Contacts of the helix formed by residues 27 - 36 (chain A) in PDB entry 5B6Q
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 ASP 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 3.2 34.0 + - + +
25A ALA 3.1 2.8 - - - +
26A HIS* 1.3 75.3 - - - +
28A ALA* 1.3 62.6 + - - +
29A ALA* 3.3 11.3 + - - +
30A ALA* 3.2 28.2 + - + +
31A TRP* 3.1 25.5 + - - -
74A MET 4.1 0.2 + - - -
75A SER 4.7 0.2 - - - -
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Residues in contact with ALA 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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26A HIS 3.4 5.9 + - - +
27A ASP* 1.3 72.8 + - - +
29A ALA* 1.3 57.9 + - - +
31A TRP* 3.4 1.2 + - - +
32A GLU* 3.0 30.5 + - - +
75A SER 3.6 21.9 - - - +
76A LYS* 4.9 6.5 - - + -
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Residues in contact with ALA 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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27A ASP* 3.2 8.4 + - - +
28A ALA* 1.3 79.9 - - - +
30A ALA* 1.3 62.6 + - - +
32A GLU* 3.6 5.7 + - - +
33A PRO* 3.3 18.9 - - - +
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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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23A PRO* 4.4 18.4 - - + -
24A LYS 4.5 1.1 - - - +
27A ASP* 3.2 34.3 + - + +
29A ALA* 1.3 76.5 - - - +
31A TRP* 1.3 62.2 + - - +
33A PRO* 3.5 9.2 - - - +
34A ARG* 2.9 29.4 + - - +
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Residues in contact with TRP 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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15A HIS* 3.6 10.5 - - - -
23A PRO* 3.3 33.1 + - + -
24A LYS 2.9 29.5 + - - -
27A ASP 3.1 19.6 + - - +
28A ALA 3.4 2.9 + - - +
30A ALA* 1.3 78.5 - - - +
32A GLU* 1.3 54.9 + - - +
33A PRO 3.4 0.4 - - - -
34A ARG* 2.9 17.5 + - + +
35A ILE* 2.7 40.5 + - + +
42A LEU* 5.0 0.4 - - + -
71A ILE* 4.1 17.9 - - + -
74A MET* 3.5 52.6 + - + +
75A SER* 3.8 23.6 - - - +
101A HEC 3.5 43.1 - + + -
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Residues in contact with GLU 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 ALA 3.0 17.3 + - - +
29A ALA* 3.8 6.1 - - - +
31A TRP* 1.3 75.7 - - - +
33A PRO* 1.4 80.3 - - + +
35A ILE* 3.4 6.7 + - + +
36A ALA* 3.0 29.7 + - - +
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Residues in contact with PRO 33 (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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29A ALA 3.3 16.8 - - - +
30A ALA 3.5 12.6 - - - +
32A GLU* 1.4 101.7 - - + +
34A ARG* 1.3 63.9 + - + +
36A ALA* 3.5 16.9 + - + +
37A GLN* 3.6 12.2 + - - +
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Residues in contact with ARG 34 (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 GLY 4.0 16.6 + - - -
23A PRO* 3.5 40.2 - - - +
30A ALA* 2.9 28.3 + - - +
31A TRP* 2.9 16.9 + - + +
33A PRO* 1.3 79.4 - - + +
35A ILE* 1.3 65.9 + - - +
36A ALA 3.1 1.6 - - - -
37A GLN* 3.1 29.9 + - - +
42A LEU* 3.3 21.5 - - + +
101A HEC 3.4 43.9 + - + +
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Residues in contact with ILE 35 (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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31A TRP* 2.7 28.0 + - + +
32A GLU* 3.8 7.0 - - - +
34A ARG* 1.3 72.6 - - - +
36A ALA* 1.3 57.4 + - - +
38A GLY* 2.9 23.4 + - - -
39A LEU* 4.2 17.9 + - + +
42A LEU* 3.9 8.1 - - + -
71A ILE* 3.7 30.3 - - + -
72A GLU* 5.7 1.6 - - + -
75A SER* 3.8 27.1 - - - +
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Residues in contact with ALA 36 (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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32A GLU* 3.0 29.2 + - - +
33A PRO* 3.5 11.9 - - + +
34A ARG 3.1 0.6 - - - -
35A ILE* 1.3 77.0 - - - +
37A GLN* 1.3 59.2 + - - +
38A GLY* 3.1 2.5 + - - -
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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