Contacts of the strand formed by residues 27 - 32 (chain E) in PDB entry 3TGX
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 THR 27 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PRO 5.1 0.9 - - - +
26E SER* 1.3 73.0 - - - +
28E LEU* 1.3 62.6 + - - +
29E THR* 5.1 5.7 + - - +
48E LEU 5.3 1.1 - - - -
78E GLN 3.6 2.1 - - - +
79E ILE* 4.4 0.2 - - - +
80E THR* 3.0 54.6 + - - +
81E ASP 4.9 4.3 - - - +
82E GLN* 3.8 20.8 - - - +
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LEU* 4.9 4.5 - - + -
16E CYS* 5.0 1.1 - - + -
18E LEU* 3.2 32.5 - - + -
21E TRP* 4.9 0.2 - - + -
26E SER* 3.3 9.3 + - - -
27E THR* 1.3 81.0 - - - +
29E THR* 1.3 62.5 + - - +
47E SER* 3.6 1.7 - - - -
48E LEU* 2.8 57.8 + - + +
60E TYR* 3.8 28.9 - - + -
77E VAL* 4.3 12.6 - - + -
78E GLN 3.5 2.5 - - - +
79E ILE* 3.6 39.0 - - + -
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Residues in contact with THR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E THR* 5.2 6.3 - - - +
28E LEU* 1.3 80.9 - - - +
30E LEU* 1.3 61.9 + - - +
31E THR* 4.0 4.1 + - - -
46E CYS 3.6 7.0 - - - -
47E SER* 3.9 18.8 - - - -
48E LEU* 4.9 0.7 - - - -
76E SER 4.0 0.9 - - - +
77E VAL* 4.6 0.9 - - - -
78E GLN* 3.1 48.8 + - - +
80E THR* 4.5 5.3 + - - +
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Residues in contact with LEU 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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14E VAL* 3.5 31.9 - - + -
16E CYS* 5.2 0.4 - - - -
28E LEU 4.3 0.2 - - - -
29E THR* 1.3 74.2 - - - +
31E THR* 1.3 63.8 + - - +
32E TRP* 4.0 16.6 - - + +
45E SER* 3.4 3.8 - - - -
46E CYS* 3.0 52.9 + - - +
48E LEU* 3.7 27.5 - - + +
62E CYS* 3.9 3.1 - - - -
64E MET* 3.9 17.5 - - - -
75E PHE* 4.2 15.9 - - + -
76E SER 3.2 12.6 - - - +
77E VAL* 4.0 13.2 - - + +
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Residues in contact with THR 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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29E THR* 4.0 4.4 + - - -
30E LEU* 1.3 74.7 + - - +
32E TRP* 1.3 75.4 + - - +
33E GLN* 3.7 1.7 + - - +
44E THR* 3.4 11.0 - - - +
45E SER* 3.5 16.3 + - - +
75E PHE* 3.4 3.4 - - - -
76E SER* 3.0 39.4 + - - -
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Residues in contact with TRP 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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8E THR* 5.2 1.3 - - - -
14E VAL* 4.7 8.5 - - + -
30E LEU* 4.0 7.9 - - + +
31E THR* 1.3 83.0 - - - +
33E GLN* 1.3 65.5 + - - +
34E ASP* 3.3 4.5 + - - +
39E LEU* 5.5 1.3 - - + -
44E THR* 2.7 40.5 + - + +
64E MET* 3.4 29.4 - - + +
66E VAL* 4.1 22.9 - - + -
69E PHE* 3.7 41.2 - + + -
73E ASP* 4.0 26.0 - - + -
74E ILE 3.5 19.1 - - - -
75E PHE* 3.5 40.2 - + + -
95E LEU* 3.9 28.3 - - + -
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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