Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 2DN0
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS* 1.3 73.7 - - - +
17A HIS* 1.3 68.0 + - - +
18A GLU* 3.4 21.3 - - - -
19A GLN* 2.7 35.7 + - - +
20A LEU* 3.2 8.2 + - - -
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Residues in contact with HIS 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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15A LYS 3.8 3.4 + - - -
16A SER* 1.3 69.6 - - - +
18A GLU* 1.3 72.3 + - - +
20A LEU* 2.7 38.5 + - + +
21A SER* 2.8 38.7 + - - -
24A LYS* 5.7 3.9 - - + +
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Residues in contact with GLU 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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16A SER* 2.8 25.5 + - - +
17A HIS* 1.3 78.7 + - - +
19A GLN* 1.3 62.5 + - + +
21A SER* 2.8 18.7 + - - -
22A ALA* 4.1 5.2 + - - +
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Residues in contact with GLN 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* 6.0 6.5 - - + +
16A SER* 2.7 30.2 + - - +
18A GLU* 1.3 77.4 - - + +
20A LEU* 1.3 68.6 + - - +
21A SER 3.3 0.2 - - - -
22A ALA* 3.0 21.6 + - - +
23A LEU* 3.3 9.6 + - + +
44A VAL 4.6 5.2 - - - +
45A THR* 3.2 48.3 + - + +
47A LEU* 4.3 17.5 - - + +
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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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15A LYS* 5.1 20.3 - - + +
16A SER 3.2 4.4 + - - +
17A HIS* 2.7 36.7 + - + +
19A GLN* 1.3 72.7 - - - +
21A SER* 1.3 67.2 + - - +
23A LEU* 2.9 25.2 + - - +
24A LYS* 3.1 38.5 + - + -
55A TRP* 4.3 20.4 - - + +
59A ARG* 3.6 14.6 - - - +
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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 HIS* 2.8 34.3 + - - -
18A GLU* 2.8 24.1 + - - -
20A LEU* 1.3 73.8 - - - +
22A ALA* 1.3 64.9 + - - +
24A LYS* 3.1 14.4 + - - +
25A GLY* 3.0 19.1 + - - -
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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 GLU 4.5 4.9 - - - +
19A GLN* 3.0 14.0 + - - +
21A SER* 1.3 81.1 + - - +
23A LEU* 1.3 67.5 + - - +
25A GLY* 3.0 14.0 + - - -
26A SER* 3.5 10.2 + - - -
41A LEU* 4.1 4.9 - - + +
44A VAL* 3.9 29.8 - - + +
45A THR* 4.7 4.9 - - + -
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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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15A LYS* 5.4 4.5 - - + -
19A GLN* 3.3 10.7 + - + +
20A LEU* 2.9 13.9 + - - +
22A ALA* 1.3 76.7 - - - +
24A LYS* 1.3 65.6 + - - +
26A SER* 2.9 21.7 + - - -
27A PHE 3.3 2.9 + - - -
41A LEU* 3.5 26.9 - - + +
45A THR* 4.1 14.8 - - + +
47A LEU* 4.8 12.6 - - + -
52A VAL* 3.8 26.0 - - + +
55A TRP* 3.5 54.0 - - + +
56A PHE* 4.3 8.1 - - + -
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Residues in contact with LYS 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 HIS* 5.7 4.3 - - + +
20A LEU* 3.1 26.2 + - + +
21A SER* 3.1 13.8 + - - +
23A LEU* 1.3 73.2 - - - +
25A GLY* 1.3 55.7 + - - +
26A SER 2.5 17.7 + - - -
27A PHE* 2.5 17.6 + - + +
28A CYS* 3.0 17.5 + - + +
55A TRP* 3.6 19.9 - - + -
59A ARG* 3.2 38.6 - - - +
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Residues in contact with GLY 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 3.0 9.3 + - - -
22A ALA* 3.0 6.8 + - - -
24A LYS* 1.3 77.9 - - - +
26A SER* 1.3 56.8 + - - +
28A CYS* 3.0 24.9 - - - -
29A ARG* 3.3 21.0 - - - -
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Residues in contact with SER 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 3.5 2.7 + - - -
23A LEU 2.9 11.7 + - - -
24A LYS 2.5 5.1 + - - -
25A GLY* 1.3 74.0 - - - +
27A PHE* 1.3 55.5 + - - -
29A ARG* 3.6 2.7 + - - +
30A ASN* 2.8 34.4 + - - +
37A GLU* 3.2 28.2 + - - +
40A HIS* 5.4 2.9 - - - -
41A LEU* 3.3 33.2 - - - +
56A PHE* 4.1 8.1 - - - -
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Residues in contact with PHE 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 3.3 1.6 + - - -
24A LYS* 2.5 13.4 + - + +
26A SER* 1.3 69.8 - - - +
28A CYS* 1.3 72.0 + - - +
29A ARG 2.8 2.6 + - - -
30A ASN 2.7 25.1 + - - +
31A GLN* 3.4 33.4 + - + +
55A TRP* 4.2 23.6 - + + -
56A PHE* 3.5 31.5 - + + -
59A ARG* 4.7 8.3 - - + -
60A ARG* 3.6 40.6 - - + -
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Residues in contact with CYS 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 LYS* 3.0 14.6 + - + +
25A GLY* 3.0 36.8 - - - -
27A PHE* 1.3 82.3 - - - +
29A ARG* 1.3 72.2 + - - +
31A GLN* 4.6 4.9 - - - +
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Residues in contact with ARG 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 GLY 3.3 21.5 - - - +
26A SER* 3.9 3.1 - - - +
27A PHE 2.8 4.9 + - - -
28A CYS* 1.3 88.6 - - - +
30A ASN* 1.3 60.2 + - + +
31A GLN* 3.9 9.2 + - - +
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Residues in contact with ASN 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 SER 2.8 22.2 + - - +
27A PHE* 2.7 19.7 - - - +
29A ARG* 1.3 72.8 - - + +
31A GLN* 1.3 75.3 + - - +
32A PHE* 3.0 29.2 + - - +
33A PRO* 4.5 5.9 - - - +
34A GLY 5.1 0.8 - - - +
37A GLU* 4.7 16.6 - - + +
56A PHE* 4.9 1.0 - - - -
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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