Contacts of the helix formed by residues 23 - 32 (chain A) in PDB entry 4FBI
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 THR 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.6 11.6 - - - +
21A GLY 5.2 2.2 - - - +
22A MET* 1.3 77.4 - - - +
24A GLN* 1.3 63.9 + - - +
25A GLU* 3.4 19.0 + - - +
26A ASP* 2.9 36.0 + - - +
27A LEU 3.1 16.6 + - - -
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Residues in contact with GLN 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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14A LYS* 5.7 1.8 - - - +
17A ARG* 3.6 25.8 - - - +
23A THR* 1.3 73.5 - - - +
25A GLU* 1.3 70.5 + - - +
27A LEU* 3.2 3.8 + - - +
28A ALA* 2.9 29.1 + - - +
35A ARG* 4.4 13.3 + - + +
38A ILE* 3.9 25.3 - - + +
39A SER* 3.5 36.3 + - - +
42A GLU* 2.8 23.4 + - - +
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Residues in contact with GLU 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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23A THR* 3.4 20.8 - - - +
24A GLN* 1.3 85.0 + - - +
26A ASP* 1.3 63.1 + - - +
28A ALA* 3.2 1.9 + - - +
29A TYR* 2.8 48.4 + - + +
35A ARG* 3.2 49.9 + - + +
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Residues in contact with ASP 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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21A GLY 3.9 5.0 - - - +
22A MET* 3.4 21.6 - - + +
23A THR* 2.9 48.7 + - - +
25A GLU* 1.3 78.2 - - - +
27A LEU* 1.3 62.5 + - - +
29A TYR* 3.4 8.0 + - - +
30A LYS* 3.1 24.1 + - - +
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Residues in contact with LEU 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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13A ILE* 4.9 4.9 - - + -
17A ARG* 4.1 16.6 - - + -
22A MET* 3.8 21.3 - - + -
23A THR 3.1 9.8 + - - +
24A GLN 3.7 5.8 - - - +
26A ASP* 1.3 76.9 - - - +
28A ALA* 1.3 60.0 - - - +
30A LYS* 3.3 1.9 + - + -
31A SER* 2.7 36.4 + - - +
38A ILE* 3.8 32.5 - - + -
56A ILE* 4.2 22.7 - - + +
59A GLY* 4.1 18.6 - - - -
60A LEU* 4.1 25.6 - - + -
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Residues in contact with ALA 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 GLN 2.9 17.2 + - - +
25A GLU* 3.5 5.6 - - - +
27A LEU* 1.3 77.7 - - - +
29A TYR* 1.3 67.9 - - + +
31A SER* 3.0 6.0 + - - -
32A ASN* 2.9 21.5 + - - -
33A LEU 3.0 27.5 + - - +
34A ASP 3.5 4.5 - - - +
35A ARG* 3.4 24.9 - - + +
38A ILE* 4.0 6.9 - - + +
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Residues in contact with TYR 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 GLU* 2.8 34.6 + - + +
26A ASP* 3.7 7.9 - - - +
28A ALA* 1.3 79.4 - - + +
30A LYS* 1.4 62.5 + - - +
32A ASN* 3.6 7.6 + - - +
33A LEU 5.0 1.3 - - - -
35A ARG* 6.3 1.8 - - + -
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Residues in contact with LYS 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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22A MET* 3.6 19.6 - - + +
26A ASP 3.1 16.3 + - - +
27A LEU* 3.8 5.2 - - - +
28A ALA 3.2 0.4 - - - -
29A TYR* 1.4 76.6 - - - +
31A SER* 1.3 60.1 + - - +
32A ASN 3.7 0.3 + - - -
55A LEU* 5.7 0.2 - - - +
58A LYS 5.1 0.9 + - - +
59A GLY* 2.6 42.9 + - - +
61A GLU* 3.1 26.1 + - - +
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Residues in contact with SER 31 (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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27A LEU* 2.7 30.9 + - - +
28A ALA* 3.2 4.7 + - - -
30A LYS* 1.3 78.2 - - - +
32A ASN* 1.3 70.4 + - - +
33A LEU* 3.3 23.3 + - - +
38A ILE* 4.8 0.2 - - - +
55A LEU* 3.4 51.4 - - - +
56A ILE* 5.3 1.1 - - - -
59A GLY* 5.5 2.5 - - - -
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Residues in contact with ASN 32 (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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28A ALA 2.9 5.4 + - - -
29A TYR* 3.6 6.1 + - - +
30A LYS 3.4 3.4 + - - -
31A SER* 1.3 81.2 - - - +
33A LEU* 1.3 65.6 + - - +
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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