Contacts of the helix formed by residues 9 - 29 (chain A) in PDB entry 4PKO
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 GLY 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 1.3 73.2 - - - +
10A ASN* 1.3 51.7 + - - -
12A ALA* 2.8 24.8 + - - +
13A ARG* 2.8 31.4 + - - +
517A THR 5.4 0.2 - - - +
518A GLU* 2.9 37.6 + - - -
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Residues in contact with ASN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE 3.6 0.2 + - - -
9A GLY* 1.3 71.0 - - - -
11A ASP* 1.3 62.0 + - - +
13A ARG* 3.2 26.8 + - - +
14A VAL* 2.9 47.6 + - - +
104A LEU 5.5 1.4 - - - +
108A ALA* 4.4 19.9 + - - +
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.5 35.5 + - - +
8A PHE 3.3 14.1 + - - +
9A GLY 3.1 0.2 - - - -
10A ASN* 1.3 81.2 - - - +
12A ALA* 1.3 62.0 + - - +
14A VAL* 3.7 4.4 + - - +
15A LYS* 3.6 18.9 + - - +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.7 38.6 - - + +
8A PHE 3.3 2.4 + - - -
9A GLY 2.8 14.5 + - - +
11A ASP* 1.3 73.4 - - - +
13A ARG* 1.3 65.1 + - - +
14A VAL 3.2 0.4 - - - -
15A LYS* 3.1 8.7 + - - +
16A MET 2.9 18.4 + - - -
66A PHE* 6.2 0.7 - - - -
517A THR* 6.0 0.7 - - + -
518A GLU 5.6 0.4 - - - -
519A CYS* 5.0 1.8 - - - +
520A MET* 3.6 29.9 - - + +
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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 GLY* 2.8 24.4 + - - +
10A ASN* 3.2 39.9 + - - +
11A ASP 3.5 0.2 - - - -
12A ALA* 1.3 72.2 - - - +
14A VAL* 1.3 51.9 + - + +
16A MET* 3.0 15.0 + - + +
17A LEU* 2.7 36.1 + - - +
104A LEU* 3.7 41.6 + - + +
107A VAL* 3.8 33.9 + - - +
108A ALA* 5.6 1.2 - - - +
113A PRO* 5.8 0.8 - - - +
515A ILE 5.2 2.9 + - - -
517A THR* 2.8 40.5 + - + +
518A GLU* 3.1 20.8 + - - -
520A MET* 5.3 0.2 - - - -
36B ARG* 4.3 4.2 - - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 2.9 40.9 + - - +
11A ASP* 3.9 5.4 - - - +
13A ARG* 1.3 77.7 - - + +
15A LYS* 1.3 64.9 + - + +
17A LEU* 3.2 13.4 + - + +
18A ARG* 3.0 36.5 + - + +
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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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7A LYS* 3.6 26.9 - - + +
11A ASP* 3.6 12.2 + - - +
12A ALA* 3.1 9.7 + - - +
14A VAL* 1.3 80.4 - - + +
16A MET* 1.3 63.7 + - - +
18A ARG* 3.4 6.5 + - - +
19A GLY 3.3 15.8 + - - -
64A ASP* 3.5 29.3 + - - +
66A PHE* 3.8 31.1 - - + -
67A GLU* 3.3 32.8 - - + +
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Residues in contact with MET 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 2.9 11.7 + - - +
13A ARG* 3.2 16.4 - - + +
15A LYS* 1.3 77.4 - - - +
17A LEU* 1.3 61.0 + - - +
19A GLY* 3.3 3.6 + - - -
20A VAL* 3.1 28.1 + - + +
66A PHE 4.6 4.9 - - - -
70A GLY* 3.8 25.1 - - - -
73A MET* 4.2 10.1 - - + -
100A ILE* 4.8 4.0 - - + -
104A LEU* 3.7 33.2 - - + -
514A MET* 3.5 48.9 - - + +
517A THR* 4.0 14.6 - - - +
520A MET* 4.0 15.2 - - - +
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Residues in contact with LEU 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 2.7 15.9 + - - +
14A VAL* 3.5 16.4 - - + +
16A MET* 1.3 70.5 - - - +
18A ARG* 1.3 62.2 + - + +
20A VAL* 3.1 11.5 + - + +
21A ASN* 2.9 48.8 + - - +
100A ILE* 4.6 7.2 - - + -
101A THR* 4.2 28.0 - - + +
104A LEU* 4.1 25.3 - - + +
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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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14A VAL* 3.0 31.6 + - + +
15A LYS* 3.7 10.3 - - - +
16A MET 3.4 0.4 - - - -
17A LEU* 1.3 79.0 - - + +
19A GLY* 1.3 60.1 + - - +
21A ASN* 3.7 11.0 + - - +
22A VAL* 3.4 32.9 + - - +
67A GLU* 2.7 45.5 + - - +
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Residues in contact with GLY 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 3.3 4.4 + - - -
16A MET 3.3 4.7 + - - -
17A LEU 3.1 0.8 - - - -
18A ARG* 1.3 77.1 - - - +
20A VAL* 1.3 65.0 - - - +
22A VAL* 3.1 15.2 + - - +
23A LEU 3.4 8.1 + - - -
62A LEU* 3.6 12.6 - - - -
67A GLU* 3.3 26.6 - - - +
71A ALA* 3.5 14.4 - - - +
