Contacts of the helix formed by residues 27 - 35 (chain D) in PDB entry 1B06
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 LYS 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL* 3.2 34.5 - - + +
19D ASP* 3.7 20.6 - - + +
22D GLU* 2.8 28.7 + - - +
25D ILE 3.8 0.2 + - - -
26D SER* 1.3 70.9 - - - +
28D ASP* 1.3 78.3 + - - +
29D ILE 3.1 0.2 - - - -
30D ILE* 3.8 0.6 - - - +
31D ASP* 2.9 34.0 + - - +
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Residues in contact with ASP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LYS* 5.0 10.0 + - - +
26D SER* 3.1 12.4 + - - +
27D LYS* 1.3 101.6 + - - +
29D ILE* 1.3 59.2 + - - +
31D ASP* 4.1 3.8 - - - +
32D VAL* 3.3 23.0 + - - +
178D LEU* 4.1 17.1 - - + +
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 4.0 13.7 - - + -
26D SER* 3.1 13.2 + - - +
28D ASP* 1.3 76.9 - - - +
30D ILE* 1.3 60.3 + - + +
32D VAL* 3.4 7.7 - - - +
33D HIS* 2.8 42.4 + - - +
174D HIS 3.8 16.4 - - - +
175D ALA 3.6 18.6 - - - +
176D TYR* 4.0 17.5 - - - +
178D LEU* 3.8 22.2 - - + +
179D GLN* 3.7 44.6 - - + +
180D TYR* 5.4 0.9 - - + -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.7 29.4 - - + -
16D TYR* 5.1 4.3 - - + -
18D VAL* 3.3 33.2 - - + +
21D LEU* 3.9 25.6 - - + -
25D ILE* 3.7 26.9 - - + +
26D SER 3.2 11.1 + - - +
27D LYS 3.4 1.1 + - - +
29D ILE* 1.3 77.1 - - + +
31D ASP* 1.3 59.3 + - - +
33D HIS* 3.7 4.8 - - - +
34D TYR* 2.9 32.1 + - + +
87D TYR* 6.1 0.4 - - + -
88D TRP* 4.1 21.3 - - + -
91D MET* 5.2 0.4 - - + -
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Residues in contact with ASP 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL* 4.2 18.2 - - + +
27D LYS 2.9 19.7 + - - +
28D ASP* 4.1 5.6 - - - +
30D ILE* 1.3 76.7 - - - +
32D VAL* 1.3 58.2 + - - +
35D ASN* 2.6 70.0 + - - +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C TYR* 3.7 22.7 - - + +
181C LYS* 4.8 12.3 - - + +
182C ASN* 3.6 35.7 - - + +
28D ASP 3.3 18.2 - - - +
29D ILE* 3.4 8.3 - - + +
31D ASP* 1.3 79.1 - - + +
33D HIS* 1.3 64.3 + - + +
35D ASN* 5.0 0.4 - - - -
36D GLY* 2.8 33.2 + - - +
37D HIS* 3.0 5.3 + - - -
174D HIS 5.7 1.1 - - - +
178D LEU* 4.6 11.2 - - + -
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 2.8 30.5 + - + +
30D ILE* 3.7 5.8 - - - +
32D VAL* 1.3 77.6 - - + +
34D TYR* 1.3 58.3 + - - +
37D HIS* 3.4 10.8 - - + +
38D HIS* 3.1 25.5 + - - +
84D HIS* 3.2 14.2 + + - -
87D TYR* 3.7 18.9 + + - -
88D TRP* 3.5 14.7 - + + -
170D ASP* 2.9 16.1 + - - -
174D HIS* 3.0 16.3 + + - +
175D ALA* 3.6 27.1 + - + -
325D FE 2.3 27.1 - - - -
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.2 47.7 - + - -
12D PRO* 2.5 28.0 + - + -
13D GLN* 3.3 13.2 - - - +
14D LEU* 3.4 48.8 + - + -
18D VAL* 5.5 2.5 - - + -
30D ILE 2.9 18.1 + - - +
31D ASP 4.1 0.2 - - - +
33D HIS* 1.3 75.2 - - - +
35D ASN* 1.3 94.5 + - - +
36D GLY 3.2 1.5 + - - -
38D HIS* 3.4 7.1 - + - +
39D LYS 3.3 12.3 + - - -
88D TRP* 4.0 24.2 - + + -
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Residues in contact with ASN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.6 5.2 - - - -
18D VAL* 4.9 4.8 - - - +
31D ASP* 2.6 45.9 + - - +
32D VAL* 5.0 0.7 - - - -
34D TYR* 1.3 99.8 - - - +
36D GLY* 1.3 57.3 + - - +
39D LYS* 3.0 37.8 + - - +
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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