Contacts of the helix formed by residues 69 - 75 (chain E) in PDB entry 4PEI
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 69 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E GLY* 3.0 23.4 + - - +
18E LYS* 3.9 2.6 - - - +
19E TYR* 3.4 17.1 + - + +
20E ARG* 2.5 67.1 + - - +
21E GLU 4.4 0.5 + - - -
68E GLY* 1.3 72.9 - - - -
70E PHE* 1.3 68.3 - - - +
71E HIS* 3.2 3.1 - - - -
72E LEU* 3.0 27.6 + - + +
73E TYR* 3.5 6.2 - - + -
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Residues in contact with PHE 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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17E GLY* 5.2 0.2 - - - -
19E TYR* 3.9 26.5 - + + -
47E GLN 3.5 20.4 + - - +
48E THR* 3.5 33.0 - - + -
49E LEU 3.4 21.5 - - - +
50E ARG* 4.4 3.8 - - + -
67E MET 4.3 1.8 + - - +
68E GLY 3.5 2.6 - - - -
69E ASP* 1.3 78.8 - - - +
71E HIS* 1.3 63.8 + - - +
73E TYR* 2.9 17.9 + - + +
74E TYR* 3.1 36.5 + + + -
106E VAL* 3.7 42.8 - - + -
107E CYS* 3.7 21.8 - - - -
110E MET* 3.9 7.2 - - - -
333E PHE* 5.7 0.9 - + - -
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Residues in contact with HIS 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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339B SER* 6.2 2.5 - - - -
342B PHE* 6.2 1.1 - + - -
343B TYR* 4.6 4.5 + + - +
49E LEU 3.7 11.9 + - - +
50E ARG 3.5 17.7 - - - +
67E MET* 4.1 24.8 - - + +
68E GLY 3.2 27.0 + - - -
69E ASP 4.2 0.7 - - - -
70E PHE* 1.3 80.9 - - - +
72E LEU* 1.3 83.2 + - + +
74E TYR* 3.6 8.3 - - - -
75E GLU* 2.7 68.2 + - - +
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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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20E ARG* 3.5 46.4 - - - +
69E ASP* 3.0 21.7 + - - +
71E HIS* 1.3 114.7 - - + +
73E TYR* 1.3 60.8 + - + +
75E GLU* 3.7 9.1 + - - +
76E GLY 3.2 2.1 + - - -
77E LYS* 3.0 44.1 + - + +
78E GLU* 3.0 22.8 + - + +
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Residues in contact with TYR 73 (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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19E TYR* 3.3 29.2 - + + -
20E ARG* 3.4 33.7 + - + +
23E TYR* 3.6 20.9 - + - +
69E ASP* 3.5 16.6 - - + -
70E PHE* 2.9 8.5 + - + +
72E LEU* 1.3 74.1 - - + +
74E TYR* 1.3 66.9 + - - +
76E GLY* 3.1 12.3 + - - -
78E GLU* 3.4 41.7 + - + +
79E LYS* 3.7 15.7 - - - -
80E ALA 3.7 13.2 - - - -
81E PRO* 5.3 0.4 - - + -
107E CYS* 4.0 26.6 - - - +
108E PHE* 5.4 0.5 + - - +
110E MET* 3.8 12.6 - - + -
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Residues in contact with TYR 74 (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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320B LYS* 5.7 2.4 + - - -
50E ARG* 3.6 56.9 + - + -
51E TYR* 4.0 16.7 + + - -
70E PHE* 3.1 27.7 + + + +
71E HIS* 3.6 9.2 - - - +
73E TYR* 1.3 79.4 - - - +
75E GLU* 1.3 66.6 + - + +
76E GLY 3.5 0.2 + - - -
106E VAL 3.5 22.4 - - - -
107E CYS* 4.0 10.0 - - + +
332E THR* 5.7 6.9 - - - +
333E PHE* 4.1 10.0 - + - -
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Residues in contact with GLU 75 (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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342B PHE* 3.6 32.3 - - + -
343B TYR* 3.8 6.1 + - - -
346B LYS* 5.9 3.4 - - - +
50E ARG 4.5 1.0 - - - +
71E HIS* 2.7 60.8 + - - +
72E LEU* 4.1 3.6 - - - +
74E TYR* 1.3 83.6 - - + +
76E GLY* 1.3 57.8 + - - +
77E LYS* 2.8 38.8 + - + +
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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