Contacts of the strand formed by residues 61 - 71 (chain E) in PDB entry 1MGQ
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 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E LEU* 3.1 6.0 - - - -
58E GLU 3.0 31.8 + - - +
59E ASP* 4.3 8.3 - - + +
60E GLY* 1.3 83.9 - - - +
62E VAL* 1.3 68.8 + - - +
63E THR* 3.5 5.7 + - + +
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Residues in contact with VAL 62 (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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55E GLU* 3.5 42.8 - - + +
56E GLU 3.5 6.7 - - - +
57E LEU* 4.2 12.8 - - + +
61E GLU* 1.3 78.3 - - - +
63E THR* 1.3 64.6 + - - +
64E ARG 3.6 22.7 - - - +
65E ARG* 4.6 7.4 - - + -
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Residues in contact with THR 63 (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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56E GLU* 2.7 32.2 + - - -
57E LEU 4.2 4.2 + - - -
58E GLU* 4.0 28.3 + - + +
61E GLU* 3.8 11.4 - - + +
62E VAL* 1.3 79.3 - - - +
64E ARG* 1.3 74.2 + - - +
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Residues in contact with ARG 64 (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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35D GLU* 5.4 7.5 + - - -
37D ARG* 6.1 1.7 - - - +
78D TYR* 4.1 18.8 + - - -
34E ARG* 5.9 0.8 - - - +
55E GLU* 3.3 6.8 - - - +
56E GLU* 2.6 75.6 + - + -
62E VAL* 3.6 3.9 - - - +
63E THR* 1.3 94.9 + - - +
65E ARG* 1.3 64.3 + - - +
66E LEU* 3.8 20.4 + - + +
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Residues in contact with ARG 65 (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 ASP* 3.3 31.1 + - - +
54E ALA 3.8 2.8 + - - -
55E GLU* 3.0 48.3 + - - +
62E VAL* 4.6 7.9 - - + -
64E ARG* 1.3 76.7 - - - +
66E LEU* 1.3 71.2 + - - +
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Residues in contact with LEU 66 (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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27D ILE* 5.4 9.9 - - + -
78D TYR* 3.9 32.1 - - + +
80D SER* 3.8 20.0 - - - +
36E PHE* 4.5 14.1 - - + -
53E ASP* 3.5 1.4 - - - -
54E ALA* 2.7 45.8 + - + +
55E GLU* 5.7 0.2 - - - -
56E GLU* 5.6 0.9 - - + +
64E ARG* 3.8 27.6 - - + +
65E ARG* 1.3 94.4 + - - +
67E GLY* 1.3 59.7 + - - +
68E THR 3.4 4.5 - - - +
69E VAL* 4.1 20.9 - - + -
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Residues in contact with GLY 67 (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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81D PRO* 5.0 5.3 + - - -
52E ASN* 3.9 3.5 - - - +
53E ASP* 3.3 26.8 + - - +
66E LEU* 1.3 73.0 - - - +
68E THR* 1.3 67.6 + - - +
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Residues in contact with THR 68 (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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17D ALA* 5.1 8.5 - - + -
80D SER* 3.4 18.9 + - - -
81D PRO* 3.5 35.7 + - + +
50E VAL* 4.4 12.3 - - + -
51E LEU 3.4 10.3 - - - +
52E ASN* 3.0 19.1 + - - +
54E ALA 4.8 0.6 - - - +
66E LEU* 3.4 2.0 + - - -
67E GLY* 1.3 82.8 + - - +
69E VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 69 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D TYR* 3.6 38.1 - - + -
79D ILE 3.5 13.0 - - - +
80D SER* 4.3 0.2 - - - -
36E PHE* 5.3 3.1 - - + -
49E LEU 3.9 0.3 - - - +
50E VAL* 3.4 6.7 - - - +
51E LEU* 3.0 40.4 + - + +
54E ALA* 3.4 28.3 - - + -
66E LEU* 4.1 16.6 - - + -
68E THR* 1.3 77.8 - - - +
70E LEU* 1.3 64.3 + - - +
71E ILE* 4.0 14.4 + - + +
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Residues in contact with LEU 70 (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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14D PRO* 3.6 33.7 - - + +
15D LEU* 4.4 2.5 - - + -
17D ALA* 4.6 8.7 - - + -
18D LEU* 3.8 33.4 - - + -
47D MET* 3.8 34.1 - - + -
78D TYR* 3.1 5.5 - - - +
79D ILE* 2.9 49.7 + - + +
81D PRO* 5.1 1.7 - - + +
48E ASN* 4.6 0.2 - - + -
49E LEU 3.4 21.5 - - - +
50E VAL* 3.9 10.3 - - + -
68E THR* 5.4 0.2 - - - +
69E VAL* 1.3 73.0 - - - +
71E ILE* 1.3 62.5 + - - +
72E ARG* 4.1 0.7 + - - +
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Residues in contact with ILE 71 (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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77D VAL 3.7 9.4 - - - +
78D TYR* 4.2 5.2 - - + -
28E ILE* 4.5 7.2 - - + -
30E LEU* 4.1 24.0 - - + -
36E PHE* 4.3 25.6 - - + -
47E MET 4.2 0.7 - - - +
48E ASN* 3.3 3.3 - - - +
49E LEU* 2.9 47.0 + - + +
51E LEU* 4.0 26.9 - - + -
69E VAL* 4.1 19.3 - - + +
70E LEU* 1.3 80.1 - - - +
72E ARG* 1.3 74.0 + - - +
75E ASN* 5.8 0.2 - - + -
76E ILE* 4.4 10.5 - - + -
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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