 78.5 - - - +
29A GLY* 1.3 56.5 + - - +
32A GLU* 5.5 0.3 - - - +
41A TYR* 3.3 29.1 + - + +
225A ILE* 5.8 1.1 - - - +
228A LEU* 2.7 45.1 + - + +
229A ARG* 3.7 35.9 + - - +
231A HIS* 4.8 10.7 + - - -
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Residues in contact with GLY 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 PHE 3.1 10.1 + - - -
26A ILE* 3.7 2.5 - - - -
28A ARG* 1.3 77.9 - - - +
30A TRP* 1.3 67.5 + - - +
31A GLY 3.3 2.2 - - - -
32A GLU* 2.9 22.2 + - - +
41A TYR* 3.6 32.3 - - - +
45A ILE* 5.9 1.3 - - - -
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 2.9 40.8 + - + +
27A ALA* 3.3 21.0 + - - +
28A ARG 3.5 0.2 - - - -
29A GLY* 1.3 76.1 - - - +
31A GLY* 1.3 61.6 + - - +
32A GLU 3.8 0.7 + - - +
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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
------------------------------------------------------------
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