Contacts of the helix formed by residues 9 - 28 (chain A) in PDB entry 3CJD
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 LYS 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 1.3 62.3 + - - +
11A ALA* 3.4 6.6 - - - +
12A LEU* 3.8 15.1 - - - +
13A ARG* 2.8 31.0 + - - +
50A THR* 5.3 11.9 - - + +
51A HIS* 3.3 27.9 + - + +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 1.3 77.7 - - - +
11A ALA* 1.3 63.1 + - - +
13A ARG* 3.9 4.6 - - - +
14A GLU* 3.3 28.1 + - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 3.4 3.9 - - - +
10A ALA* 1.3 76.4 - - - +
12A LEU* 1.3 59.2 + - - +
14A GLU* 3.4 6.1 + - - +
15A LYS* 2.9 31.1 + - - +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 3.7 16.2 + - - +
10A ALA 3.4 0.2 - - - -
11A ALA* 1.3 76.4 - - - +
13A ARG* 1.3 64.2 + - - +
15A LYS* 3.2 9.6 + - + +
16A LEU* 2.9 40.8 + - + +
41A ALA* 3.9 32.1 - - + +
43A CYS* 4.1 14.6 - - + -
47A ALA* 4.0 22.7 - - + -
51A HIS* 3.5 22.4 - - + +
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 2.8 23.6 + - - +
10A ALA* 3.9 6.5 - - - +
11A ALA 3.4 0.2 - - - -
12A LEU* 1.3 72.8 - - - +
14A GLU* 1.3 86.2 + - - +
16A LEU* 3.4 2.4 + - - +
17A ILE* 3.3 30.6 + - + +
51A HIS* 3.9 27.9 + - + -
52A PHE* 3.7 24.6 - - + -
61A GLU* 3.4 33.7 + - - +
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Residues in contact with GLU 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 ALA 3.3 17.4 + - - +
11A ALA* 3.8 4.9 - - - +
12A LEU 3.3 0.2 - - - -
13A ARG* 1.3 99.6 + - - +
15A LYS* 1.3 58.9 + - - +
17A ILE* 3.2 10.4 + - - +
18A ASP* 3.0 38.2 + - - +
65A ARG* 3.2 25.5 + - - -
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Residues in contact with LYS 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 ALA 2.9 20.6 + - - +
12A LEU* 3.6 11.9 - - + +
14A GLU* 1.3 71.3 - - - +
16A LEU* 1.3 57.7 + - - +
18A ASP* 3.3 12.2 + - + +
19A LEU* 2.9 45.7 + - + +
40A GLN 4.3 6.3 - - - -
41A ALA* 3.9 37.9 - - + +
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Residues in contact with LEU 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 LEU* 2.9 40.0 + - + +
13A ARG* 3.7 3.8 - - - +
14A GLU 3.3 0.2 - - - -
15A LYS* 1.3 75.3 - - - +
17A ILE* 1.3 51.8 + - - +
19A LEU* 3.4 4.6 + - + +
20A ALA* 2.8 35.7 + - - +
37A LEU* 4.2 14.8 - - + +
41A ALA* 3.7 25.8 - - + -
43A CYS* 4.4 1.6 - - - -
47A ALA 4.4 0.7 - - - +
48A ILE* 4.1 36.8 - - + +
51A HIS* 4.1 12.1 - - - +
52A PHE* 3.9 26.0 - - + -
58A LEU* 4.0 9.1 - - + +
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Residues in contact with ILE 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 ARG* 3.3 43.5 + - - +
14A GLU* 3.2 17.5 + - - +
16A LEU* 1.3 75.2 - - - +
18A ASP* 1.3 56.4 + - - +
20A ALA* 3.3 2.3 + - - +
21A GLU* 2.9 28.8 + - - +
52A PHE* 3.7 15.9 - - + -
58A LEU* 3.9 11.0 - - + -
61A GLU* 4.0 35.4 - - + +
62A VAL* 3.9 5.2 - - + +
65A ARG* 3.4 32.5 - - - +
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Residues in contact with ASP 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 GLU* 3.0 25.9 + - - +
15A LYS* 3.5 12.8 - - + +
17A ILE* 1.3 75.4 - - - +
19A LEU* 1.3 60.2 + - + +
21A GLU* 3.5 5.2 + - - +
22A ALA* 3.0 27.8 + - - +
65A ARG* 2.9 34.4 + - - +
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Residues in contact with LEU 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 LYS* 2.9 33.3 + - + +
16A LEU* 3.9 4.9 - - + +
18A ASP* 1.3 74.3 - - + +
20A ALA* 1.3 60.2 + - - +
22A ALA* 3.3 10.4 + - + +
23A GLN* 2.9 29.6 + - - +
37A LEU* 3.8 16.6 - - + +
40A GLN* 3.7 32.0 - - + +
