Contacts of the helix formed by residues 103 - 109 (chain X) in PDB entry 1M6E
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 ASP 103 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9X MET* 5.9 0.2 - - - +
10X LYS 5.8 1.6 + - - +
12X GLY* 3.5 27.0 - - - -
13X ALA 3.7 4.2 + - - +
62X SER* 3.1 19.0 + - - +
102X ASN* 1.3 84.7 + - - +
104X PHE* 1.3 60.9 + - - +
105X ASN* 3.8 9.2 + - - +
106X ALA* 3.2 36.9 + - + +
107X ILE* 3.4 17.2 + - - +
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Residues in contact with PHE 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X CYS* 4.8 1.8 - - - -
96X LEU* 3.5 27.4 - - + -
98X ASP* 3.6 33.2 - - + -
99X LEU 3.7 19.5 - - - -
100X PRO* 5.1 0.7 - - + -
101X GLY 5.2 1.8 - - - -
102X ASN* 3.2 27.7 + - + -
103X ASP* 1.3 71.8 - - - +
105X ASN* 1.3 65.4 + - - +
107X ILE* 3.2 11.2 + - + +
108X PHE* 2.9 64.2 + + + -
125X GLY* 4.0 8.5 - - - -
126X VAL 4.2 0.9 - - - -
127X PRO* 4.4 20.0 - - + -
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Residues in contact with ASN 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X ASP* 3.3 8.9 + - - +
104X PHE* 1.3 79.3 - - - +
106X ALA* 1.3 56.9 + - - +
108X PHE* 3.4 9.3 + - - -
109X ARG* 2.8 76.9 + - - +
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Residues in contact with ALA 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X ALA* 4.0 23.3 - - + +
62X SER* 4.7 2.2 - - - -
63X GLY 5.3 1.6 - - - +
103X ASP* 3.2 35.3 + - + +
104X PHE 3.2 0.2 - - - -
105X ASN* 1.3 79.7 - - - +
107X ILE* 1.3 61.4 + - - +
109X ARG* 4.6 3.1 - - - +
110X SER* 3.1 28.6 + - - +
111X LEU* 3.7 5.2 + - - +
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Residues in contact with ILE 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X CYS* 4.5 5.4 - - - -
61X SER 3.0 26.5 - - - +
62X SER* 4.1 9.0 - - - -
66X ALA* 4.0 15.3 - - + -
67X LEU* 4.9 3.8 - - + -
96X LEU* 4.1 27.6 - - + -
102X ASN* 4.4 5.4 - - - +
103X ASP 3.4 14.6 - - - +
104X PHE* 3.2 12.9 + - + +
106X ALA* 1.3 72.5 - - - +
108X PHE* 1.3 64.4 + - + +
109X ARG 2.8 3.0 + - - -
111X LEU* 3.0 35.8 + - + -
112X PRO* 2.5 35.4 - - + +
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Residues in contact with PHE 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96X LEU* 4.9 6.5 - - + -
104X PHE* 2.9 46.0 + + + +
105X ASN* 3.8 9.9 - - - +
107X ILE* 1.3 78.7 - - + +
109X ARG* 1.3 64.7 + - + +
112X PRO* 4.0 19.5 - - + +
113X ILE* 4.6 1.6 + - - -
123X ILE* 4.7 16.8 - - + -
124X ASN* 5.5 0.4 - - - -
125X GLY* 3.7 36.8 - - - -
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Residues in contact with ARG 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X ASN* 2.8 68.7 + - - +
106X ALA* 4.0 3.1 - - - +
107X ILE 2.8 0.8 + - - -
108X PHE* 1.3 79.2 - - + +
110X SER* 1.3 57.0 + - - +
111X LEU 2.4 17.5 + - - -
113X ILE* 2.9 29.9 + - - +
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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