Contacts of the strand formed by residues 42 - 48 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41P CYS* 1.3 71.2 - - - +
43P ILE* 1.3 67.8 + - - +
59P SER* 3.4 11.7 - - - +
60P THR* 4.3 7.5 + - + +
64P ARG* 4.2 28.4 + - - +
65P VAL* 4.0 24.2 + - + +
68P LYS* 2.5 37.0 + - - +
46Q ILE 3.8 0.5 - - - +
47Q ILE* 3.5 0.3 - - - -
48Q PHE* 2.9 43.3 + - + +
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Residues in contact with ILE 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA* 3.6 30.7 - - + +
35P LEU* 4.0 21.5 - - + -
36P SER* 3.8 17.3 - - - +
41P CYS* 4.1 5.8 - - - +
42P GLU* 1.3 81.4 - - - +
44P ALA* 1.3 72.3 + - - +
45P LEU 4.3 0.2 - - - -
57P TYR* 3.8 15.1 - - + -
58P ALA* 3.4 4.5 - - - +
59P SER* 3.0 32.7 + - - -
65P VAL* 4.4 6.2 - - - +
28Q LEU* 4.6 2.0 - - + -
45Q LEU* 3.7 18.4 - - + -
46Q ILE 3.1 13.0 - - - +
47Q ILE* 3.7 14.4 - - + -
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Residues in contact with ALA 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P ILE* 1.3 75.1 - - - +
45P LEU* 1.3 61.1 + - - +
46P ILE* 4.2 3.4 - - + -
57P TYR 3.6 5.4 - - - -
62P MET* 3.6 24.2 - - + -
65P VAL* 3.6 26.4 - - + +
66P LEU* 5.0 0.9 - - + -
45Q LEU* 3.5 6.2 - - - +
46Q ILE* 2.8 44.3 + - + -
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Residues in contact with LEU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P LEU* 3.8 33.0 - - + -
29P MET* 4.0 30.3 - - + -
32P ALA* 4.6 7.6 - - + -
43P ILE* 5.1 0.2 - - + -
44P ALA* 1.3 74.8 - - - +
46P ILE* 1.3 62.3 + - - +
47P ILE* 4.4 10.0 - - + +
56P GLN* 3.1 8.8 - - - +
57P TYR* 3.0 48.7 + - + +
62P MET* 4.2 0.2 - - - +
28Q LEU* 6.0 0.9 - - + -
32Q ALA* 5.5 0.2 - - + -
43Q ILE* 3.8 17.9 - - + -
44Q ALA 3.6 9.4 - - - +
45Q LEU* 3.5 26.7 - - + -
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Residues in contact with ILE 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ALA* 5.4 2.0 - - + -
45P LEU* 1.3 76.8 - - - +
47P ILE* 1.3 65.3 + - - +
48P PHE* 4.4 8.5 - - + -
54P LEU* 4.1 15.9 - - + -
55P PHE 3.8 2.2 - - - -
56P GLN* 4.8 4.0 - - + -
62P MET* 4.8 7.9 - - + -
66P LEU* 4.6 7.0 - - + -
42Q GLU 3.8 0.2 - - - +
43Q ILE* 3.0 7.3 - - - +
44Q ALA* 2.8 45.0 + - + +
46Q ILE* 6.4 0.2 - - + -
65Q VAL* 3.7 19.5 - - + -
66Q LEU* 3.6 30.7 - - + -
69Q TYR* 3.5 37.0 - - + -
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Residues in contact with ILE 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P PHE* 4.1 26.2 - - + -
25P LYS* 3.6 31.6 - - + +
28P LEU* 4.4 11.4 - - + -
29P MET* 4.8 4.3 - - + -
45P LEU* 4.4 17.3 - - + +
46P ILE* 1.3 77.9 - - - +
48P PHE* 1.3 64.9 + - - +
53P ARG 4.5 0.7 - - - -
54P LEU* 3.3 8.7 - - - +
55P PHE* 2.7 49.5 + - + +
35Q LEU* 4.0 14.4 - - + -
41Q CYS* 4.1 5.6 - - - -
42Q GLU 3.5 2.2 - - - +
43Q ILE* 3.8 20.2 - - + -
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Residues in contact with PHE 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ILE* 4.4 4.9 - - + -
47P ILE* 1.3 81.5 - - - +
49P ASN* 1.3 57.1 + - - +
52P ASN* 3.9 16.2 - - + -
53P ARG 3.6 1.8 - - - -
54P LEU* 3.5 37.0 - - + -
41Q CYS* 2.7 30.6 - - - +
42Q GLU* 2.9 37.7 + - + +
65Q VAL* 3.8 38.8 - - + -
68Q LYS* 3.8 24.9 - - + -
69Q TYR* 4.0 21.5 - - + -
72Q TYR* 3.9 16.6 - + - -
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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