Contacts of the helix formed by residues 18 - 32 (chain A) in PDB entry 1B0K
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 TYR 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.6 23.3 + - + -
17A ARG* 1.3 74.6 - - - +
19A ASP* 1.3 57.8 + - - +
21A LEU* 3.7 20.2 - - + +
22A GLU* 3.1 28.1 + - - +
156A TYR* 3.8 11.5 - + - -
157A PRO* 2.6 44.7 + - - +
158A GLY* 4.4 7.2 - - - -
288A ILE* 4.7 5.7 - - + +
291A LEU* 3.6 33.9 - - + -
292A ALA* 3.8 26.2 - - - +
295A PHE* 3.6 39.9 - + + -
299A LEU* 4.3 10.8 - - + -
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.6 52.4 + - + +
16A ILE 4.6 1.0 - - - +
17A ARG* 2.8 48.0 + - - -
18A TYR* 1.3 80.4 + - - +
20A LEU* 1.3 63.5 + - - +
22A GLU* 3.7 2.6 - - - +
23A LYS* 3.2 25.3 + - - +
295A PHE* 4.2 2.9 - - - -
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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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17A ARG* 3.3 47.7 + - + +
19A ASP* 1.3 84.7 + - - +
21A LEU* 1.3 63.8 + - - +
23A LYS* 3.5 19.4 + - + +
24A ASN* 3.3 43.5 + - - +
45A GLY 4.8 0.4 - - - -
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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 ARG 3.2 10.7 + - - +
18A TYR* 3.7 30.1 - - + +
20A LEU* 1.3 78.0 - - - +
22A GLU* 1.4 56.9 + - - +
25A ILE* 3.0 44.6 + - + +
41A LYS 4.0 10.1 - - - +
42A ILE* 4.3 8.5 - - + -
45A GLY* 3.8 33.5 - - - -
46A HIS* 4.2 19.5 - - + +
158A GLY* 4.7 9.2 - - - +
295A PHE* 6.5 1.3 - - + -
298A HIS* 4.5 10.5 - - + +
299A LEU* 4.4 18.8 - - + -
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Residues in contact with GLU 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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2A ARG* 2.9 39.0 + - - -
18A TYR 3.1 18.6 + - - +
19A ASP 3.7 4.2 - - - +
21A LEU* 1.4 74.6 - - - +
23A LYS* 1.3 63.2 + - - +
24A ASN 3.2 0.2 + - - -
25A ILE* 3.3 9.2 + - - +
26A ASP* 3.0 27.2 + - + +
295A PHE* 3.8 9.7 - - + -
298A HIS* 3.3 37.2 + - + +
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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 ASP 3.2 16.2 + - - +
20A LEU* 3.7 22.9 - - + +
21A LEU 3.5 0.2 - - - -
22A GLU* 1.3 76.8 - - - +
24A ASN* 1.3 81.8 + - - +
26A ASP* 3.4 6.9 - - - +
27A ILE* 3.2 54.8 + - + +
50A PRO* 4.6 3.8 - - - +
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Residues in contact with ASN 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* 3.3 28.7 + - - +
22A GLU 3.2 0.8 - - - -
23A LYS* 1.3 102.2 + - - +
25A ILE* 1.3 66.2 + - - +
26A ASP 3.0 1.3 - - - -
27A ILE* 3.5 6.0 + - - +
28A VAL* 3.1 27.4 + - - +
44A TYR 4.1 4.3 - - - +
45A GLY* 2.9 35.1 + - - +
46A HIS* 5.0 0.2 - - - +
47A LEU 4.3 12.1 + - - -
50A PRO* 3.5 19.2 - - + +
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Residues in contact with ILE 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* 3.0 41.5 + - + +
22A GLU 3.5 4.7 - - - +
24A ASN* 1.3 75.1 - - - +
26A ASP* 1.3 60.0 + - + +
28A VAL* 3.3 6.0 + - - +
29A ARG* 2.9 51.2 + - - +
36A LEU* 4.6 5.4 - - + +
41A LYS* 3.3 44.2 - - + +
44A TYR* 5.4 1.1 - - + -
45A GLY* 4.2 4.6 - - - +
298A HIS* 3.8 40.6 - - + +
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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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22A GLU* 3.0 18.7 + - + +
23A LYS* 3.4 8.5 - - - +
24A ASN 3.0 0.8 - - - -
25A ILE* 1.3 79.4 - - + +
27A ILE* 1.3 67.0 + - - +
28A VAL 3.1 1.2 + - - -
29A ARG* 3.3 26.1 + - - +
30A LYS* 2.7 49.3 + - - +
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Residues in contact with ILE 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* 3.2 47.1 - - + +
24A ASN* 3.7 8.1 - - - +
26A ASP* 1.3 78.8 + - - +
28A VAL* 1.3 61.1 + - - +
30A LYS* 3.8 8.1 + - - +
31A ARG* 3.3 22.6 + - + +
50A PRO* 4.1 13.5 - - + +
51A ALA* 4.1 33.2 - - + +
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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 ASN 3.1 18.9 + - - +
25A ILE* 3.6 4.5 - - - +
26A ASP 3.1 0.6 - - - -
27A ILE* 1.3 73.9 - - - +
29A ARG* 1.3 61.8 + - - +
30A LYS 3.2 2.0 - - - -
31A ARG* 3.0 24.9 + - - +
32A LEU* 3.1 25.4 + - + +
36A LEU* 4.8 5.4 - - + -
44A TYR* 3.8 35.4 - - + +
47A LEU* 4.2 16.4 - - + -
50A PRO* 3.9 30.5 - - + +
55A ILE* 4.0 8.5 - - + -
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Residues in contact with ARG 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 ILE* 2.9 34.9 + - - +
26A ASP* 3.4 26.6 + - - +
28A VAL* 1.3 72.1 - - - +
30A LYS* 1.3 60.5 + - + +
32A LEU* 4.4 5.2 - - - +
33A ASN* 2.9 29.5 + - - +
34A ARG 4.1 14.3 + - - +
35A PRO* 5.1 0.4 - - - +
36A LEU* 4.2 14.8 - - + +
41A LYS* 4.0 10.3 - - - +
298A HIS* 5.6 3.4 + - - -
302A ASP* 2.8 43.0 + - - -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASP* 2.7 54.0 + - - +
27A ILE* 3.9 11.0 - - - +
28A VAL 3.2 0.6 - - - -
29A ARG* 1.3 79.2 - - + +
31A ARG* 1.3 65.8 + - + +
33A ASN* 3.3 20.8 + - - -
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Residues in contact with ARG 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 ILE* 3.3 19.3 + - + +
28A VAL* 3.0 9.0 + - - +
30A LYS* 1.3 79.5 - - + +
32A LEU* 1.3 71.2 + - + +
33A ASN* 4.1 5.0 + - - -
50A PRO 2.9 31.8 + - - -
51A ALA* 3.2 26.3 + - - +
52A ASN* 4.5 3.2 + - - +
53A GLN 2.9 31.3 + - - -
54A GLU* 4.7 3.4 - - - +
55A ILE* 4.5 13.6 - - - +
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Residues in contact with LEU 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 VAL* 3.1 33.4 + - + +
29A ARG* 4.6 3.1 - - - +
31A ARG* 1.3 85.3 - - + +
33A ASN* 1.3 72.1 + - - +
34A ARG* 3.2 37.9 + - + +
36A LEU* 3.9 20.2 - - + -
44A TYR* 4.3 8.3 - - + -
55A ILE* 4.4 26.2 - - + +
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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