Contacts of the helix formed by residues 94 - 106 (chain B) in PDB entry 4O6M
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 ASN 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B PHE* 4.2 0.4 - - - -
92B ASP* 3.0 13.0 + - - +
93B GLY* 1.3 77.0 - - - +
95B LEU* 1.3 57.6 + - - +
96B GLN* 3.4 12.0 + - - +
97B SER* 2.8 37.5 + - - -
98B SER* 2.6 37.7 + - - -
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Residues in contact with LEU 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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7B LYS* 5.1 5.4 - - + -
39B PHE* 3.6 37.5 - - + -
42B LEU* 4.1 26.0 - - + +
52B ILE* 4.4 10.5 - - + -
54B LEU* 3.8 15.9 - - + -
87B PHE* 4.8 3.8 - - + -
91B PHE* 4.1 16.4 - - + -
93B GLY 4.0 2.6 + - - -
94B ASN* 1.3 70.3 - - - +
96B GLN* 1.3 68.7 + - - +
98B SER* 3.1 0.9 + - - -
99B ILE* 2.9 53.2 + - + +
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASN* 3.4 11.1 + - - +
95B LEU* 1.3 79.8 - - - +
97B SER* 1.3 64.3 + - - +
99B ILE* 3.5 7.6 + - - +
100B GLU* 3.2 20.7 + - + +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP* 3.6 13.9 + - - -
94B ASN* 2.8 30.5 + - - -
96B GLN* 1.3 74.7 - - - +
98B SER* 1.3 57.7 + - - +
100B GLU* 3.2 13.9 + - - +
101B LYS* 2.9 38.4 + - - +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.8 8.8 - - - -
90B VAL* 3.6 7.8 - - - +
91B PHE* 3.4 28.8 - - - -
92B ASP* 2.9 33.2 + - - -
94B ASN 2.6 23.2 + - - -
95B LEU 3.7 2.9 - - - -
97B SER* 1.3 73.6 - - - +
99B ILE* 1.3 60.6 + - - +
101B LYS* 3.5 3.8 + - - -
102B TYR* 2.9 29.8 + - - +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 4.6 4.5 - - + -
54B LEU* 4.0 26.0 - - + -
81B TYR* 4.3 24.2 - - + +
83B PHE* 4.1 18.6 - - + -
87B PHE* 4.7 2.9 - - + -
95B LEU* 2.9 46.8 + - + +
96B GLN* 3.8 6.3 - - - +
98B SER* 1.3 74.5 - - - +
100B GLU* 1.3 66.1 + - - +
102B TYR* 3.2 5.0 + - - +
103B LEU* 2.9 46.5 + - + +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN* 3.2 11.2 + - + +
97B SER* 3.4 17.6 + - - +
99B ILE* 1.3 81.8 - - - +
101B LYS* 1.3 64.3 + - + +
103B LEU* 3.4 7.5 + - - +
104B SER* 3.1 23.8 + - - -
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Residues in contact with LYS 101 (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 VAL* 3.9 22.7 + - + +
92B ASP* 3.5 29.9 + - - +
97B SER* 2.9 25.0 + - - +
98B SER* 3.8 5.2 - - - +
100B GLU* 1.3 79.6 - - + +
102B TYR* 1.3 62.5 + - - +
104B SER* 2.6 25.0 + - - +
105B LEU* 3.1 17.1 + - + +
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Residues in contact with TYR 102 (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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69B ARG* 5.1 7.8 + - - +
83B PHE* 3.2 47.7 - + + -
84B GLY* 3.2 14.2 + - - -
86B ASP* 2.8 36.0 + - - -
87B PHE* 3.7 32.3 - + + -
90B VAL* 3.9 20.1 - - + +
98B SER 2.9 18.5 + - - +
99B ILE 3.2 3.6 + - - +
101B LYS* 1.3 75.6 - - - +
103B LEU* 1.3 63.1 + - - +
105B LEU* 3.4 4.1 + - - -
106B ASN* 2.6 59.8 + - + +
108B LEU* 4.7 6.3 - - + -
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Residues in contact with LEU 103 (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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71B ILE* 3.8 17.0 - - + -
81B TYR* 4.2 12.3 - - + +
83B PHE* 4.1 9.4 - - + -
99B ILE* 2.9 38.2 + - + +
100B GLU* 3.8 6.5 - - - +
102B TYR* 1.3 77.4 - - - +
104B SER* 1.3 56.7 + - - +
106B ASN* 2.7 26.0 - - - +
108B LEU* 3.4 34.1 - - + -
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Residues in contact with SER 104 (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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100B GLU* 3.1 13.8 + - - -
101B LYS* 2.6 25.2 + - - +
103B LEU* 1.3 78.0 - - - +
105B LEU* 1.3 67.2 + - - +
106B ASN 3.3 2.0 - - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 5.1 0.7 + - - -
90B VAL* 4.0 27.8 - - + -
101B LYS* 3.1 21.2 + - + +
102B TYR* 3.4 4.9 + - - +
103B LEU 3.3 0.2 - - - -
104B SER* 1.3 83.4 + - - +
106B ASN* 1.3 67.5 + - - +
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Residues in contact with ASN 106 (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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69B ARG* 2.8 40.3 + - - +
86B ASP* 5.0 1.6 - - - +
102B TYR* 2.6 61.8 + - + +
103B LEU 2.7 23.3 - - - +
104B SER 4.3 2.3 - - - +
105B LEU* 1.3 89.3 - - - +
107B ASN* 1.3 60.3 + - - +
108B LEU* 3.7 19.5 + - + +
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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