Contacts of the helix formed by residues 45 - 57 (chain E) in PDB entry 7CR3
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 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E ASN 5.1 0.5 + - - -
44E PRO* 1.3 77.7 - - - +
46E GLU* 1.3 79.9 + - + +
47E ALA* 3.4 9.9 - - + +
48E GLU* 3.2 39.1 + - - +
49E LEU* 3.4 12.9 + - - +
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Residues in contact with GLU 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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30E THR* 4.7 4.2 + - - +
31E LYS* 2.4 35.2 + - - -
45E THR* 1.3 80.0 - - + +
47E ALA* 1.3 63.0 + - - +
48E GLU 3.2 0.5 + - - -
49E LEU* 3.2 13.0 + - - +
50E GLN* 3.1 21.4 + - - +
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Residues in contact with ALA 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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45E THR* 3.4 7.8 - - + +
46E GLU* 1.3 79.0 - - - +
48E GLU* 1.3 57.1 + - + +
50E GLN* 3.1 16.6 - - - +
51E ASP* 2.8 38.8 + - - +
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Residues in contact with GLU 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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550D VAL* 4.5 0.9 - - - +
42E GLN* 4.7 9.6 + - - +
44E PRO* 3.5 19.1 - - + +
45E THR* 3.2 39.9 + - - +
46E GLU 3.1 0.6 - - - -
47E ALA* 1.3 78.5 - - + +
49E LEU* 1.3 62.6 + - + +
51E ASP* 3.1 10.9 + - - +
52E MET* 3.0 28.9 + - + +
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Residues in contact with LEU 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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30E THR* 3.1 38.1 - - - +
31E LYS* 4.8 10.3 - - - +
33E LEU* 3.8 16.2 - - + +
34E GLY* 3.5 32.3 - - - +
37E MET* 5.1 2.2 - - + -
44E PRO* 3.8 21.1 - - + +
45E THR 3.5 15.3 - - - +
46E GLU* 3.2 10.9 + - - +
48E GLU* 1.3 75.3 - - + +
50E GLN* 1.3 62.4 + - - +
52E MET* 3.1 20.3 + - + +
53E ILE* 3.0 24.1 + - - +
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Residues in contact with GLN 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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30E THR* 4.2 2.8 + - - +
46E GLU 3.1 13.6 + - - +
47E ALA* 3.1 27.5 - - - +
48E GLU 3.2 0.2 - - - -
49E LEU* 1.3 77.2 - - - +
51E ASP* 1.3 67.5 + - - +
53E ILE* 3.0 26.1 + - + +
54E ASN* 2.6 46.7 + - - +
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Residues in contact with ASP 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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550D VAL* 3.5 16.4 - - + -
554D LYS* 6.0 8.0 - - - +
557D GLU* 5.1 6.8 - - - +
47E ALA* 2.8 27.1 + - - +
48E GLU* 3.4 9.6 - - - +
50E GLN* 1.3 89.1 + - - +
52E MET* 1.3 62.8 + - - +
54E ASN* 3.1 13.7 + - - +
55E GLU* 3.0 27.6 + - - +
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Residues in contact with MET 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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543D VAL* 4.0 14.4 - - + +
546D MET* 3.4 57.7 - - + +
547D ARG* 3.8 20.4 - - + -
550D VAL* 3.6 21.1 - - - -
33E LEU* 4.5 7.9 - - + -
37E MET* 5.5 4.0 - - - -
48E GLU* 3.0 18.8 + - + +
49E LEU* 3.1 22.9 + - + +
51E ASP* 1.3 76.2 - - - +
53E ILE* 1.3 62.2 + - - +
55E GLU* 3.0 8.1 + - - +
56E VAL* 3.0 26.8 + - - +
64E ILE* 5.1 0.9 - - - -
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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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30E THR* 3.6 28.3 - - + +
33E LEU* 4.1 13.0 - - + -
49E LEU 3.0 14.7 + - - +
50E GLN* 3.0 15.0 + - + +
52E MET* 1.3 76.8 - - - +
54E ASN* 1.3 61.5 + - - +
56E VAL 4.4 0.4 - - - +
57E ASP* 2.8 37.5 + - + +
62E GLY* 3.2 37.0 - - - +
63E THR* 4.1 15.3 - - - +
64E ILE* 4.4 14.1 - - + -
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Residues in contact with ASN 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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553D ARG* 2.6 41.2 + - - +
50E GLN* 2.6 46.6 + - - +
51E ASP* 3.1 14.0 + - - +
53E ILE* 1.3 78.9 - - - +
55E GLU* 1.3 55.2 + - - +
57E ASP 4.0 8.9 - - - +
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Residues in contact with GLU 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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546D MET* 4.4 2.0 - - + +
549D LEU* 3.0 59.9 - - + +
550D VAL* 3.5 23.0 - - + +
553D ARG* 2.7 54.7 + - - +
51E ASP* 3.1 19.8 - - - +
52E MET* 3.0 7.8 + - - +
54E ASN* 1.3 80.0 - - - +
56E VAL* 1.3 63.6 + - + +
57E ASP 4.7 0.9 - - - +
72E MET* 5.6 0.5 - - - +
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Residues in contact with VAL 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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546D MET* 3.5 31.2 - - + -
52E MET 3.0 15.5 + - - +
55E GLU* 1.3 81.5 - - + +
57E ASP* 1.3 69.1 + - - +
58E ALA* 3.7 1.9 + - - +
64E ILE* 3.5 36.1 - - + -
68E GLU* 3.5 37.0 - - + +
69E PHE* 3.9 4.0 - - + +
71E THR* 5.1 1.6 + - - -
72E MET* 3.5 20.4 - - + -
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Residues in contact with ASP 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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53E ILE* 2.8 26.9 + - + +
54E ASN* 4.0 9.5 - - - +
55E GLU 4.7 0.3 - - - +
56E VAL* 1.3 80.3 - - - +
58E ALA* 1.3 73.2 + - - +
59E ASP* 2.7 26.5 + - - +
60E GLY* 2.9 9.2 + - - +
61E ASN* 2.7 32.3 + - - +
63E THR 2.7 19.1 - - - +
64E ILE* 5.2 0.2 - - - -
65E ASP* 4.6 0.2 - - - +
68E GLU* 2.9 22.2 - - - +
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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