Contacts of the helix formed by residues 18 - 29 (chain L) in PDB entry 6BCH
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 SER 18 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L ASN 3.7 2.3 + - - -
17L ILE* 1.3 78.3 - - - +
19L PRO* 1.3 75.4 - - - +
20L TRP* 3.2 16.8 + - - +
21L THR* 3.1 28.8 + - - -
22L ILE* 3.2 14.0 + - - +
70L TYR* 4.7 0.2 - - - -
173L ASP* 5.0 0.2 + - - -
175L ASN* 3.6 24.2 + - - -
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Residues in contact with PRO 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ILE 3.9 0.6 - - - +
18L SER* 1.3 89.3 - - - +
20L TRP* 1.3 60.3 + - + +
22L ILE* 3.2 8.7 + - + +
23L THR* 2.9 30.5 + - - -
70L TYR* 3.2 37.2 - - + +
98L HIS* 3.7 9.1 + - + -
102L TYR* 3.5 43.3 - - + +
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Residues in contact with TRP 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L SER* 3.2 10.4 + - - +
19L PRO* 1.3 79.0 - - + +
21L THR* 1.3 61.1 + - - +
23L THR* 3.4 6.2 + - + -
24L GLY 2.9 22.9 + - - -
101L LYS 4.7 1.8 - - - -
102L TYR* 3.7 36.2 - + + -
103L PRO* 3.2 47.1 - - + -
105L ILE* 5.0 1.6 - - + -
172L PRO* 3.4 43.3 + - + -
173L ASP* 3.8 25.8 - - + +
175L ASN* 4.5 0.2 - - + -
176L TRP* 3.3 36.9 - + - +
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Residues in contact with THR 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ILE* 3.8 23.3 - - + +
18L SER* 3.1 18.8 + - - -
20L TRP* 1.3 77.5 - - - +
22L ILE* 1.3 58.0 + - - +
24L GLY 3.4 0.2 + - - -
25L PHE* 2.9 29.1 + - - +
175L ASN* 3.2 34.9 + - - +
178L ALA* 4.9 4.2 - - + +
179L GLY* 3.6 18.9 - - - +
269L HIS 5.6 1.1 - - - +
271L ILE* 4.4 19.1 - - + -
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Residues in contact with ILE 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ILE* 3.8 23.6 - - + -
18L SER 3.5 10.3 - - - +
19L PRO* 3.2 9.4 + - + +
21L THR* 1.3 77.7 - - - +
23L THR* 1.3 57.2 + - - +
25L PHE* 3.4 5.4 + - - +
26L ALA* 2.9 32.8 + - + +
67L ILE* 4.2 34.5 - - + +
70L TYR* 3.6 46.9 - - + -
71L LEU* 5.2 4.7 - - + -
98L HIS* 3.8 17.7 - - + +
99L PHE* 5.6 2.0 - - + -
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Residues in contact with THR 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L PRO 2.9 13.6 + - - -
20L TRP* 3.8 10.5 - - + -
22L ILE* 1.3 77.4 - - - +
24L GLY* 1.3 56.4 + - - +
27L ASP* 2.8 30.4 + - - +
98L HIS* 3.3 15.9 + - - -
99L PHE* 4.0 9.6 - - + -
102L TYR* 2.6 31.4 + - - +
103L PRO 3.3 23.3 - - - +
104L LEU* 3.6 16.3 - - + +
176L TRP* 4.0 7.0 - - + -
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Residues in contact with GLY 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TRP 2.9 12.6 + - - -
21L THR 3.8 0.7 - - - -
23L THR* 1.3 76.6 - - - +
25L PHE* 1.3 56.1 + - - +
27L ASP* 3.0 19.6 - - - +
28L ALA 3.0 8.0 + - - -
176L TRP* 3.4 38.0 - - - -
180L PHE* 3.6 17.1 - - - -
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Residues in contact with PHE 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ILE* 6.4 0.7 - - + -
21L THR 2.9 17.8 + - - +
22L ILE* 3.8 5.2 - - - +
24L GLY* 1.3 73.6 - - - +
26L ALA* 1.3 60.8 + - - +
28L ALA* 3.1 4.1 + - - +
29L ASP* 2.9 29.4 + - - +
54L ILE* 3.3 26.2 - - + +
56L LEU* 3.5 48.7 - - + -
60L ASP* 5.8 2.5 - - - -
63L ILE* 5.2 5.2 - - + -
67L ILE* 4.8 11.4 - - + -
179L GLY* 3.3 24.0 - - - +
182L ALA* 3.7 30.7 - - + -
183L GLY* 3.8 8.1 - - - -
271L ILE* 4.4 19.1 - - + -
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Residues in contact with ALA 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ILE* 2.9 19.9 + - + +
23L THR 3.8 3.4 - - - +
25L PHE* 1.3 73.6 - - - +
27L ASP* 1.3 66.3 + - - +
28L ALA 3.0 0.2 - - - -
30L SER* 2.7 51.0 + - - +
52L PHE* 4.4 4.3 - - + -
54L ILE* 4.1 8.0 - - + +
99L PHE* 3.9 25.1 - - + -
104L LEU* 4.3 2.0 - - + +
108L LYS* 5.6 2.3 - - - +
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Residues in contact with ASP 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L THR 2.8 14.2 + - - +
24L GLY* 3.0 16.6 - - - +
26L ALA* 1.3 76.5 - - - +
28L ALA* 1.3 58.9 + - - +
104L LEU* 3.5 16.5 - - - +
105L ILE 2.9 17.5 + - - -
106L THR* 2.4 61.5 + - + +
108L LYS* 5.1 4.9 - - - +
176L TRP* 2.8 25.9 + - + -
180L PHE* 4.1 7.0 - - + -
184L GLU* 4.6 1.0 - - - +
211L GLN* 4.8 3.3 + - - -
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Residues in contact with ALA 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L GLY 3.0 11.0 + - - +
25L PHE* 3.4 8.7 - - - +
26L ALA 3.0 0.4 - - - -
27L ASP* 1.3 80.0 - - - +
29L ASP* 1.3 71.4 + - - +
30L SER 3.8 1.5 + - - +
180L PHE* 4.1 6.5 - - + +
183L GLY* 3.7 15.3 - - - -
184L GLU* 3.2 43.8 - - + +
15O C 5.7 0.3 + - - -
17P A 4.1 9.7 + - - +
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Residues in contact with ASP 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L PHE* 2.9 19.8 + - + +
28L ALA* 1.3 89.8 - - - +
30L SER* 1.3 63.5 + - - +
31L SER* 5.4 0.3 - - - -
54L ILE* 4.4 5.8 - - + -
55L GLY 4.1 11.3 + - - +
56L LEU* 3.4 23.3 - - + +
183L GLY* 3.9 15.5 - - - +
184L GLU* 3.6 5.4 - - - +
16N T 5.5 1.6 + - - -
16O G 4.5 0.6 + - - -
16P T 3.7 28.2 + - - +
17P A 3.4 29.6 + - - +
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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