Contacts of the helix formed by residues 49 - 58 (chain B) in PDB entry 6BZE
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 ARG 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B LYS* 3.2 38.4 - - - +
47B LEU 5.4 0.2 - - - +
48B SER* 1.3 80.0 + - - +
50B GLU* 1.3 60.5 + - + +
52B THR* 2.4 27.3 + - - -
53B GLU* 2.5 33.3 + - - +
62C ARG* 6.0 5.2 - - - +
37F HIS* 3.3 3.0 + - - -
90F LYS* 3.9 16.3 - - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 1.3 73.9 - - + +
51B ASP* 1.3 63.6 + - - +
52B THR 3.1 1.3 - - - -
53B GLU* 2.9 29.2 + - - +
54B GLU* 2.8 31.4 + - - +
60C SER* 2.6 25.6 + - - +
62C ARG* 3.4 28.8 + - + +
63C LYS* 2.8 22.8 + - - -
36F ARG* 2.8 28.3 + - - +
37F HIS* 2.8 23.4 - - - +
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B SER* 3.2 9.0 - - - +
50B GLU* 1.3 75.9 - - - +
52B THR* 1.3 55.3 + - - +
54B GLU* 2.5 13.6 + - - -
55B ILE* 2.2 55.4 + - + +
71B TYR* 3.0 25.1 + - - -
33F ILE* 3.8 5.4 - - - +
36F ARG* 2.7 37.5 + - - +
37F HIS* 3.0 33.7 + - - +
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B HIS* 3.7 27.9 + - + +
44B LYS* 5.6 7.7 + - + -
47B LEU* 3.5 31.0 - - + -
48B SER* 3.6 16.8 - - - +
49B ARG* 2.4 30.5 + - - -
51B ASP* 1.3 77.8 - - - +
53B GLU* 1.3 63.9 + - - +
55B ILE* 4.2 7.5 - - + +
56B SER* 3.0 29.3 + - - -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 2.5 35.9 + - - +
50B GLU* 3.0 36.2 - - - +
52B THR* 1.3 80.0 - - - +
54B GLU* 1.3 54.1 + - - +
56B SER* 3.9 2.5 - - - -
57B CYS* 3.1 29.9 + - - +
60C SER* 3.0 29.1 - - - +
61C SER* 3.8 7.5 + - - -
62C ARG* 4.4 3.7 - - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLU* 2.8 15.8 + - - +
51B ASP 2.5 9.7 + - - +
53B GLU* 1.3 69.0 - - - +
55B ILE* 1.3 67.9 + - - +
56B SER 3.0 2.6 + - - -
57B CYS* 3.0 32.0 + - - -
58B ARG* 3.9 2.1 + - - +
67B LYS* 4.9 1.4 - - - -
59C THR* 5.7 1.3 - - - -
60C SER* 3.1 21.8 + - - +
63C LYS* 4.1 3.2 - - - -
36F ARG* 2.1 55.1 + - - +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B HIS* 5.9 4.9 - - + -
47B LEU* 6.5 0.2 - - + -
48B SER* 5.3 3.1 - - - +
51B ASP* 2.2 45.0 + - + +
52B THR* 4.2 7.2 - - + +
54B GLU* 1.3 69.6 - - - +
56B SER* 1.3 57.9 - - - +
58B ARG 4.4 0.3 + - - -
59B THR* 3.2 7.4 - - - +
64B ARG* 3.3 20.1 - - + +
67B LYS* 2.1 64.4 + - + +
68B LEU* 4.6 6.7 - - + +
71B TYR* 3.4 46.0 - - + +
36F ARG* 4.8 2.0 - - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B HIS* 4.6 9.8 + - - -
52B THR 3.0 21.0 + - - -
53B GLU* 3.9 2.9 - - - -
54B GLU 3.0 1.0 - - - -
55B ILE* 1.3 77.8 - - - +
57B CYS* 1.3 65.4 + - - +
58B ARG 2.9 4.8 + - - -
59B THR* 3.4 14.7 + - - +
64B ARG* 3.3 22.9 + - - +
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Residues in contact with CYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 3.9 20.4 + - - +
53B GLU 3.1 14.6 + - - +
54B GLU* 3.0 32.5 + - - -
56B SER* 1.3 76.2 - - - +
58B ARG* 1.3 90.4 + - - +
59B THR 3.9 0.8 + - - -
59C THR 5.1 13.0 - - - +
60C SER* 5.8 0.7 - - - -
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 3.7 36.9 - - - +
54B GLU 3.9 2.9 + - - +
56B SER 2.9 1.6 + - - -
57B CYS* 1.3 105.3 + - - +
59B THR* 1.3 67.0 + - - +
63B LYS* 4.9 3.6 - - - +
67B LYS* 4.9 2.3 + - - -
57C CYS* 3.8 19.6 + - - +
58C ARG* 3.8 27.8 - - - +
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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