Contacts of the helix formed by residues 64 - 72 (chain N) in PDB entry 5MS0
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 HIS 64 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122M GLU 5.4 0.4 - - - +
125M MET* 3.4 35.8 + - + +
126M VAL* 3.8 12.8 - - + +
129M GLN* 4.6 10.8 - - + +
63N TYR* 1.3 75.9 - - - +
65N LYS* 1.3 61.8 + - - +
66N GLN 3.3 2.7 - - - -
67N ILE* 3.9 8.7 - - + +
68N GLU* 3.4 23.4 + - - +
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Residues in contact with LYS 65 (chain N).
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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156M ASN* 4.6 19.3 - - + +
157M ASN 6.3 0.2 - - - -
158M ALA* 6.1 4.5 - - + +
62N GLU* 4.4 24.7 - - + +
63N TYR 3.2 2.0 - - - +
64N HIS* 1.3 78.4 - - - +
66N GLN* 1.3 63.7 + - - +
68N GLU* 4.0 3.6 + - - +
69N SER* 3.8 17.7 + - - -
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Residues in contact with GLN 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M GLU 5.5 7.0 - - - +
62N GLU 5.6 0.2 + - - -
63N TYR 4.3 7.7 + - - +
64N HIS* 3.3 0.6 - - - +
65N LYS* 1.3 80.1 - - - +
67N ILE* 1.3 63.0 + - - +
68N GLU 3.4 0.3 + - - -
69N SER* 3.4 6.3 + - - -
70N ASN* 3.2 20.3 + - - +
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Residues in contact with ILE 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M GLU* 5.6 4.0 - - - -
16M LYS* 5.6 10.1 - - + -
121M ALA 5.7 0.4 - - - +
122M GLU* 5.1 15.2 - - - +
125M MET* 4.3 23.1 - - + -
63N TYR 4.9 0.8 + - - +
64N HIS* 3.6 11.8 + - + +
65N LYS 3.4 0.4 - - - -
66N GLN* 1.3 79.3 - - - +
68N GLU* 1.3 57.1 + - - +
70N ASN* 3.3 8.5 + - - +
71N LEU* 3.1 27.5 + - - +
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Residues in contact with GLU 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M GLU* 6.1 1.6 - - - -
193M ALA* 6.2 3.6 - - + -
64N HIS 3.4 15.3 + - - +
65N LYS* 4.6 3.8 - - - +
66N GLN 3.3 0.4 - - - -
67N ILE* 1.3 75.9 - - - +
69N SER* 1.3 63.4 + - - +
71N LEU* 3.4 17.4 + - - +
72N GLN* 3.9 9.5 + - - +
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Residues in contact with SER 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N LYS 3.8 11.2 + - - -
66N GLN* 3.4 9.5 + - - -
67N ILE 3.3 0.4 - - - -
68N GLU* 1.3 79.1 - - - +
70N ASN* 1.3 61.0 + - - +
73N ARG* 3.4 21.8 + - - +
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Residues in contact with ASN 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M VAL* 5.4 3.7 - - - +
15M GLU* 3.7 31.4 - - + +
66N GLN 3.2 13.5 + - - +
67N ILE* 3.3 11.6 + - - +
68N GLU 3.2 0.4 - - - -
69N SER* 1.3 76.7 - - - +
71N LEU* 1.3 63.6 + - - +
73N ARG* 4.2 6.8 + - - +
74N ILE* 4.5 9.5 + - - +
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Residues in contact with LEU 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M VAL* 5.4 11.6 - - + +
122M GLU* 4.7 17.0 - - + -
67N ILE 3.1 15.1 + - - +
68N GLU* 3.8 10.5 - - - +
69N SER 3.3 1.6 - - - -
70N ASN* 1.3 80.0 - - - +
72N GLN* 1.3 66.7 + - - +
73N ARG 3.4 0.5 + - - -
74N ILE* 3.9 8.8 + - - +
75N GLU* 4.7 3.1 + - - +
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Residues in contact with GLN 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N GLU 3.9 8.1 + - - +
69N SER 4.7 0.2 + - - -
71N LEU* 1.3 75.3 - - + +
73N ARG* 1.3 57.8 + - - +
74N ILE 3.1 5.5 + - - -
75N GLU* 3.6 5.9 + - - +
76N ARG* 3.0 29.6 + - + +
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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