Contacts of the strand formed by residues 129 - 133 (chain E) in PDB entry 1TYE
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 SER 129 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107E CYS* 3.4 1.7 - - - +
108E ALA* 2.7 40.2 + - - +
111E GLN* 3.1 39.7 + - - -
128E GLY* 1.3 72.3 - - - -
130E CYS* 1.3 65.1 + - - +
131E PHE* 4.3 5.5 - - - -
142E GLU* 4.1 11.1 + - - +
143E TYR 3.6 8.2 + - - -
144E SER* 3.5 16.6 - - - +
147E ARG* 3.9 3.3 + - - -
169E ALA* 3.6 6.0 + - - +
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Residues in contact with CYS 130 (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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105E VAL* 4.2 10.3 - - + -
106E ALA 3.5 3.8 - - - +
107E CYS* 2.0 45.5 - - - -
129E SER* 1.3 74.8 + - - +
131E PHE* 1.3 61.7 + - - +
132E LEU* 3.5 6.4 - - + +
142E GLU* 3.4 5.0 - - - +
143E TYR* 2.8 42.1 + - + +
169E ALA 4.6 0.2 - - - -
170E GLY* 3.8 4.9 - - - -
181E LEU* 4.9 1.3 - - + -
183E LEU* 3.5 37.0 - - + +
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Residues in contact with PHE 131 (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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70E PHE* 3.6 41.2 - + + -
71E ASP 3.8 21.5 - - - -
72E LEU* 5.5 0.7 - - + -
88E LYS* 4.0 11.0 - - + -
91E GLN* 3.4 29.4 - - - -
93E LEU* 3.7 25.6 - - + -
104E ILE 3.9 0.5 - - - +
105E VAL* 3.6 2.8 - - - -
106E ALA 2.7 36.3 + - - +
108E ALA* 4.2 8.1 - - + -
111E GLN* 3.6 15.0 - - - -
129E SER* 4.3 7.9 - - - -
130E CYS* 1.3 78.8 - - - +
132E LEU* 1.3 63.0 + - - +
141E ALA 3.7 4.7 - - - +
142E GLU* 4.2 23.8 - - + -
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Residues in contact with LEU 132 (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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70E PHE* 3.8 1.8 - - - -
103E VAL* 4.2 3.8 - - + -
104E ILE 3.6 3.6 - - - +
105E VAL* 3.6 26.9 - - + -
130E CYS* 3.5 20.9 - - + +
131E PHE* 1.3 81.0 - - - +
133E ALA* 1.3 63.1 + - - +
140E ARG* 3.3 8.1 - - - -
141E ALA* 2.7 41.0 + - + +
142E GLU* 4.2 2.2 - - - -
143E TYR* 4.3 6.5 - - + +
181E LEU* 4.6 9.9 - - + -
200E VAL* 4.4 10.1 - - + -
203E ILE* 3.9 29.4 - - + -
204E PHE* 3.6 30.3 - - + -
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Residues in contact with ALA 133 (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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68E LEU* 4.2 9.4 - - + -
70E PHE* 3.6 20.2 - - + -
103E VAL* 3.4 3.3 - - - +
104E ILE* 2.9 34.3 + - + +
132E LEU* 1.3 76.9 - - - +
134E GLN* 1.3 59.3 + - - +
135E PRO* 3.2 11.2 - - + +
139E ARG 3.4 6.1 - - - -
140E ARG* 3.4 24.9 - - - +
204E PHE* 4.1 4.9 - - - -
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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