Contacts of the helix formed by residues 75 - 82 (chain B) in PDB entry 1MNM
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 PRO 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASP 6.0 2.0 - - - +
57B GLN* 4.4 8.1 - - - +
74B THR* 1.3 85.9 - - - -
76B LYS* 1.3 68.3 + - + +
77B PHE 3.1 1.6 + - - -
78B GLU* 3.2 32.8 + - + +
79B PRO* 4.0 2.8 - - - +
121C GLN* 3.1 31.9 - - + +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A CYS* 3.0 47.2 - - - +
94A LEU* 3.6 21.6 + - + +
96A ALA* 2.9 34.2 + - + +
97A PRO 4.2 3.8 - - - +
98A ASP* 2.9 36.8 + - - +
57B GLN* 3.1 39.5 + - + +
75B PRO* 1.3 75.2 - - + +
77B PHE* 1.3 59.8 + - - +
79B PRO* 3.6 6.4 - - - +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.4 17.0 - - + -
63A VAL* 3.9 13.5 - - + -
69A VAL* 5.7 0.2 - - + -
90A ILE* 4.0 23.6 - - + -
93A CYS* 4.2 9.4 - - + -
94A LEU* 3.8 25.4 - - + -
57B GLN* 3.5 29.4 - - + -
58B VAL* 3.5 27.1 - - - +
59B LEU* 3.8 22.4 - - + +
73B SER* 3.2 16.1 + - - +
74B THR* 2.9 8.9 + - - +
76B LYS* 1.3 81.3 - - - +
78B GLU* 1.3 65.3 + - - +
79B PRO* 3.3 3.8 - - - -
80B ILE* 3.0 33.8 + - + +
81B VAL* 4.1 1.0 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER* 3.1 14.3 + - - +
74B THR 3.8 9.9 - - - +
75B PRO* 3.2 28.8 + - + +
77B PHE* 1.3 76.7 - - - +
79B PRO* 1.3 62.9 - - + +
80B ILE 3.0 0.5 + - - -
81B VAL* 3.1 8.0 + - + +
82B THR* 2.7 48.2 + - + +
120C THR* 3.5 35.2 - - + +
121C GLN 5.1 0.5 + - - -
122C ASP* 5.3 0.9 - - - +
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 5.6 5.4 - - + +
93A CYS* 4.2 13.7 - - - -
75B PRO 4.0 2.7 - - - +
76B LYS* 3.6 15.3 - - - +
77B PHE 3.3 4.9 - - - -
78B GLU* 1.3 92.8 - - + +
80B ILE* 1.3 61.2 + - - +
82B THR* 3.5 9.9 - - - +
83B GLN* 3.2 50.5 + - - +
85B GLU* 5.9 0.2 - - - +
86B GLY 4.4 4.3 + - - -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 6.4 0.4 - - + -
80A ILE* 6.4 3.6 - - + -
89A LEU* 3.5 28.0 - - + +
90A ILE* 4.8 10.1 - - + -
93A CYS* 3.4 27.6 - - + -
59B LEU* 4.1 22.0 - - + -
61B LEU* 5.7 1.1 - - + -
77B PHE* 3.0 30.4 + - + +
79B PRO* 1.3 77.5 - - - +
81B VAL* 1.3 61.7 + - + +
83B GLN 3.9 0.2 - - - +
86B GLY* 3.3 36.5 - - - -
87B ARG* 3.4 4.3 + - - -
90B ILE* 4.2 19.1 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.4 7.4 - - + -
61B LEU* 3.8 13.7 - - + -
71B THR* 3.5 35.0 - - + +
73B SER* 4.4 4.7 - - - -
77B PHE 4.6 0.7 - - - +
78B GLU* 3.4 15.0 - - - +
80B ILE* 1.3 81.3 - - + +
82B THR* 1.3 64.5 + - + +
83B GLN 3.5 1.1 - - - -
87B ARG* 2.8 32.3 + - - +
90B ILE* 4.5 8.5 - - + -
116C PHE* 4.0 13.1 - - + +
118C VAL* 3.8 32.2 - - + +
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 2.7 55.1 + - + +
79B PRO* 3.5 4.5 - - - +
81B VAL* 1.3 81.6 - - + +
83B GLN* 1.3 69.0 + - - +
87B ARG* 4.1 11.1 + - - +
118C VAL* 4.8 14.1 - - + -
120C THR* 5.8 0.9 - - + -
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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