Contacts of the helix formed by residues 85 - 97 (chain B) in PDB entry 1M6X
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 LYS 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B THR* 3.9 42.4 + - + +
83B THR* 3.2 12.7 + - - +
84B GLN* 1.3 78.6 - - + +
86B ALA* 1.3 65.5 + - - +
87B THR* 3.3 3.4 - - - -
88B ILE* 3.3 44.9 + - + +
89B LEU* 3.5 9.2 + - - +
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Residues in contact with ALA 86 (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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83B THR* 4.2 10.0 + - + -
84B GLN* 3.3 4.9 + - - +
85B LYS* 1.3 74.3 - - - +
87B THR* 1.3 66.2 + - - +
89B LEU* 2.9 8.2 + - - +
90B GLU* 2.9 32.9 + - - +
104B ILE* 3.5 34.8 - - + +
106B PRO* 5.0 11.0 - - + -
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Residues in contact with THR 87 (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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85B LYS 3.3 0.9 - - - -
86B ALA* 1.3 78.5 - - - +
88B ILE* 1.3 69.0 + - + +
90B GLU* 2.9 14.5 + - + +
91B ALA* 2.9 26.4 + - + +
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Residues in contact with ILE 88 (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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45B ILE* 5.3 6.7 - - + -
46B THR* 6.4 1.1 - - + -
85B LYS* 3.3 44.3 + - + +
87B THR* 1.3 79.8 - - + +
89B LEU* 1.3 60.7 + - - +
91B ALA* 3.5 7.3 + - - +
92B SER* 2.9 31.9 + - - +
114D SER 6.2 2.7 - - - +
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Residues in contact with LEU 89 (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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42B CYS* 3.7 40.8 - - + +
45B ILE* 3.6 42.2 - - + -
46B THR* 4.0 13.0 - - + -
81B TYR* 4.2 13.5 - - + -
83B THR* 4.4 6.5 - - + +
85B LYS 3.5 6.7 + - - +
86B ALA 2.9 9.7 + - - +
88B ILE* 1.3 78.8 - - - +
90B GLU* 1.3 65.8 + - - +
92B SER* 3.2 6.2 + - - -
93B LEU* 2.9 28.3 + - + +
104B ILE* 4.0 26.5 - - + -
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Residues in contact with GLU 90 (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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86B ALA* 2.9 33.5 + - - +
87B THR* 2.9 11.4 + - + +
89B LEU* 1.3 75.1 - - - +
91B ALA* 1.3 64.2 + - - +
93B LEU* 3.2 4.5 + - - +
94B LYS* 2.9 23.5 + - - +
101B GLU* 4.9 2.3 - - - +
102B PHE* 2.7 38.0 - - + +
103B THR* 3.6 7.5 + - - +
104B ILE* 3.3 38.6 + - + +
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Residues in contact with ALA 91 (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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87B THR* 2.9 14.6 + - + +
88B ILE* 3.6 12.6 - - - +
90B GLU* 1.3 77.0 - - - +
92B SER* 1.3 63.2 + - - +
94B LYS* 3.0 17.1 + - - +
95B LYS* 3.0 24.1 + - - +
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Residues in contact with SER 92 (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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45B ILE* 3.5 34.0 - - - +
88B ILE* 2.9 16.1 + - - +
89B LEU 3.2 8.2 + - - -
91B ALA* 1.3 78.1 - - - +
93B LEU* 1.3 65.8 + - - +
95B LYS* 3.1 21.5 + - - +
96B LEU 3.4 2.4 + - - -
114D SER 4.6 9.8 + - - -
116D ILE* 2.9 27.6 - - - +
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Residues in contact with LEU 93 (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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19B PHE* 4.6 7.7 - - + -
38B LEU* 4.0 17.9 - - + -
41B LEU* 4.5 20.2 - - + -
42B CYS* 4.4 6.7 - - - -
45B ILE* 4.5 15.3 - - + -
79B PHE* 3.9 11.4 - - + -
89B LEU* 2.9 17.8 + - + +
90B GLU 3.6 6.1 - - - +
92B SER* 1.3 75.1 - - - +
94B LYS* 1.3 64.0 + - - +
96B LEU* 3.0 21.1 + - + +
97B ILE* 3.2 5.4 + - - +
102B PHE* 3.8 36.8 - - + -
104B ILE* 3.7 30.1 - - + -
116D ILE* 4.3 4.0 - - + -
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Residues in contact with LYS 94 (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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90B GLU 2.9 13.5 + - - +
91B ALA* 3.4 11.2 - - - +
93B LEU* 1.3 71.8 - - - +
95B LYS* 1.3 57.2 + - - +
96B LEU 2.9 1.8 - - - -
97B ILE 2.6 22.4 + - - -
98B PRO* 2.7 47.5 + - + +
100B TRP 3.2 16.8 + - - +
101B GLU* 3.3 26.5 + - - +
102B PHE* 3.8 15.0 - - + +
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Residues in contact with LYS 95 (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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91B ALA* 3.0 22.2 + - - +
92B SER* 3.1 13.4 + - - +
94B LYS* 1.3 76.7 - - - +
96B LEU* 1.3 60.8 + - - +
98B PRO* 3.8 14.5 - - - +
114D SER 5.1 5.7 + - - -
115D ASP* 3.7 31.2 + - - +
116D ILE* 5.2 5.2 - - + +
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Residues in contact with LEU 96 (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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16B VAL* 3.8 33.2 - - + -
19B PHE* 4.0 10.5 - - + -
20B VAL* 4.4 19.9 - - + +
41B LEU* 3.9 26.0 - - + -
92B SER 3.4 5.9 + - - +
93B LEU* 3.0 14.1 + - + +
94B LYS 2.9 1.0 - - - -
95B LYS* 1.3 82.4 - - - +
97B ILE* 1.3 66.1 + - + +
98B PRO* 3.7 3.2 - - - +
116D ILE* 4.3 28.3 - - + -
117D THR* 4.4 18.8 - - + -
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Residues in contact with ILE 97 (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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19B PHE* 3.6 28.0 - - + +
20B VAL* 4.5 13.5 - - + -
23B PHE* 3.4 44.2 - - + -
93B LEU 3.2 2.6 + - - +
94B LYS* 2.6 15.2 + - - +
96B LEU* 1.3 86.1 - - + +
98B PRO* 1.4 60.3 - - + +
99B ALA* 4.5 4.3 - - + +
100B TRP* 3.0 53.2 + - + +
102B PHE* 3.9 11.2 - - + -
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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