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Residues in contact with VAL 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 MET* 3.1 17.7 + - + +
17A LEU* 3.1 13.6 + - + +
19A GLY* 1.3 75.0 - - - +
21A ASN* 1.3 65.4 + - - +
22A VAL 3.2 0.3 + - - -
23A LEU* 3.4 2.6 + - - +
24A ALA* 3.0 25.5 + - + +
70A GLY* 3.6 21.5 - - - +
71A ALA* 4.0 0.8 - - - +
74A VAL* 3.7 35.1 - - + +
97A GLN* 4.8 16.8 - - + -
100A ILE* 4.3 17.9 - - + -
514A MET* 4.4 10.1 - - - -
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Residues in contact with ASN 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 LEU* 2.9 48.2 + - - +
18A ARG* 3.8 10.3 - - - +
20A VAL* 1.3 78.8 - - - +
22A VAL* 1.3 57.5 + - + +
24A ALA* 4.5 0.2 - - - -
25A ASP* 2.8 46.0 + - - +
97A GLN* 3.3 29.0 + - - +
101A THR* 4.5 3.8 + - - -
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Residues in contact with VAL 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 23.1 + - - +
19A GLY 3.1 8.4 + - - +
21A ASN* 1.3 75.2 - - + +
23A LEU* 1.3 68.4 + - - +
25A ASP* 3.9 2.5 - - - +
26A ALA* 3.0 26.1 + - + +
60A ILE* 4.6 9.9 - - + -
62A LEU* 4.2 29.2 - - + -
67A GLU* 5.4 2.9 - - - +
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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 GLY 3.4 1.6 + - - -
20A VAL 3.4 5.9 + - - +
22A VAL* 1.3 80.2 - - - +
24A ALA* 1.3 68.0 + - - +
26A ALA* 3.5 1.7 + - - +
27A VAL* 3.1 29.1 + - + +
57A ALA* 3.6 36.6 - - + +
60A ILE* 3.7 34.9 - - + +
71A ALA* 3.5 30.3 - - + +
74A VAL* 4.0 19.1 - - + +
75A LYS* 3.7 17.0 - - + +
78A ALA* 5.7 0.2 - - + -
93A THR* 4.4 15.5 - - + +
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Residues in contact with ALA 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 VAL* 3.0 19.6 + - + +
21A ASN 4.1 0.2 - - - +
23A LEU* 1.3 76.0 - - + +
25A ASP* 1.3 56.2 + - - +
27A VAL* 2.8 5.2 + - - +
28A LYS* 2.7 38.9 + - + +
74A VAL* 6.2 0.4 - - + -
93A THR* 4.1 22.2 - - + +
97A GLN* 3.9 37.9 - - + +
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Residues in contact with ASP 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 ASN* 2.8 37.5 + - - +
22A VAL* 4.1 2.5 - - - +
24A ALA* 1.3 74.3 - - - +
26A ALA* 1.3 59.8 + - - +
28A LYS* 3.0 31.8 + - - +
29A VAL* 3.8 16.8 - - - +
97A GLN* 2.8 26.7 + - - -
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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 VAL* 3.0 20.9 + - + +
23A LEU* 3.7 6.1 - - - +
25A ASP* 1.3 78.5 - - - +
27A VAL* 1.3 59.1 + - - +
29A VAL* 3.0 23.5 - - - +
38A VAL* 3.7 15.6 - - + +
56A VAL* 4.1 8.1 - - + +
60A ILE* 4.6 15.0 - - + -
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Residues in contact with VAL 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* 3.1 19.7 + - + +
24A ALA 2.8 5.0 + - - +
26A ALA* 1.3 75.6 - - - +
28A LYS* 1.3 65.3 + - - +
29A VAL 3.1 2.7 - - - -
30A THR* 3.1 23.3 + - - +
53A GLY* 3.8 19.5 - - - +
56A VAL* 3.8 23.8 - - + -
57A ALA* 4.0 16.6 - - + -
60A ILE* 5.8 0.2 - - + -
89A THR 5.4 0.2 - - - -
90A THR* 3.2 33.9 - - + +
93A THR* 4.4 17.0 - - + +
94A VAL* 5.9 0.2 - - + -
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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 ALA* 2.7 28.6 + - + +
25A ASP* 3.0 35.2 + - - +
26A ALA 3.5 0.4 - - - -
27A VAL* 1.3 73.6 - - - +
29A VAL* 1.3 57.3 + - + +
30A THR 3.0 0.2 - - - -
31A LEU* 2.9 22.3 + - - +
90A THR* 4.4 6.3 - - - -
93A THR* 6.1 0.7 - - + -
94A VAL* 4.0 18.8 - - + -
97A GLN* 3.2 24.4 + - - +
453A GLN* 3.3 42.9 - - + +
456A LEU* 5.5 1.6 - - - +
457A ASN* 3.2 12.3 + - - -
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Residues in contact with VAL 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 ASP 3.8 13.0 - - - +
26A ALA* 3.0 25.6 - - - +
28A LYS* 1.3 77.7 - - + +
30A THR* 1.3 51.9 + - + +
31A LEU 3.3 0.9 - - - -
35A GLY* 3.3 5.7 - - - -
36A ARG* 2.4 44.1 + - + +
37A ASN 5.5 1.1 - - - +
38A VAL* 3.8 18.2 - - + -
457A ASN* 4.0 12.8 + - - +
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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