41A ALA* 3.6 42.2 - - + +
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Residues in contact with ALA 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 LEU 2.8 21.6 + - - +
17A ILE 3.6 4.3 - - - +
19A LEU* 1.3 68.4 - - - +
21A GLU* 1.3 65.2 + - - +
23A GLN* 3.4 2.6 + - - +
24A ILE* 3.0 29.3 + - - +
32A LEU* 4.0 14.5 - - + +
37A LEU* 3.8 8.9 - - + +
58A LEU* 3.6 31.2 - - + -
62A VAL* 3.6 13.7 - - + -
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Residues in contact with GLU 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 ILE 2.9 15.1 + - - +
18A ASP* 3.6 6.2 - - - +
20A ALA* 1.3 77.6 - - - +
22A ALA* 1.3 56.5 + - - +
24A ILE* 3.3 2.4 + - - +
25A GLU* 3.0 46.1 + - - +
62A VAL* 3.6 19.4 - - + +
65A ARG* 3.1 43.9 + - - +
66A THR* 5.3 0.5 + - - -
69A ARG* 3.2 30.9 + - - -
107A LEU* 4.1 13.5 - - + +
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Residues in contact with ALA 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 ASP 3.0 17.7 + - - +
19A LEU* 3.3 15.7 + - + +
21A GLU* 1.3 75.4 - - - +
23A GLN* 1.3 55.9 + - - +
25A GLU* 3.5 14.5 + - - +
26A ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 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 LEU 2.9 16.7 + - - +
20A ALA 3.7 4.5 - - - +
22A ALA* 1.3 74.1 - - - +
24A ILE* 1.3 60.1 + - - +
26A ALA* 3.2 4.1 + - - +
27A GLU* 2.9 55.5 + - - +
28A GLY 3.6 2.5 + - - +
31A SER* 2.9 34.0 + - - +
32A LEU* 3.9 28.3 - - + -
33A ARG 5.4 1.1 - - - +
36A GLU* 4.6 13.7 - - + +
37A LEU* 4.9 5.2 - - + -
40A GLN* 4.5 18.8 + - - +
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Residues in contact with ILE 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 ALA 3.0 21.7 + - - +
21A GLU 3.8 4.0 - - - +
23A GLN* 1.3 73.0 - - - +
25A GLU* 1.3 59.8 + - - +
28A GLY* 2.8 32.5 + - - +
29A LEU* 3.8 43.1 - - + +
32A LEU* 4.6 11.7 - - + -
59A THR* 4.3 10.8 - - + +
62A VAL* 4.0 26.5 - - + -
106A LYS* 3.2 31.1 - - - +
107A LEU* 3.9 15.0 - - + -
110A ALA* 4.1 7.9 - - + -
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Residues in contact with GLU 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 GLU* 3.0 28.8 + - - +
22A ALA* 3.5 17.0 - - - +
24A ILE* 1.3 78.0 - - - +
26A ALA* 1.3 60.9 + - - +
69A ARG* 3.4 25.5 + - - -
104A HIS* 5.7 0.3 + - - -
106A LYS* 3.4 15.8 + - - +
107A LEU* 3.7 22.9 - - + +
202A CL 4.2 15.7 - - + -
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Residues in contact with ALA 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 ALA 3.0 16.9 + - - +
23A GLN* 3.2 9.4 + - - +
25A GLU* 1.3 77.4 - - - +
27A GLU* 1.3 71.6 + - + +
106A LYS* 2.6 22.0 + - - -
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Residues in contact with GLU 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 GLN* 2.9 27.0 + - - +
26A ALA* 1.3 86.5 - - + +
28A GLY* 1.3 60.9 + - - +
30A ALA* 6.1 0.2 - - - +
31A SER* 3.3 26.7 + - - +
106A LYS* 3.9 7.9 - - - +
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Residues in contact with GLY 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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23A GLN 3.6 0.6 + - - -
24A ILE* 2.8 34.0 + - - +
27A GLU* 1.3 71.2 - - - +
29A LEU* 1.3 65.1 + - - +
30A ALA 3.3 2.5 - - - -
31A SER* 2.7 25.6 + - - -
32A LEU 4.1 0.9 + - - -
106A LYS* 3.7 14.5 - - - +
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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
------------------------------------------------------------
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