Contacts of the helix formed by residues 17 - 28 (chain A) in PDB entry 2EW9
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A CYS 3.4 1.2 + - - -
16A ALA* 1.3 90.0 + - - +
18A CYS* 1.3 62.5 + - - +
19A VAL 3.4 2.0 - - - -
20A SER* 3.1 17.1 + - - -
21A ASN* 2.8 28.6 + - - +
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Residues in contact with CYS 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 THR* 3.3 35.9 - - - +
15A CYS 4.7 2.2 + - - +
16A ALA 4.8 0.8 - - - +
17A SER* 1.3 74.1 - - - +
19A VAL* 1.3 59.6 + - - +
21A ASN* 3.2 15.3 + - - +
22A ILE* 2.8 37.0 + - - +
65A LEU 5.7 5.4 - - - -
67A PHE* 3.8 14.4 - - + -
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Residues in contact with VAL 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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10A ILE* 5.2 6.1 - - + -
13A MET* 4.3 17.3 - - + -
15A CYS 5.4 2.6 + - - +
18A CYS* 1.3 74.1 - - - +
20A SER* 1.3 58.1 + - - +
22A ILE* 3.0 13.6 + - + +
23A GLU* 2.8 35.7 + - + +
37A VAL* 3.7 36.3 - - + -
39A LEU* 3.8 36.3 - - + -
67A PHE* 3.8 21.3 - - + -
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Residues in contact with SER 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 ALA 4.1 4.7 + - - -
17A SER* 3.1 25.6 + - - -
19A VAL* 1.3 82.2 - - - +
21A ASN* 1.3 61.0 + - - +
23A GLU* 3.5 17.8 + - - +
24A ARG* 3.4 24.3 + - - +
39A LEU* 5.1 5.0 - - - +
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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 SER 2.8 15.0 + - - +
18A CYS* 3.5 19.8 + - - +
20A SER* 1.3 70.3 - - - +
22A ILE* 1.3 68.1 + - - +
24A ARG* 2.9 12.6 + - - +
25A ASN* 2.8 48.9 + - - +
65A LEU* 3.9 19.0 - - - +
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Residues in contact with ILE 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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10A ILE* 5.6 7.9 - - + -
18A CYS* 2.8 21.4 + - + +
19A VAL* 3.3 11.7 - - + +
21A ASN* 1.3 78.3 - - - +
23A GLU* 1.3 64.7 + - + +
25A ASN* 3.0 9.0 + - - +
26A LEU* 2.8 43.8 + - + +
37A VAL* 6.1 2.5 - - + -
62A ILE* 4.5 11.9 - - + -
65A LEU* 3.9 26.5 - - + -
67A PHE* 3.2 52.0 - - + -
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Residues in contact with GLU 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 VAL* 2.8 20.9 + - - +
20A SER* 3.6 22.8 + - - +
22A ILE* 1.3 74.0 - - + +
24A ARG* 1.3 58.1 + - + +
26A LEU* 3.4 2.8 + - - -
27A GLN* 2.8 36.6 + - - +
35A VAL* 3.6 35.5 - - + +
37A VAL* 3.6 45.4 + - + +
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Residues in contact with ARG 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 SER 3.8 13.0 - - - +
21A ASN* 2.9 13.2 + - - +
23A GLU* 1.3 74.1 - - + +
25A ASN* 1.3 70.1 + - - +
27A GLN* 3.4 13.5 + - - +
28A LYS* 3.3 27.6 + - - +
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Residues in contact with ASN 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 52.1 + - - +
22A ILE 3.3 7.0 - - - +
24A ARG* 1.3 76.8 - - - +
26A LEU* 1.3 58.0 + - - +
28A LYS* 2.8 24.8 + - - +
29A GLU* 3.0 10.7 + - - +
61A PHE* 4.2 18.9 - - + -
65A LEU* 3.7 35.1 - - + +
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Residues in contact with LEU 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 ILE* 2.8 46.8 + - + +
23A GLU* 3.8 5.8 - - - +
25A ASN* 1.3 72.0 - - + +
27A GLN* 1.3 58.2 + - - +
29A GLU* 2.8 45.3 + - - +
32A VAL* 3.3 28.2 - - + +
35A VAL* 4.5 11.9 - - + -
46A ILE* 4.9 13.5 - - + -
58A ILE* 3.8 22.4 - - + -
61A PHE* 5.2 4.7 - - + -
62A ILE* 3.9 22.2 - - + -
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Residues in contact with GLN 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 GLU* 2.8 34.4 + - - +
24A ARG* 3.5 15.9 - - - +
25A ASN 3.3 0.2 - - - -
26A LEU* 1.3 74.1 - - - +
28A LYS* 1.3 61.5 + - + +
30A ALA 5.2 1.7 - - - +
32A VAL 3.9 13.2 - - - +
33A LEU* 4.6 21.6 - - + +
34A SER* 4.9 1.1 - - - +
35A VAL* 3.3 34.3 - - + +
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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 ARG* 3.3 16.1 + - - +
25A ASN* 2.8 12.7 + - - +
27A GLN* 1.3 83.3 - - + +
29A GLU* 1.3 64.9 + - - +
30A ALA 3.6 1.3 - - - -
61A PHE* 5.4 2.0 - - - -
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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