Contacts of the helix formed by residues 61 - 72 (chain F) in PDB entry 1M5P
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F HIS* 4.3 6.2 + - - -
59F PHE* 3.5 7.4 - - - +
60F LYS* 1.3 112.4 + - + +
62F VAL* 1.3 67.6 + - - +
63F SER* 4.2 11.5 + - - +
64F SER* 3.0 34.3 + - - +
65F ALA 3.3 4.2 + - - -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO* 4.0 28.5 - - + +
9F ASN* 4.0 10.8 - - - +
10F HIS* 3.2 45.7 - - + +
61F GLU* 1.3 73.0 + - - +
63F SER* 1.3 60.2 + - - +
65F ALA* 2.7 27.6 + - + +
66F THR* 2.9 17.2 + - - +
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Residues in contact with SER 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F GLU* 3.3 9.4 + - - +
62F VAL* 1.3 78.6 - - - +
64F SER* 1.3 78.0 + - - +
66F THR* 3.2 6.9 + - - -
67F ASN* 3.1 32.1 + - - +
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Residues in contact with SER 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 2.7 38.1 + - - +
38F GLY* 3.7 8.8 - - - -
59F PHE* 3.8 20.7 - - - -
61F GLU* 3.0 28.0 + - - +
62F VAL 3.0 0.8 - - - -
63F SER* 1.3 86.2 + - - +
65F ALA* 1.3 58.2 + - - +
67F ASN* 3.5 3.1 + - - +
68F ALA* 3.2 18.4 + - - +
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASN 3.2 27.1 - - - +
10F HIS 3.9 6.7 - - - +
12F ILE* 3.9 14.1 - - + +
59F PHE* 3.7 24.0 - - + -
61F GLU 3.3 2.5 + - - +
62F VAL 2.7 14.9 + - - +
64F SER* 1.3 70.9 - - - +
66F THR* 1.3 64.5 + - - +
67F ASN 3.1 2.0 - - - -
68F ALA* 3.3 1.4 + - - +
69F LEU* 3.0 25.5 + - - +
86F TYR* 4.0 3.6 - - + -
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Residues in contact with THR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO* 4.4 4.6 - - + +
62F VAL* 2.9 19.1 + - - +
63F SER* 3.7 10.4 - - - -
65F ALA* 1.3 76.7 - - - +
67F ASN* 1.3 67.1 + - - +
69F LEU* 3.5 1.6 + - - +
70F ARG* 3.2 61.2 + - - +
86F TYR* 2.6 30.8 + - - +
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Residues in contact with ASN 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 3.9 17.2 - - + +
63F SER* 3.1 22.0 + - - +
64F SER* 3.8 5.8 - - - +
65F ALA 3.1 0.6 - - - -
66F THR* 1.3 84.1 - - - +
68F ALA* 1.3 64.8 + - - +
70F ARG* 3.4 9.7 + - - +
71F SER* 3.0 30.7 + - - +
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Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 4.3 3.6 - - + -
34F PHE* 4.0 11.4 - - + -
37F PHE* 3.7 31.8 - - + -
59F PHE* 3.7 28.0 - - + -
64F SER 3.2 7.1 + - - +
65F ALA 3.3 2.4 + - - +
67F ASN* 1.3 79.8 - - - +
69F LEU* 1.3 61.6 + - - +
72F MET* 3.1 29.6 + - - +
84F ILE* 4.0 2.6 - - - +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 4.7 3.3 - - + +
65F ALA 3.0 16.8 + - - +
66F THR 3.8 3.6 - - - +
68F ALA* 1.3 79.1 - - - +
70F ARG* 1.3 67.3 + - + +
73F GLN* 3.6 30.1 + - - +
84F ILE* 2.7 52.4 - - + +
85F GLN* 4.1 3.8 - - - +
86F TYR* 3.7 40.8 - - + +
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Residues in contact with ARG 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 5.7 1.0 - - - +
79C ASP* 3.7 39.8 - - + +
66F THR* 3.2 41.7 + - + +
67F ASN* 3.9 9.2 - - - +
69F LEU* 1.3 84.1 - - + +
71F SER* 1.3 60.0 + - - +
72F MET 3.5 0.4 + - - -
73F GLN* 4.5 8.2 + - - +
86F TYR* 5.4 0.2 + - - -
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 3.7 18.8 - - - +
79C ASP* 2.9 25.7 + - - +
36F ARG* 4.8 7.1 + - - -
37F PHE* 3.7 23.4 - - - -
67F ASN* 3.0 20.2 + - - +
70F ARG* 1.3 76.9 - - - +
72F MET* 1.3 69.8 + - - +
73F GLN 3.6 0.9 - - - -
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Residues in contact with MET 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 4.3 1.3 - - - -
33F ILE* 3.0 40.4 - - + +
34F PHE* 3.6 16.2 - - + -
36F ARG* 4.5 7.4 - - - -
37F PHE* 3.7 23.3 - - + -
68F ALA 3.1 17.8 + - - +
71F SER* 1.3 94.9 - - - +
73F GLN* 1.3 67.5 + - - +
74F GLY 3.1 1.0 + - - -
75F PHE* 3.0 55.7 + - + +
82F MET* 3.7 2.9 - - - +
84F ILE* 3.4 21.2 - - + +
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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