Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 2DHY
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 PHE 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.3 1.3 - - + -
17A GLU* 1.3 74.3 - - - +
19A ASN* 1.3 86.4 + - + +
20A GLN 3.3 1.3 - - - +
21A ALA* 3.2 4.0 + - - +
22A MET* 2.9 37.6 + - + +
34A TYR* 5.1 1.3 - - - -
38A GLU* 3.0 43.3 - - - -
41A LEU* 3.9 18.8 - - + -
42A ARG* 5.2 4.7 - - - -
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Residues in contact with ASN 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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18A PHE* 1.3 96.6 - - + +
20A GLN* 1.3 69.9 + - + +
22A MET* 3.2 15.7 + - - +
23A ASP* 3.3 11.7 + - - +
34A TYR* 5.6 2.3 + - - -
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Residues in contact with GLN 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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17A GLU* 3.4 41.7 + - + +
18A PHE 3.3 0.8 - - - +
19A ASN* 1.3 75.2 - - + +
21A ALA* 1.3 68.4 + - - +
23A ASP* 2.9 12.4 + - - +
24A ASP* 2.8 20.6 + - - +
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Residues in contact with ALA 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 GLU* 3.6 20.6 + - + +
18A PHE* 3.2 13.1 + - - +
20A GLN* 1.3 75.4 - - - +
22A MET* 1.3 66.3 + - - +
24A ASP* 2.7 22.3 + - - +
25A PHE* 2.8 35.9 + - + -
41A LEU* 4.7 5.2 - - + -
48A VAL* 4.1 16.2 - - + -
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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 PHE* 2.9 34.0 + - + +
19A ASN* 3.3 12.3 - - - +
21A ALA* 1.3 75.5 - - - +
23A ASP* 1.3 51.6 + - - +
25A PHE* 3.2 11.5 + - - +
26A LYS* 2.7 40.4 + - - +
34A TYR* 2.9 59.0 - - + +
37A ILE* 3.9 15.2 - - + +
38A GLU* 2.9 44.2 - - + +
41A LEU* 4.1 4.7 - - + -
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Residues in contact with ASP 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 ASN 3.3 6.1 + - - +
20A GLN* 2.9 14.7 + - - +
22A MET* 1.3 78.5 - - - +
24A ASP* 1.3 66.1 + - - +
26A LYS* 2.8 22.9 + - - +
27A THR* 2.8 14.9 + - - -
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Residues in contact with ASP 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 GLN 2.8 11.0 + - - +
21A ALA* 2.7 18.4 + - - +
23A ASP* 1.3 71.2 - - - +
25A PHE* 1.3 59.6 + - + +
27A THR* 3.1 9.4 + - - +
28A MET* 2.6 68.8 + - - +
48A VAL* 4.9 8.0 - - + +
52A ILE* 4.9 2.1 - - - +
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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 ALA* 2.8 36.2 + - + -
22A MET* 3.3 5.6 - - - +
24A ASP* 1.3 77.5 - - - +
26A LYS* 1.3 60.6 + - - +
28A MET* 3.8 10.1 - - + -
29A PHE* 2.6 38.7 + + - +
37A ILE* 3.3 37.4 - - + +
41A LEU* 3.2 28.0 - - + -
48A VAL* 3.9 19.3 - - + -
51A THR* 3.5 26.2 - - + -
52A ILE* 3.9 27.8 - - + -
55A LEU* 4.1 13.9 - - + -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A MET* 2.7 23.0 + - + +
23A ASP* 3.2 19.3 - - - +
25A PHE* 1.3 73.6 - - - +
27A THR* 1.3 59.5 + - - +
29A PHE 3.6 15.7 - - - +
30A PRO* 3.7 13.4 + - + +
32A MET 5.2 6.0 + - - +
34A TYR* 3.6 44.0 - - + +
37A ILE* 4.0 14.6 - - + -
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Residues in contact with THR 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 ASP 2.8 10.4 + - - -
24A ASP* 3.6 10.8 - - - +
26A LYS* 1.3 77.7 - - - +
28A MET* 1.3 70.4 + - + +
30A PRO* 4.3 7.6 - - - +
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Residues in contact with MET 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 ASP* 2.6 53.2 + - - +
25A PHE* 3.6 4.3 - - + +
27A THR* 1.3 79.7 - - + +
29A PHE* 1.3 98.2 + - + +
30A PRO* 3.7 5.0 - - - +
52A ILE* 3.8 34.3 - - + -
56A LEU* 5.6 1.6 - - + -
59A ASN* 5.5 0.2 + - - -
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Residues in contact with PHE 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* 2.6 22.0 + + - +
26A LYS* 3.6 6.9 - - - +
28A MET* 1.3 112.5 - - + +
30A PRO* 1.4 64.2 - - - +
31A ASN 3.4 1.6 - - - -
32A MET* 3.2 38.0 - - + +
37A ILE* 4.2 0.9 - - - +
52A ILE* 4.2 3.8 - - - -
55A LEU* 3.4 47.8 - - + -
56A LEU* 3.4 39.0 - - + -
59A ASN* 3.5 27.6 - - + +
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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