Contacts of the helix formed by residues 28 - 32 (chain E) in PDB entry 6XOX
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 ALA 28 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU 3.4 5.9 + - - -
132B ASN* 3.8 40.4 + - + +
27E PHE* 1.3 68.9 - - - +
29E PHE* 1.3 65.0 + - - +
30E SER* 3.3 6.5 + - - +
31E SER* 3.6 9.6 + - - +
32E PHE* 3.2 19.9 - - - -
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Residues in contact with PHE 29 (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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4E LEU* 5.4 0.2 - - + -
22E CYS 5.4 0.7 - - - -
24E ALA* 3.6 24.0 - - + -
27E PHE* 2.9 24.3 + + + +
28E ALA* 1.3 72.9 - - - +
30E SER* 1.3 52.5 + - - +
31E SER 3.0 6.3 + - - -
32E PHE* 3.4 8.3 + - - +
34E MET* 3.8 35.0 - - + -
72E ARG* 2.6 65.0 + - + -
73E ASP 4.2 0.7 - - - -
74E ASP* 3.6 12.1 - - - -
77E ASN* 3.3 42.0 + - + +
78E THR 3.8 31.0 - - - -
79E LEU* 4.5 5.8 - - + -
96E CYS* 5.9 0.4 - - - -
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Residues in contact with SER 30 (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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25A MET* 4.6 5.5 - - - +
28E ALA* 3.3 4.6 - - - +
29E PHE* 1.3 77.3 - - - +
31E SER* 1.3 60.1 + - - +
32E PHE 3.5 0.9 - - - -
53E SER* 2.9 15.2 + - - -
54E GLY* 4.1 6.4 + - - -
72E ARG* 3.6 11.3 + - - +
74E ASP* 4.1 29.6 - - - +
77E ASN* 5.1 0.6 + - - -
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Residues in contact with SER 31 (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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22A ARG* 4.3 15.7 + - - -
25A MET* 6.2 0.4 - - - -
131B GLY 5.3 0.7 - - - -
132B ASN* 5.2 6.8 + - - +
28E ALA* 3.6 15.8 + - - +
29E PHE 3.0 1.6 + - - -
30E SER* 1.3 82.5 + - - +
32E PHE* 1.3 63.9 + - - +
53E SER* 3.3 14.3 - - - -
100E ILE* 3.3 28.2 - - - +
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Residues in contact with PHE 32 (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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131B GLY* 3.5 26.2 - - - -
27E PHE* 3.4 23.1 - + + -
28E ALA 3.2 28.5 - - - -
29E PHE 3.4 7.0 + - - +
30E SER 3.5 1.8 + - - -
31E SER* 1.3 80.5 - - - +
33E GLY* 1.3 62.7 + - - +
34E MET* 3.5 12.8 - - - +
53E SER* 4.0 3.7 - - - -
72E ARG* 2.4 34.7 + - - -
98E ARG* 3.4 44.4 - - + -
99E SER 3.9 0.9 - - - -
100E ILE* 3.5 41.5 - - + +
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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