Contacts of the strand formed by residues 42 - 48 (chain S) in PDB entry 1TQE
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 GLU 42 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R ILE 3.7 0.7 - - - +
47R ILE* 3.5 0.7 - - - -
48R PHE* 2.8 56.0 + - + +
52R ASN* 5.6 4.5 + - - +
41S CYS* 1.3 71.4 - - - +
43S ILE* 1.3 66.3 + - - +
59S SER* 3.4 11.9 - - - +
60S THR* 4.2 6.7 + - + +
64S ARG* 3.0 36.3 + - - +
65S VAL* 4.4 19.8 - - + +
68S LYS* 5.8 3.8 - - - +
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Residues in contact with ILE 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R LEU* 4.6 1.3 - - + -
45R LEU* 3.8 17.7 - - + -
46R ILE 3.0 12.1 - - - +
47R ILE* 3.8 15.7 - - + -
32S ALA* 3.7 29.8 - - + +
35S LEU* 4.0 22.4 - - + -
36S SER* 3.9 17.0 - - - +
41S CYS* 4.2 4.7 - - - +
42S GLU* 1.3 82.7 - - - +
44S ALA* 1.3 73.7 + - - +
57S TYR* 3.9 16.1 - - + -
58S ALA* 3.3 4.9 - - - +
59S SER* 2.9 32.2 + - - -
65S VAL* 4.4 6.3 - - - +
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Residues in contact with ALA 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R ALA 4.1 0.2 - - - +
45R LEU* 3.6 5.2 - - - +
46R ILE* 2.8 41.7 + - + +
43S ILE* 1.3 75.4 - - - +
45S LEU* 1.3 62.1 + - - +
46S ILE* 5.4 1.8 - - + -
57S TYR 3.6 5.6 - - - -
58S ALA* 4.5 0.9 - - - +
62S MET* 4.0 21.8 - - + -
65S VAL* 3.5 24.4 - - + +
66S LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R ALA* 5.6 0.4 - - + -
43R ILE* 3.7 19.1 - - + -
44R ALA 3.4 15.0 - - - +
45R LEU* 3.5 22.4 - - + -
28S LEU* 3.8 32.5 - - + -
29S MET* 4.0 30.1 - - + -
32S ALA* 4.6 7.6 - - + -
44S ALA* 1.3 76.0 - - - +
46S ILE* 1.3 61.8 + - - +
47S ILE* 4.4 10.8 - - + -
56S GLN* 3.2 8.7 - - - +
57S TYR* 3.0 48.3 + - + +
62S MET* 3.8 0.3 - - - +
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Residues in contact with ILE 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R ILE* 3.1 6.8 - - - +
44R ALA* 2.8 49.2 + - + -
46R ILE* 6.3 0.7 - - + -
65R VAL* 3.7 24.7 - - + -
66R LEU* 5.3 7.4 - - + -
69R TYR* 3.5 37.7 - - + -
44S ALA* 4.2 1.5 - - + -
45S LEU* 1.3 76.6 - - - +
47S ILE* 1.3 65.5 + - - +
48S PHE* 4.4 7.2 - - + -
54S LEU* 4.2 15.3 - - + -
55S PHE 3.8 2.2 - - - -
56S GLN* 4.8 0.7 - - + -
62S MET* 4.2 14.4 - - + -
66S LEU* 4.3 20.6 - - + -
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Residues in contact with ILE 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R LEU* 4.1 13.9 - - + -
41R CYS* 4.1 15.7 - - - -
42R GLU 3.5 1.8 - - - +
43R ILE* 3.7 24.5 - - + -
21S PHE* 4.1 16.2 - - + -
25S LYS* 3.6 31.2 - - + +
28S LEU* 4.3 12.8 - - + -
29S MET* 4.9 4.3 - - + -
45S LEU* 4.4 13.0 - - + +
46S ILE* 1.3 79.5 - - - +
48S PHE* 1.3 65.8 + - - +
53S ARG 4.4 0.4 - - - -
54S LEU* 3.2 8.7 - - - +
55S PHE* 2.7 50.7 + - + +
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Residues in contact with PHE 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R CYS* 2.8 22.5 - - - +
42R GLU* 2.9 38.5 + - + +
65R VAL* 4.0 18.6 - - + -
68R LYS* 3.3 65.5 - - + +
69R TYR* 3.9 10.5 - - + -
72R TYR* 4.1 9.9 - + - -
46S ILE* 4.4 9.4 - - + -
47S ILE* 1.3 80.9 - - - +
49S ASN* 1.3 64.5 + - - +
52S ASN* 4.0 13.5 - - - -
53S ARG 3.6 3.4 - - - -
54S LEU* 3.4 37.5 - - + -
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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