Contacts of the helix formed by residues 8 - 29 (chain A) in PDB entry 2DME
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 SER 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY* 1.3 70.8 - - - -
9A ALA* 1.3 67.5 + - - +
10A ASP* 4.3 6.7 - - - -
11A GLN* 2.8 41.8 + - - +
12A ILE* 3.5 7.3 + - - +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 3.8 3.6 + - - -
8A SER* 1.3 70.7 - - - +
10A ASP* 1.3 65.9 + - - +
12A ILE* 3.3 24.5 + - - +
13A ARG* 3.2 44.1 + - - +
58A THR* 4.0 13.4 - - - +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 2.9 7.1 + - - -
9A ALA* 1.3 79.2 - - - +
11A GLN* 1.3 64.7 + - - +
13A ARG* 3.0 21.5 + - - +
14A GLN* 2.8 45.9 + - - +
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Residues in contact with GLN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 2.8 32.1 + - - +
10A ASP* 1.3 73.5 + - - +
12A ILE* 1.3 67.3 + - + +
14A GLN* 2.8 37.2 + - - +
15A SER* 2.8 20.8 + - - +
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY* 5.9 3.4 - - - -
8A SER 4.2 6.1 - - - +
9A ALA* 3.3 18.7 + - - +
11A GLN* 1.3 79.4 - - + +
13A ARG* 1.3 61.1 + - + +
15A SER* 3.5 5.6 + - - -
16A VAL* 2.9 30.5 + - + +
58A THR* 4.3 24.5 - - + +
62A TYR* 4.1 25.4 - - + -
63A LYS* 4.0 35.4 - - + +
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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 ALA* 3.2 41.2 + - - +
10A ASP* 3.0 17.8 + - - +
12A ILE* 1.3 72.5 - - - +
14A GLN* 1.3 68.3 + - - +
16A VAL* 3.2 23.1 + - - +
17A ARG* 3.3 11.4 + - - +
48A GLU* 3.8 11.1 - - + +
52A PHE* 2.7 62.4 - - + -
58A THR* 3.6 12.1 + - + +
62A TYR* 4.1 16.8 - - - +
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Residues in contact with GLN 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 ASP* 2.8 32.1 + - - +
11A GLN* 2.8 32.0 + - - +
13A ARG* 1.3 70.3 - - - +
15A SER* 1.3 65.7 + - - +
17A ARG* 2.9 55.5 + - - +
18A HIS* 3.6 3.1 + - - +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 2.8 21.7 + - - +
12A ILE* 3.8 5.2 - - - -
14A GLN* 1.3 72.7 - - - +
16A VAL* 1.3 66.7 + - - +
17A ARG 2.9 1.0 + - - -
18A HIS* 3.0 8.8 + - - +
19A SER* 2.9 33.0 + - - -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 2.9 31.4 - - + +
13A ARG* 3.2 11.8 + - - +
15A SER* 1.3 76.6 + - - +
17A ARG* 1.3 65.8 + - - +
19A SER* 3.7 0.7 - - - -
20A LEU* 3.0 30.7 + - + +
47A ILE* 5.2 1.8 - - + -
48A GLU* 2.9 28.7 - - + +
51A LEU* 5.9 1.1 - - + -
62A TYR* 4.2 13.0 - - + +
66A TYR* 3.5 50.5 - - + -
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Residues in contact with ARG 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 3.4 9.9 - - - +
14A GLN* 2.9 46.0 + - - +
16A VAL* 1.3 79.5 - - - +
18A HIS* 1.3 64.4 + - - +
20A LEU* 3.2 2.8 + - - +
21A LYS* 3.0 22.8 + - - +
44A ALA* 3.7 7.4 - - + +
45A THR* 4.2 33.8 + - - +
48A GLU* 3.3 26.9 - - + +
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Residues in contact with HIS 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 GLN 3.6 2.8 + - - +
15A SER* 3.0 10.1 + - - +
17A ARG* 1.3 77.8 - - - +
19A SER* 1.3 67.3 + - - +
20A LEU 3.0 0.7 + - - -
21A LYS* 3.0 26.9 + - + +
22A ASP* 2.8 40.1 + - - +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 2.9 31.5 + - - -
16A VAL* 3.7 1.8 - - - -
18A HIS* 1.3 73.9 - - - +
20A LEU* 1.3 66.1 + - - +
22A ASP* 3.1 18.1 - - - +
23A ILE* 3.4 4.7 + - - +
66A TYR* 3.3 25.3 + - - -
70A MET* 4.1 14.1 - - - +
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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 VAL* 3.0 29.0 + - + +
17A ARG 3.4 2.2 - - - +
19A SER* 1.3 72.0 - - - +
21A LYS* 1.3 69.8 + - - +
22A ASP 2.9 1.3 - - - -
23A ILE* 2.7 20.3 + - - +
24A LEU* 3.2 17.7 + - + +
44A ALA* 3.7 12.8 - - + +
47A ILE* 3.8 25.8 - - + -
48A GLU* 2.8 31.6 - - - +
66A TYR* 4.0 12.8 - - + -
