Contacts of the helix formed by residues 19 - 31 (chain A) in PDB entry 4BSX
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 GLY 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU 4.3 0.4 + - - -
16A GLY 3.9 6.4 + - - -
17A ALA 3.3 3.8 + - - -
18A ALA* 1.3 80.6 - - - +
20A GLN* 1.3 65.2 + - - -
21A ASP* 3.3 3.5 + - - -
22A LYS 3.7 1.0 + - - -
23A LEU* 3.1 29.3 + - - +
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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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16A GLY* 5.2 5.7 + - - -
19A GLY* 1.3 72.1 - - - -
21A ASP* 1.3 63.7 + - - +
23A LEU* 3.7 21.3 - - - +
24A LEU* 2.9 39.4 + - + +
50A LYS 4.7 5.6 + - - +
51A LEU* 3.8 26.1 - - + +
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Residues in contact with ASP 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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19A GLY* 3.3 1.0 - - - -
20A GLN* 1.3 79.0 - - - +
22A LYS* 1.3 59.0 + - - +
24A LEU* 3.0 17.2 + - - +
25A TYR* 2.8 27.1 + - - +
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Residues in contact with LYS 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 ALA* 3.4 39.1 + - + +
19A GLY* 3.7 2.5 + - - +
20A GLN 3.5 0.2 - - - -
21A ASP* 1.3 77.7 - - - +
23A LEU* 1.3 56.1 + - - +
25A TYR* 3.2 36.7 + - + +
26A LEU* 2.8 36.9 + - + +
106A GLU* 4.7 7.8 + - + +
108A LEU* 3.9 24.5 - - + +
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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 LEU* 3.5 50.5 - - + +
16A GLY* 5.2 1.1 - - - +
18A ALA* 4.8 3.8 - - + -
19A GLY 3.1 14.5 + - - +
20A GLN* 3.7 31.0 - - - +
21A ASP 3.3 0.4 - - - -
22A LYS* 1.3 75.5 - - - +
24A LEU* 1.3 58.0 + - - +
26A LEU* 3.1 4.6 + - + -
27A LYS* 2.7 30.8 + - - +
47A VAL* 3.4 16.4 - - + +
50A LYS* 4.1 27.6 - - + +
51A LEU* 3.8 21.8 - - + -
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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 GLN* 2.9 23.7 + - + +
21A ASP* 3.3 15.5 - - - +
23A LEU* 1.3 75.0 - - - +
25A TYR* 1.3 62.7 + - - +
27A LYS* 3.3 16.1 + - + +
28A HIS* 2.9 53.1 + - + +
51A LEU* 4.3 22.2 - - + -
53A GLN* 4.7 5.6 - - - +
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Residues in contact with TYR 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 ASP 2.8 15.2 + - - +
22A LYS* 3.2 35.4 - - + +
24A LEU* 1.3 72.9 - - - +
26A LEU* 1.3 62.1 + - + +
28A HIS* 3.3 7.5 + - + +
29A LYS* 2.7 74.5 + - + +
106A GLU* 3.4 23.3 + - - -
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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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15A LEU* 4.2 16.6 - - + -
22A LYS* 2.8 26.3 + - + +
23A LEU* 3.7 8.7 - - + +
25A TYR* 1.3 80.5 - - + +
27A LYS* 1.3 59.5 + - - +
29A LYS* 4.4 3.1 - - + -
30A LEU* 2.7 56.0 + - + +
43A LEU* 5.6 3.8 - - + -
47A VAL* 3.9 17.0 - - + -
103A LEU* 5.4 1.6 - - + -
106A GLU* 3.8 35.2 - - + +
108A LEU* 3.5 31.2 - - + -
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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 LEU 2.7 19.5 + - - +
24A LEU* 3.6 10.4 - - + +
26A LEU* 1.3 74.8 - - - +
28A HIS* 1.3 85.0 + - + +
31A LYS* 3.5 20.1 + - - +
44A HIS* 3.5 14.3 - - + -
47A VAL* 3.7 16.4 - - + +
48A LEU* 4.0 20.2 - - + -
51A LEU* 4.1 12.1 - - + -
53A GLN* 2.7 33.8 + - - +
56A GLU* 4.1 14.9 + - - -
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Residues in contact with HIS 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 46.6 + - + +
25A TYR* 3.8 7.2 - - + +
27A LYS* 1.3 102.1 - - + +
29A LYS* 1.3 61.2 + - - +
31A LYS* 3.9 11.2 - - - +
32A THR* 4.9 5.5 + - - +
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Residues in contact with LYS 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 TYR* 2.7 60.9 + - + +
26A LEU* 3.9 6.7 - - + +
28A HIS* 1.3 76.5 - - - +
30A LEU* 1.3 69.4 + - + +
31A LYS 3.1 3.5 + - - -
32A THR* 3.7 2.4 + - - +
34A ARG* 2.5 54.6 + - - +
106A GLU* 2.8 28.1 + - - +
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Residues in contact with LEU 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 LEU* 2.7 51.1 + - + +
29A LYS* 1.3 80.3 - - + +
31A LYS* 1.3 63.2 + - - +
32A THR 3.2 7.9 + - - +
33A PRO* 5.2 0.2 - - - +
40A GLN* 3.9 44.9 + - + +
41A ASP* 4.6 5.5 - - - +
43A LEU* 3.6 41.5 - - + +
44A HIS* 3.8 31.6 - - + +
47A VAL* 4.2 1.6 - - + -
102A LEU* 5.2 4.7 - - + -
106A GLU* 5.5 4.3 - - + +
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Residues in contact with LYS 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 LYS 3.5 18.6 + - - +
28A HIS* 3.9 8.7 - - - +
29A LYS 3.1 1.0 - - - -
30A LEU* 1.3 78.6 - - - +
32A THR* 1.3 66.3 + - + +
33A PRO* 4.2 3.5 - - - +
41A ASP* 5.0 5.9 - - - +
44A HIS* 3.6 29.4 + - + +
56A GLU* 4.3 15.7 + - - +
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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