Contacts of the strand formed by residues 45 - 53 (chain E) in PDB entry 1TH7
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 LEU 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ALA* 5.4 1.6 - - - -
14E LEU* 5.9 0.4 - - + -
24E VAL* 3.9 33.9 - - + -
36E LEU* 4.1 14.6 - - + -
38E SER* 3.3 7.2 - - - +
39E TYR* 3.7 22.9 - - + -
43E MET* 3.3 18.8 - - - +
44E ASN* 1.3 81.3 - - - +
46E VAL* 1.3 67.1 + - - +
47E LEU* 5.1 1.1 - - + -
66E VAL* 3.3 7.3 - - - +
67E ILE* 2.7 49.4 + - + +
72E VAL* 4.3 6.7 - - + -
75E ILE* 3.9 31.6 - - + -
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Residues in contact with VAL 46 (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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9D THR* 4.6 2.0 - - + -
10D ALA* 3.4 38.6 - - + +
13D VAL* 4.0 19.7 - - + -
36E LEU* 3.8 1.4 - - - +
37E ARG* 2.9 40.3 + - + -
38E SER* 3.2 18.5 + - - -
45E LEU* 1.3 80.0 - - - +
47E LEU* 1.3 74.6 + - - +
48E SER* 5.6 0.4 - - - -
64E THR* 4.2 7.4 - - + -
65E ILE 3.2 9.0 - - - +
66E VAL* 4.1 13.9 - - + -
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Residues in contact with LEU 47 (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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22E VAL* 3.6 26.5 - - + -
24E VAL* 4.1 14.1 - - + -
32E VAL* 3.9 28.3 - - + +
33E ARG 4.1 3.1 - - - -
34E GLY* 3.9 20.9 - - - +
35E MET 3.2 5.2 - - - +
36E LEU* 3.7 18.8 - - + +
45E LEU* 5.1 1.8 - - + -
46E VAL* 1.3 85.3 - - - +
48E SER* 1.3 60.4 + - - +
50E SER* 4.0 7.4 - - - -
63E GLY 3.7 1.5 - - - +
64E THR* 3.3 3.8 - - - +
65E ILE* 2.9 43.0 + - + -
67E ILE* 4.1 14.1 - - + -
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Residues in contact with SER 48 (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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34E GLY* 3.7 0.3 - - - -
35E MET* 2.9 35.9 + - - +
37E ARG* 2.8 41.0 + - - +
46E VAL* 5.7 0.2 - - - -
47E LEU* 1.3 72.8 - - - +
49E ASP* 1.3 73.1 + - - +
50E SER 3.0 3.6 + - - -
63E GLY 3.9 2.5 - - - -
64E THR* 4.0 15.5 - - - -
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Residues in contact with ASP 49 (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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21E LEU* 5.9 1.0 - - - +
33E ARG 4.2 0.3 - - - +
34E GLY* 4.1 6.1 - - - -
35E MET* 4.8 11.0 - - + +
37E ARG* 5.5 2.8 + - - -
48E SER* 1.3 80.6 + - - +
50E SER* 1.3 63.4 + - - +
51E GLU* 4.2 3.8 + - - +
63E GLY* 3.3 15.6 + - - -
64E THR* 4.7 0.8 + - - -
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Residues in contact with SER 50 (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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32E VAL* 5.3 0.4 - - - -
33E ARG 3.0 15.9 - - - -
47E LEU* 4.0 24.0 - - - -
48E SER 3.0 0.9 + - - -
49E ASP* 1.3 79.1 - - - +
51E GLU* 1.3 65.8 + - - +
61E LYS* 3.6 4.7 - - - +
62E LEU* 2.9 36.2 + - - +
63E GLY 2.7 25.6 + - - -
65E ILE* 3.6 17.0 - - - +
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Residues in contact with GLU 51 (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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32E VAL* 3.4 2.6 - - - -
33E ARG* 2.8 75.4 + - + +
49E ASP 5.2 3.6 - - - +
50E SER* 1.3 77.6 - - - +
52E GLU* 1.3 61.6 + - - +
53E ILE* 3.6 3.6 + - + +
59E GLY* 3.1 22.2 + - - -
60E LYS 3.0 20.0 - - - +
61E LYS* 4.2 6.1 - - + +
62E LEU* 4.2 5.2 - - - +
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Residues in contact with GLU 52 (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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25D LYS* 5.3 0.7 + - - -
74D LEU* 5.3 1.2 - - - +
29E ASN* 3.6 21.4 + - - +
30E LYS* 3.4 38.7 - - + +
31E GLU 3.6 7.0 - - - +
32E VAL* 4.1 3.1 - - + -
51E GLU* 1.3 70.1 - - - +
53E ILE* 1.3 58.5 + - - +
54E GLN* 3.1 31.0 + - - +
60E LYS* 2.6 53.7 + - + +
62E LEU* 3.9 23.7 - - + +
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Residues in contact with ILE 53 (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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23E LEU* 5.0 1.8 - - + -
30E LYS* 3.4 23.7 - - - +
31E GLU* 2.9 37.5 + - + +
33E ARG* 3.0 58.6 - - + +
51E GLU* 4.3 9.9 - - + +
52E GLU* 1.3 71.3 - - - +
54E GLN* 1.3 74.2 + - - +
57E GLY* 4.2 16.4 - - - +
58E SER 3.7 5.6 - - - +
59E GLY* 4.6 0.2 - - - -
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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