Contacts of the helix formed by residues 53 - 64 (chain E) in PDB entry 5MNI
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 ILE 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E LYS* 3.8 17.0 - - + +
43E PRO 3.2 8.8 + - - +
45E VAL* 3.2 22.8 + - + +
47E PHE* 4.4 9.6 - - + +
52E ARG* 1.3 70.9 - - - +
54E ILE* 1.3 64.7 + - - +
56E PHE* 2.9 29.0 + - - +
57E ALA 4.1 0.3 + - - -
141E GLY 3.6 5.6 - - - +
142E ASP* 3.6 24.2 - - + +
143E HIS 3.5 23.9 - - - +
144E ILE* 4.0 15.9 - - + -
277E VAL* 3.2 34.8 - - + -
283E TYR* 5.5 0.4 - - + -
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Residues in contact with ILE 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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24E ILE* 4.1 21.1 - - + -
26E ALA* 4.8 0.4 - - + -
43E PRO* 2.7 35.4 + - + +
52E ARG* 3.0 4.2 + - + +
53E ILE* 1.3 72.0 - - - +
55E ASP* 1.3 68.1 + - - +
56E PHE 2.9 1.4 + - - -
57E ALA* 3.0 12.9 + - + +
58E LEU* 3.1 36.6 + - + +
71E VAL* 3.9 25.1 - - + -
80E LEU* 3.8 31.0 - - + -
83E HIS* 4.3 16.8 - - + -
84E ILE* 4.3 2.2 - - + -
141E GLY* 3.6 10.5 - - - +
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Residues in contact with ASP 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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51E PHE* 3.6 3.5 - - + -
52E ARG 2.8 31.2 + - - +
54E ILE* 1.3 80.4 - - - +
56E PHE* 1.3 49.6 + - + +
58E LEU* 3.8 0.3 - - - +
59E SER* 2.6 43.3 + - - -
83E HIS* 2.6 27.1 + - - -
88E TRP* 2.9 19.6 + - - +
306E ILE* 4.1 10.3 - - + -
307E ARG 3.2 19.7 - - - +
308E THR* 2.7 24.0 + - - -
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Residues in contact with PHE 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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47E PHE* 3.7 29.2 - + - -
51E PHE* 4.6 11.7 - - + -
52E ARG 4.4 2.7 - - - -
53E ILE* 2.9 19.6 + - - +
54E ILE 2.9 1.2 + - - -
55E ASP* 1.3 73.7 - - - +
57E ALA* 1.3 67.0 + - - +
59E SER* 3.0 6.6 + - - -
60E ASN* 2.8 28.7 + - - +
143E HIS 4.0 9.9 - - - +
144E ILE* 3.6 36.6 - - + -
145E TYR* 3.9 20.0 - - + +
146E LYS* 5.9 0.7 - - + -
297E LEU* 4.0 7.6 - - + -
299E MET* 3.7 37.7 - - + -
306E ILE* 3.9 21.8 - - + -
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Residues in contact with ALA 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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24E ILE* 4.2 20.2 - - + -
53E ILE 4.1 0.8 + - - -
54E ILE* 3.0 8.5 + - - +
56E PHE* 1.3 80.0 - - - +
58E LEU* 1.3 64.9 + - - +
60E ASN* 3.0 12.7 + - - +
61E CYS* 3.0 17.6 + - - -
139E LEU* 4.5 8.3 - - + -
140E ALA 4.5 6.5 - - - +
141E GLY* 4.3 20.0 - - - -
143E HIS 4.9 2.9 + - - +
145E TYR* 4.7 5.3 - - + +
149E TYR* 4.1 12.4 - - - +
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Residues in contact with LEU 58 (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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24E ILE* 4.3 11.2 - - + +
54E ILE* 3.1 28.1 + - + +
55E ASP 3.8 1.8 - - - +
57E ALA* 1.3 76.7 - - - +
59E SER* 1.3 64.5 + - - +
61E CYS* 3.0 16.6 + - - +
62E ILE* 3.0 14.7 + - - +
69E MET* 3.6 24.1 - - + +
71E VAL* 4.1 20.9 - - + -
84E ILE* 3.6 24.5 - - + -
88E TRP* 3.3 42.8 - - + +
99E VAL* 4.2 10.8 - - + -
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Residues in contact with SER 59 (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 ASP 2.6 27.8 + - - -
56E PHE 3.4 4.0 - - - -
58E LEU* 1.3 71.7 - - - +
60E ASN* 1.3 64.7 + - - +
62E ILE* 3.0 6.2 + - - +
63E ASN* 2.9 27.7 + - - +
88E TRP* 3.7 9.5 - - - -
305E PRO 3.9 8.7 - - - -
306E ILE* 3.4 24.4 - - - +
307E ARG* 2.9 28.5 + - - -
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Residues in contact with ASN 60 (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 PHE 2.8 20.7 + - - +
57E ALA 3.3 3.1 - - - +
59E SER* 1.3 72.6 - - - +
61E CYS* 1.3 65.8 + - - +
63E ASN 3.0 2.8 + - - -
64E SER* 2.7 28.2 + - - -
145E TYR* 3.0 36.1 + - - +
146E LYS* 3.4 5.4 - - - +
147E GLN 3.4 17.8 + - - +
149E TYR* 3.2 32.6 + - + -
304E TRP* 2.9 28.6 + - - +
306E ILE* 5.2 1.7 - - - +
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Residues in contact with CYS 61 (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 ALA* 3.4 29.8 - - - -
24E ILE* 4.4 2.5 - - - -
57E ALA 3.0 12.8 + - - -
58E LEU 3.0 9.5 + - - +
60E ASN* 1.3 77.1 - - - +
62E ILE* 1.3 64.0 + - - +
64E SER* 3.2 3.7 + - - -
66E ILE* 2.7 43.1 + - + +
69E MET* 3.6 18.8 - - + -
139E LEU* 3.4 23.6 - - - -
149E TYR* 3.6 11.2 - - - -
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Residues in contact with ILE 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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58E LEU 3.0 7.5 + - - +
59E SER* 3.0 9.9 + - - +
61E CYS* 1.3 73.5 - - - +
63E ASN* 1.3 73.3 + - - +
65E GLY* 3.1 15.8 + - - -
66E ILE 3.8 2.0 - - - -
67E ARG* 3.9 38.2 + - - +
69E MET* 3.5 22.4 - - + -
88E TRP* 3.5 27.1 - - + -
90E PHE* 4.8 4.7 - - + -
91E PHE* 3.6 25.1 - - + -
307E ARG* 6.4 0.7 - - + -
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Residues in contact with ASN 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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59E SER* 2.9 18.6 + - - +
62E ILE* 1.3 85.1 - - - +
64E SER* 1.3 59.9 + - - +
65E GLY 3.2 0.7 + - - -
148E ASP* 5.4 0.3 - - - +
303E ASN 5.3 0.9 - - - +
304E TRP* 3.4 58.1 - - + -
305E PRO* 2.9 46.1 + - - +
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Residues in contact with SER 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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17E PRO* 3.5 20.3 - - - +
60E ASN 2.7 20.3 + - - -
61E CYS* 3.8 5.2 - - - -
62E ILE 3.1 0.2 - - - -
63E ASN* 1.3 77.3 - - - +
65E GLY* 1.3 57.6 + - - +
66E ILE* 3.4 4.5 - - - -
147E GLN 3.5 7.8 + - - -
148E ASP* 3.5 5.3 - - - -
149E TYR* 2.9 40.2 + - - +
150E SER* 3.5 15.1 - - - -
304E TRP* 3.5 7.4 - - - -
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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