Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 4B23
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 ASP 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU 4.6 0.2 - - - +
17A ILE* 1.3 85.6 + - - +
19A ASN* 1.3 62.1 + - - +
20A LYS* 3.1 40.7 + - - +
21A TRP* 3.5 29.2 + - - +
22A SER* 3.8 2.3 + - - -
173A PHE* 5.8 1.9 - - - -
190A PRO* 5.9 4.0 - - - +
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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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17A ILE 4.4 0.9 - - - +
18A ASP* 1.3 73.5 - - - +
20A LYS* 1.3 64.3 + - - +
21A TRP 3.1 1.8 - - - -
22A SER* 3.6 14.3 - - - -
23A SER* 3.0 27.2 + - - -
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Residues in contact with LYS 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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18A ASP* 3.1 27.4 + - - +
19A ASN* 1.3 81.0 - - - +
21A TRP* 1.3 58.8 + - - +
23A SER* 3.4 7.0 + - - -
24A LEU* 2.9 29.1 + - - +
172A PHE* 3.4 45.3 - - + +
173A PHE* 3.8 29.6 - - - +
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Residues in contact with TRP 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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14A LEU* 3.1 29.6 - - + +
17A ILE* 3.8 20.2 - - + +
18A ASP* 3.5 26.4 + - - +
19A ASN 3.1 0.2 - - - -
20A LYS* 1.3 77.3 - - - +
22A SER* 1.3 64.9 + - - +
24A LEU* 3.4 21.4 + - + +
25A VAL* 3.0 31.3 + - + +
172A PHE* 3.5 26.6 - + - -
173A PHE* 4.1 19.9 - + - -
187A LEU 5.0 2.8 + - - -
188A THR* 4.5 5.2 - - + -
190A PRO* 5.9 2.3 - - + +
191A CYS* 3.4 24.6 - - - -
198A ALA* 3.7 41.1 - - + -
201A TYR* 4.4 4.3 - - + -
202A LEU* 3.8 19.1 - - + -
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Residues in contact with SER 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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14A LEU 3.6 1.2 + - - -
15A SER* 3.9 39.0 + - - +
18A ASP 3.8 1.5 + - - -
19A ASN* 3.4 23.8 + - - -
21A TRP* 1.3 78.6 - - - +
23A SER* 1.3 61.9 + - - +
25A VAL* 3.6 2.6 + - - +
26A LYS* 3.2 23.6 + - - +
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Residues in contact with SER 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* 3.0 20.8 + - - -
20A LYS* 3.5 8.3 - - - -
21A TRP 3.2 0.2 - - - -
22A SER* 1.3 74.8 - - - +
24A LEU* 1.3 64.4 + - - +
26A LYS* 3.4 5.9 + - - +
27A LYS* 3.1 48.4 + - - +
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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 LYS 2.9 16.5 + - - +
21A TRP* 3.8 16.4 - - + +
23A SER* 1.3 72.9 - - - +
25A VAL* 1.3 67.7 + - - +
27A LYS* 3.2 6.5 + - + +
28A VAL* 2.9 48.5 + - + +
172A PHE* 3.8 26.2 - - + -
201A TYR* 3.8 33.7 - - + +
202A LEU* 4.1 5.2 - - + +
205A ILE* 3.7 22.7 - - + -
208A LEU* 4.2 11.0 - - + -
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Residues in contact with VAL 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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11A GLU* 4.2 14.6 - - + +
14A LEU* 3.8 28.0 - - + -
15A SER* 3.9 17.3 - - - +
21A TRP* 3.0 20.7 + - + +
22A SER 3.8 4.3 - - - +
24A LEU* 1.3 76.7 - - + +
26A LYS* 1.3 57.6 + - - +
29A GLY* 2.9 32.0 + - - +
201A TYR* 3.7 39.0 - - + +
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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 SER 3.2 15.9 + - - +
23A SER* 3.8 5.6 - - - +
24A LEU 3.2 0.4 - - - -
25A VAL* 1.3 82.3 - - - +
27A LYS* 1.3 62.4 + - + +
29A GLY* 3.7 7.7 + - - -
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Residues in contact with LYS 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 SER* 3.1 34.9 + - - +
24A LEU* 3.7 6.5 - - + +
26A LYS* 1.3 77.7 - - + +
28A VAL* 1.3 61.6 + - - +
208A LEU* 4.2 30.6 - - + +
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Residues in contact with VAL 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 40.6 + - + +
27A LYS* 1.3 76.9 - - - +
29A GLY* 1.3 60.5 + - - +
30A PRO* 4.7 2.1 - - - +
200A TRP* 3.7 33.4 - - + -
201A TYR* 3.7 15.0 - - + +
204A GLN* 3.9 22.2 - - + -
208A LEU* 4.0 21.5 - - + -
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Residues in contact with GLY 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 VAL* 2.9 14.4 + - - +
26A LYS 4.2 5.6 - - - -
27A LYS 3.4 2.2 - - - -
28A VAL* 1.3 79.0 - - - +
30A PRO* 1.3 67.5 - - - +
201A TYR* 2.7 33.4 + - - -
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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