Contacts of the strand formed by residues 53 - 57 (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 VAL 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.2 15.3 - - + -
37E VAL 3.5 9.0 - - - +
52E GLY* 1.3 79.7 - - - +
54E PHE* 1.3 79.1 + - - +
55E LEU* 6.0 0.2 - - + -
67E SER* 3.7 5.2 - - - -
68E LEU* 3.2 55.2 + - + +
70E PHE* 3.9 10.3 - - + -
93E LEU* 4.3 9.6 - - + +
94E GLY* 4.5 4.7 - - - -
97E VAL* 4.8 2.7 - - + -
104E ILE* 4.8 0.7 - - + -
106E ALA* 3.4 32.3 - - + -
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Residues in contact with PHE 54 (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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13E GLY* 5.3 1.3 - - - -
14E PRO* 3.6 29.8 - - + -
19E PHE* 3.7 34.1 - + + -
35E ILE 3.6 0.2 - - - +
36E VAL* 3.5 4.0 - - - +
37E VAL* 2.9 38.1 + - + +
39E ALA* 3.8 22.4 - - + -
42E THR* 4.2 13.2 - - + -
52E GLY* 4.5 0.9 - - - -
53E VAL* 1.3 89.3 - - - +
55E LEU* 1.3 60.7 + - - +
56E CYS 3.9 0.9 - - - -
64E GLN* 6.1 2.0 - - + -
65E CYS* 3.6 29.2 - - + -
66E PRO 3.5 8.1 - - - +
67E SER* 3.6 20.2 - - - +
68E LEU 5.1 0.7 - - - -
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Residues in contact with LEU 55 (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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217C SER* 5.1 11.0 - - - +
26E HIS* 4.4 9.6 - - + -
34E ALA* 4.1 21.8 - - + -
35E ILE 4.1 0.2 - - - +
36E VAL* 4.0 22.7 - - + -
54E PHE* 1.3 74.4 - - - +
56E CYS* 1.3 61.1 + - - +
57E PRO* 3.6 2.9 - - - +
65E CYS* 4.2 0.4 - - - -
66E PRO* 3.0 33.8 + - + +
67E SER* 4.9 0.6 - - - +
68E LEU* 4.7 15.5 - - + -
104E ILE* 3.7 33.0 - - + -
135E PRO* 4.2 17.9 - - + -
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Residues in contact with CYS 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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11E TYR* 3.8 22.9 - - + -
19E PHE* 4.0 7.4 - - - -
34E ALA* 3.1 5.2 - - - +
35E ILE* 2.7 53.3 + - + +
37E VAL* 4.0 18.8 - - - -
54E PHE* 4.7 1.8 - - - -
55E LEU* 1.3 70.3 - - - +
57E PRO* 1.3 66.8 - - - +
65E CYS* 2.0 45.8 - - - -
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Residues in contact with PRO 57 (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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11E TYR* 2.5 26.3 + - + -
32E ARG* 6.3 4.9 - - - +
34E ALA* 4.1 8.7 - - + -
55E LEU 3.6 8.3 - - - +
56E CYS* 1.3 85.3 - - + +
58E TRP* 1.3 59.5 + - - +
59E ARG* 3.2 36.7 + - + +
65E CYS* 4.9 1.3 - - + -
66E PRO* 4.1 10.8 - - + -
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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