69A LEU* 5.9 2.0 - - + -
70A MET* 3.9 31.9 - - + +
73A LEU* 4.8 10.5 - - + -
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Residues in contact with LYS 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 ARG 3.0 10.2 + - - +
18A HIS* 3.6 26.4 - - - +
20A LEU* 1.3 77.7 - - - +
22A ASP* 1.3 54.0 + - - +
24A LEU* 3.6 8.3 - - - +
25A MET* 2.8 57.4 + - + +
37A GLU* 4.9 12.2 + - + +
40A ALA* 4.4 1.8 - - + -
41A ALA* 3.5 40.7 - - + +
44A ALA* 3.9 10.4 - - + +
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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
----------------------------------------------------------
18A HIS* 2.8 29.2 + - + +
19A SER* 3.1 16.6 - - - +
20A LEU 2.7 4.0 + - - -
21A LYS* 1.3 73.3 - - - +
23A ILE* 1.3 59.2 + - + +
25A MET* 3.1 6.2 + - - +
26A LYS* 2.8 37.1 + - - +
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Residues in contact with ILE 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 SER 4.1 6.5 - - - +
20A LEU* 2.7 13.9 + - - +
22A ASP* 1.3 72.4 - - + +
24A LEU* 1.3 60.8 + - + +
25A MET 2.8 14.0 + - - -
26A LYS* 3.1 9.9 + - + +
27A ARG* 2.8 44.5 + - + +
70A MET* 3.7 49.1 - - + +
73A LEU* 3.9 25.6 - - + -
74A LYS* 4.0 20.9 - - + +
82A PHE* 5.5 0.4 - - + -
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Residues in contact with LEU 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* 3.2 20.7 + - + +
21A LYS 3.6 2.9 - - - +
23A ILE* 1.3 80.7 - - + +
25A MET* 1.3 55.9 + - - +
27A ARG* 4.5 4.5 - - - -
28A LEU* 2.9 37.1 - - - +
40A ALA* 3.8 33.0 - - + +
43A VAL* 4.4 14.8 - - + -
44A ALA* 4.8 4.7 - - + +
47A ILE* 6.4 0.4 - - + -
73A LEU* 4.2 20.6 - - + -
82A PHE* 3.9 23.6 - - + -
85A VAL* 5.8 2.0 - - + -
86A LEU* 3.4 31.5 - - + +
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Residues in contact with MET 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 LYS* 2.8 38.4 + - + +
22A ASP* 3.2 7.9 - - - +
23A ILE 2.8 1.6 + - - -
24A LEU* 1.3 78.5 - - - +
26A LYS* 1.3 58.1 + - - +
27A ARG 3.1 4.7 - - - -
28A LEU* 3.7 23.1 - - + +
29A THR* 3.0 34.5 + - - -
37A GLU* 3.5 56.1 - - + +
40A ALA* 4.1 5.2 - - + -
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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 ASP* 2.8 22.8 + - - +
23A ILE* 3.3 15.9 - - + +
25A MET* 1.3 72.3 - - - +
27A ARG* 1.3 88.3 + - - +
29A THR* 3.4 20.1 - - - +
30A ASP* 3.7 9.5 - - - +
74A LYS 5.9 0.8 + - - -
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Residues in contact with ARG 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 ILE* 2.8 38.6 + - + +
24A LEU* 4.5 2.0 - - - -
26A LYS* 1.3 101.7 - - + +
28A LEU* 1.3 60.9 + - - +
29A THR 3.2 1.1 - - - -
30A ASP* 2.9 8.7 + - - +
31A SER* 2.9 31.8 + - - -
73A LEU 3.4 18.6 + - - -
74A LYS* 3.9 15.2 + - - +
75A ASP 3.6 6.0 + - - -
76A PRO* 4.9 5.7 + - - +
78A ASN 2.8 29.3 + - - -
79A ASN* 3.8 15.0 - - - +
82A PHE* 4.0 31.1 - - + -
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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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24A LEU 2.9 26.2 + - - +
25A MET* 3.7 27.6 - - + +
27A ARG* 1.3 77.9 - - - +
29A THR* 1.3 70.4 + - - +
31A SER* 2.8 17.0 + - - -
33A LEU* 3.2 70.1 + - + +
35A VAL* 3.6 24.7 - - + +
36A PRO 5.6 0.4 - - - +
37A GLU* 5.8 0.2 - - - -
40A ALA* 4.2 8.5 - - + +
82A PHE* 4.4 1.6 - - - -
86A LEU* 3.8 5.2 - - + -
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Residues in contact with THR 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 MET 3.0 20.0 + - - +
26A LYS* 3.4 18.2 - - - +
28A LEU* 1.3 90.3 - - - +
30A ASP* 1.3 64.3 + - + +
31A SER 3.8 0.2 + - - -
32A ASN* 4.1 7.3 + - - -
33A LEU 5.6 0.2 - - - -
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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