Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 2BZG
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 THR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.7 8.3 - - + +
24A LEU* 1.3 77.5 - - - +
26A LEU* 1.3 66.0 + - - +
27A GLU* 3.6 15.4 + - - +
28A GLU* 3.0 49.7 + - - +
29A TRP* 3.2 19.1 + - - -
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Residues in contact with LEU 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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24A LEU 4.3 0.2 + - - -
25A THR* 1.3 75.0 - - - +
27A GLU* 1.3 66.8 + - - +
29A TRP* 3.2 7.7 + - + +
30A GLN* 2.9 37.4 + - - +
91A ILE* 3.9 34.8 - - + +
134A SER* 4.3 12.8 - - - +
1246A SAH 3.4 43.5 - - + +
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Residues in contact with GLU 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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25A THR* 3.2 12.9 - - - +
26A LEU* 1.3 88.7 + - - +
28A GLU* 1.3 54.3 + - + +
30A GLN* 3.7 17.2 + - - +
31A ASP* 2.8 47.1 + - - +
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Residues in contact with GLU 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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23A VAL 4.5 2.2 - - - +
24A LEU* 3.4 18.9 - - + +
25A THR* 3.0 46.2 + - - +
27A GLU* 1.3 75.4 - - + +
29A TRP* 1.3 62.5 + - + +
31A ASP* 3.4 10.2 + - - +
32A LYS* 3.1 31.5 + - - +
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Residues in contact with TRP 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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24A LEU* 3.8 33.9 - - + +
25A THR 3.2 23.9 + - - -
26A LEU* 3.2 8.3 + - + +
28A GLU* 1.3 75.7 - - + +
30A GLN* 1.3 66.2 + - - +
32A LYS* 3.2 39.4 + - + +
33A TRP* 3.4 18.9 - - - -
40A PHE* 4.5 10.3 - + - -
91A ILE* 4.3 3.6 - - + -
157A ALA* 3.6 39.7 + - + -
159A ASN* 5.3 1.0 + - - -
195A PRO* 3.9 19.3 - - + -
1246A SAH 3.4 74.9 + + + +
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Residues in contact with GLN 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 LEU* 2.9 32.1 + - - +
27A GLU* 3.2 24.3 + - - +
29A TRP* 1.3 72.4 - - - +
31A ASP* 1.3 65.1 - - - +
33A TRP* 3.1 6.9 + - - +
34A VAL* 3.0 27.0 + - + +
91A ILE* 3.5 38.9 - - + +
92A SER* 4.3 15.3 + - - +
93A GLU 5.2 1.0 + - - -
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Residues in contact with ASP 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 GLU* 2.8 29.4 + - - +
28A GLU* 3.6 9.5 - - - +
30A GLN* 1.3 71.4 - - - +
32A LYS* 1.3 58.8 + - - +
34A VAL* 3.2 11.5 + - - +
35A ASN* 2.8 47.1 + - - +
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Residues in contact with LYS 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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24A LEU* 4.7 3.8 - - - +
28A GLU* 3.1 23.6 + - - +
29A TRP* 3.2 41.2 + - + +
31A ASP* 1.3 76.4 - - - +
33A TRP* 1.3 58.2 + - + +
35A ASN* 3.3 2.5 + - - +
36A GLY 3.0 8.5 + - - -
37A LYS* 2.9 57.8 + - + +
38A THR* 4.4 1.1 - - + -
40A PHE* 5.2 4.5 - - + -
195A PRO* 3.6 31.3 - - - +
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Residues in contact with TRP 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 TRP* 3.4 22.4 + + - -
30A GLN 3.1 7.0 + - - +
32A LYS* 1.3 76.2 - - + +
34A VAL* 1.3 65.5 + - - +
36A GLY* 3.2 12.1 + - - -
38A THR* 3.6 20.4 - - + -
40A PHE* 3.7 25.9 - + - -
41A HIS* 5.5 1.1 - - + -
71A GLY* 3.6 13.7 - - - -
72A LYS* 3.8 33.9 - - + -
90A GLU* 3.8 2.4 + - - -
92A SER* 3.3 28.9 - - - +
94A LEU* 3.5 16.5 - - + +
95A GLY* 3.5 24.5 - - - -
98A GLU* 3.3 33.4 - - - +
1246A SAH 2.8 37.1 + - - -
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Residues in contact with VAL 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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30A GLN* 3.0 20.5 + - + +
31A ASP* 3.6 14.8 - - - +
33A TRP* 1.3 76.6 - - + +
35A ASN* 1.3 70.2 + - - +
36A GLY 3.6 0.5 + - - -
94A LEU* 3.7 19.8 - - + +
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Residues in contact with ASN 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 ASP* 2.8 36.6 + - - +
32A LYS* 4.0 3.3 - - - +
34A VAL* 1.3 84.6 - - - +
36A GLY* 1.3 61.7 + - - +
37A LYS* 3.2 22.7 + - + +
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Residues in contact with GLY 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 LYS 3.0 4.7 + - - -
33A TRP 3.2 12.0 + - - -
34A VAL 3.4 1.6 + - - -
35A ASN* 1.3 77.5 - - - +
37A LYS* 1.3 60.0 + - - +
38A THR* 3.1 17.5 + - - -
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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