Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 1BUO
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 HIS 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 3.3 34.2 + - + +
15A SER* 1.3 72.6 - - - +
17A PRO* 1.3 66.4 - - + +
19A GLY* 3.2 1.9 + - - +
20A LEU* 2.7 74.8 + - + +
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Residues in contact with PRO 17 (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 ASN 4.0 4.5 - - - +
14A PRO 3.7 12.3 - - - +
15A SER 3.6 3.4 - - - -
16A HIS* 1.3 99.8 - - + +
18A THR* 1.3 57.3 + - - +
20A LEU* 3.6 8.8 - - + +
21A LEU* 3.1 28.6 + - - +
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Residues in contact with THR 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 PRO 5.3 0.4 + - - -
15A SER* 3.3 11.3 + - - -
16A HIS 3.3 0.4 - - - -
17A PRO* 1.3 77.1 - - - +
19A GLY* 1.3 58.2 + - - +
21A LEU* 3.3 5.6 + - - +
22A CYS* 3.0 31.1 + - + +
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Residues in contact with GLY 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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15A SER 2.8 15.7 + - - -
16A HIS* 3.6 3.1 - - - -
18A THR* 1.3 77.2 - - - +
20A LEU* 1.3 61.7 + - - +
22A CYS* 3.3 7.0 + - - +
23A LYS* 3.0 24.9 + - - +
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Residues in contact with LEU 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 HIS* 2.7 53.4 + - + +
17A PRO* 3.6 7.9 - - + +
19A GLY* 1.3 74.1 - - - +
21A LEU* 1.3 58.0 + - - +
23A LYS* 3.2 6.1 + - + +
24A ALA* 2.9 28.0 + - - +
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Residues in contact with LEU 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 PRO 3.1 17.4 + - - +
18A THR* 3.3 6.3 + - - +
20A LEU* 1.3 72.9 - - - +
22A CYS* 1.3 59.8 + - - +
24A ALA* 3.1 14.7 + - + +
25A ASN* 2.8 29.6 + - - +
51A VAL* 4.7 11.4 - - + -
87A ALA 3.7 20.6 - - - +
88A TYR* 3.3 30.1 - - - +
89A THR* 4.1 15.3 - - - +
90A ALA* 4.3 8.5 - - + +
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Residues in contact with CYS 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 THR* 3.0 20.9 + - + +
19A GLY* 3.7 8.1 - - - +
20A LEU 3.3 0.2 - - - -
21A LEU* 1.3 76.7 - - - +
23A LYS* 1.3 55.9 + - - +
25A ASN* 3.3 7.4 + - - +
26A GLN* 3.0 50.0 + - - +
88A TYR 5.3 0.4 - - - -
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Residues in contact with LYS 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 GLY 3.0 13.0 + - - +
20A LEU* 3.5 10.3 - - + +
22A CYS* 1.3 72.2 - - - +
24A ALA* 1.3 69.1 + - - +
26A GLN* 3.4 30.3 + - + +
27A MET* 2.9 54.8 + - + +
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Residues in contact with ALA 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 LEU 2.9 14.1 + - - +
21A LEU* 3.1 12.8 + - + +
23A LYS* 1.3 78.7 - - - +
25A ASN* 1.3 57.2 + - - +
27A MET* 3.3 11.5 + - - +
28A ARG* 2.8 29.5 + - - +
48A HIS* 3.8 5.3 + - + -
51A VAL* 4.2 14.6 - - + -
88A TYR* 3.6 19.6 - - + -
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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 LEU 2.8 14.4 + - - +
22A CYS* 3.6 6.7 - - - +
23A LYS 3.2 0.2 - - - -
24A ALA* 1.3 70.3 - - - +
26A GLN* 1.3 66.0 + - - +
28A ARG* 2.8 44.0 + - - +
29A LEU* 3.0 33.5 + - - +
88A TYR* 3.4 36.5 - - + +
89A THR* 3.7 15.3 - - + +
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Residues in contact with GLN 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 CYS* 3.0 41.5 + - - +
23A LYS* 3.7 35.7 + - + +
25A ASN* 1.3 77.6 + - - +
27A MET* 1.3 59.9 + - + +
29A LEU* 3.3 9.0 + - - +
30A ALA* 3.1 23.2 + - - +
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Residues in contact with MET 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 LYS* 2.9 54.1 + - + +
24A ALA* 3.3 11.2 + - - +
26A GLN* 1.3 69.0 - - - +
28A ARG* 1.3 64.2 + - - +
30A ALA* 3.1 2.6 + - - -
31A GLY 2.9 4.0 + - - -
32A THR* 2.8 62.6 + - + +
33A LEU* 3.9 29.8 - - + -
48A HIS* 4.0 8.3 - - - +
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Residues in contact with ARG 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 ALA 2.8 17.8 + - - +
25A ASN* 2.8 38.6 + - - +
27A MET* 1.3 73.7 - - - +
29A LEU* 1.3 89.2 + - - +
31A GLY* 3.0 13.9 + - - -
34A CYS* 4.0 7.0 - - - -
46A HIS* 3.7 23.7 - - - +
47A ALA* 4.8 0.2 - - - -
48A HIS* 3.7 10.7 + - - +
81A GLN* 4.6 10.5 + - - +
84A LEU* 3.8 26.9 - - - +
85A GLU* 4.4 17.9 + - - +
88A TYR* 3.6 40.3 - - + +
89A THR* 5.6 1.0 - - - +
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Residues in contact with LEU 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 ASN* 3.0 34.6 + - - +
26A GLN* 3.9 7.0 - - - +
27A MET 3.3 0.2 - - - -
28A ARG* 1.3 107.5 - - - +
30A ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 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 GLN 3.1 13.7 + - - +
27A MET* 3.1 2.9 + - - +
29A LEU* 1.3 76.4 - - - +
31A GLY* 1.3 60.6 + - - +
32A THR* 3.5 17.9 + - - +
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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