Contacts of the helix formed by residues 55 - 59 (chain E) in PDB entry 3PB1
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 55 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E SER* 1.3 83.8 + - - +
56E THR* 1.3 65.2 + - - +
57E HIS* 3.3 3.6 + - + +
58E CYS* 3.4 13.8 + - - +
59E PHE* 3.2 18.5 - - - -
102E ASP* 3.4 32.3 - - - +
104E ALA* 3.7 3.1 - - - -
196E GLY* 3.7 21.7 - - - +
212E ILE* 4.1 2.2 - - + -
213E VAL 4.1 7.4 - - - +
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Residues in contact with THR 56 (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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55E ALA* 1.3 71.2 - - - +
57E HIS* 1.3 63.3 + - - +
59E PHE* 2.9 16.3 + - - +
60E ILE* 3.0 17.2 + - + -
90E LEU* 3.6 21.8 - - + +
91E HIS* 3.1 14.5 + - - +
94E TYR* 3.6 37.5 - - + -
102E ASP* 3.0 8.4 + - - -
103E ILE 2.5 32.5 + - - +
104E ALA* 3.6 8.5 - - - +
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Residues in contact with HIS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ALA* 3.3 4.2 - - + +
56E THR* 1.3 73.2 - - - +
58E CYS* 1.3 63.6 + - - +
59E PHE 3.1 0.6 + - - -
60E ILE* 3.4 23.8 + - + +
94E TYR* 3.3 24.2 - - + +
99E HIS* 3.9 7.9 - + + +
102E ASP* 2.5 38.7 + - - +
195E ALA* 3.6 14.1 - - + +
214E SER* 3.1 28.3 - - - -
345I ALA* 3.6 20.2 - - + -
346I ARG 3.4 4.5 + - - -
347I MET* 3.2 45.9 + - + +
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Residues in contact with CYS 58 (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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41E VAL* 3.5 18.1 - - + +
42E CYS* 2.0 51.4 - - + -
54E SER* 4.4 2.9 - - - -
55E ALA* 3.4 22.7 - - - +
56E THR 3.1 0.2 + - - -
57E HIS* 1.3 78.5 - - - +
59E PHE* 1.3 70.5 + - + +
60E TYR* 5.7 1.4 + - - +
64E TYR* 4.1 4.5 + - - -
195E ALA* 4.0 18.8 - - - -
347I MET* 3.7 17.5 - - - +
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Residues in contact with PHE 59 (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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33E ILE* 3.7 30.7 - - + -
41E VAL* 5.1 1.8 - - + -
42E CYS* 4.9 0.9 - - + -
54E SER* 3.8 16.6 - - - -
55E ALA 3.2 23.1 - - - -
56E THR 2.9 1.6 + - - -
58E CYS* 1.3 89.8 - - + +
60E ILE* 1.3 99.9 + - - +
64E TYR* 3.6 33.0 - + - +
88E LEU* 4.0 15.9 - - + -
90E LEU* 3.7 28.5 - - + -
104E ALA* 4.0 6.1 - - + -
106E LEU* 3.8 33.7 - - + -
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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