Contacts of the helix formed by residues 62 - 72 (chain E) 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 62 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 6.0 5.1 - - - +
50D GLU* 3.5 48.2 + - + +
53D GLU* 4.3 4.0 - - - +
28E LEU* 3.3 33.2 + - - +
29E CYS* 4.7 18.4 - - - +
60E SER* 3.2 1.2 - - - +
61E SER* 1.3 81.7 - - - +
63E LYS* 1.3 64.3 + - + +
65E ALA* 3.1 4.0 - - - +
66E GLY* 2.9 21.3 + - - -
37H HIS* 2.9 31.1 + - - -
38H PHE* 4.7 7.4 - - - +
41H LEU* 4.7 17.1 - - - +
88H ARG* 5.7 4.4 - - - +
90H LYS* 5.2 4.2 - - - +
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Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLU* 2.8 23.5 + - - -
54D GLU* 3.9 4.7 - - - +
58E ARG 4.6 2.9 - - - +
59E THR* 3.5 15.7 - - + -
60E SER* 3.6 17.0 - - - +
61E SER 4.4 0.2 - - - +
62E ARG* 1.3 76.9 - - + +
64E ARG* 1.3 54.3 + - - +
66E GLY* 2.8 5.8 + - - -
67E LYS* 2.5 45.0 + - + +
35H GLU 5.0 0.2 + - - -
36H ARG* 2.2 57.6 + - - +
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ILE* 6.2 0.6 - - - +
35E GLU* 3.0 72.5 + - + +
36E ARG* 3.4 21.0 - - - +
40E HIS* 4.4 9.7 - - - -
55E ILE* 3.4 14.6 - - + -
56E SER* 3.4 39.8 + - - +
59E THR* 3.2 22.7 + - - +
61E SER* 4.5 12.3 - - - +
63E LYS* 1.3 75.8 - - - +
65E ALA* 1.3 58.5 + - - +
67E LYS* 3.0 19.3 - - - +
68E LEU* 2.6 36.4 + - + +
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 3.4 24.0 - - + +
32E ILE* 3.5 16.2 - - + -
35E GLU* 2.9 16.0 + - - +
61E SER 3.1 19.3 + - - +
62E ARG* 3.1 14.5 - - - +
64E ARG* 1.3 79.6 - - - +
66E GLY* 1.3 62.2 + - - +
68E LEU* 3.4 0.7 + - - +
69E LEU* 3.1 27.0 + - - +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ARG* 3.4 18.5 + - - -
28E LEU* 3.4 20.5 - - - +
62E ARG 2.9 9.8 + - - -
63E LYS* 2.8 8.9 + - - -
65E ALA* 1.3 69.9 - - - +
67E LYS* 1.3 65.7 + - - +
69E LEU* 3.4 1.0 + - - +
70E ASP* 2.9 25.8 + - - +
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Residues in contact with LYS 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E GLU 4.8 1.6 - - - -
55E ILE* 2.1 71.5 + - + +
58E ARG 4.8 2.0 - - - -
59E THR* 2.8 24.5 - - - +
63E LYS* 2.5 33.9 + - + +
64E ARG* 3.0 13.5 - - - +
66E GLY* 1.3 70.8 - - - +
68E LEU* 1.3 57.2 + - - +
70E ASP* 2.8 28.1 + - - +
71E TYR* 3.0 29.1 - - + +
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Residues in contact with LEU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ILE* 5.2 1.8 - - + -
35E GLU* 3.4 32.3 - - + +
39E ASP* 3.9 30.5 - - + +
40E HIS* 4.9 16.2 - - + +
47E LEU* 5.3 14.2 - - + +
55E ILE* 4.7 7.6 - - + +
64E ARG* 2.6 23.3 + - + +
65E ALA 3.7 2.9 - - - +
67E LYS* 1.3 72.7 - - - +
69E LEU* 1.3 78.8 + - + +
71E TYR* 3.9 9.0 + - - +
72E LEU* 3.4 31.4 - - + +
81E THR* 5.4 8.1 - - + +
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 3.7 39.2 - - + +
24E LEU* 4.9 8.3 - - + +
25E ARG* 5.0 12.6 - - - +
27E TYR 4.8 5.2 - - - +
28E LEU* 3.7 17.3 - - + -
32E ILE* 3.7 34.1 - - + -
65E ALA 3.1 24.0 + - - +
66E GLY* 3.8 4.0 - - - +
67E LYS 3.1 1.0 - - - -
68E LEU* 1.3 91.2 - - + +
70E ASP* 1.3 66.7 + - - +
72E LEU* 3.1 25.3 + - + +
73E GLN* 4.3 0.4 - - - +
81E THR* 6.5 0.9 - - + -
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Residues in contact with ASP 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ARG* 4.5 9.3 + - - +
66E GLY 2.9 18.5 + - - +
67E LYS* 2.8 15.5 + - - +
69E LEU* 1.3 72.5 - - - +
71E TYR* 1.3 70.4 + - + +
72E LEU 3.4 0.3 + - - -
73E GLN* 3.6 27.7 + - - +
74E GLU* 4.6 9.4 + - - +
44H LYS* 3.8 6.8 + - - -
49H ARG* 2.4 41.3 + - - -
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Residues in contact with TYR 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 6.2 3.6 - - + -
48E SER* 5.3 7.6 - - - -
51E ASP* 3.4 31.6 + - + -
55E ILE* 3.6 32.0 - - + +
67E LYS* 3.0 35.4 - - + +
68E LEU* 4.1 7.9 - - - +
69E LEU 3.2 1.0 - - - -
70E ASP* 1.3 86.4 - - + +
72E LEU* 1.3 68.5 + - + +
73E GLN 3.1 1.4 + - - -
74E GLU* 3.1 40.9 + - - +
75E ASN* 3.9 2.1 + - - +
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 4.7 10.1 - - + -
43E ALA* 6.4 0.9 - - + -
47E LEU* 4.9 16.8 - - + -
68E LEU* 3.4 29.4 - - + +
69E LEU* 3.1 15.7 + - + +
71E TYR* 1.3 82.9 - - + +
73E GLN* 1.3 59.0 + - - +
74E GLU 3.2 0.2 - - - -
75E ASN* 2.8 45.1 + - - +
78E GLY* 4.8 7.7 - - - -
81E THR* 3.4 25.6 - - - +
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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