Contacts of the helix formed by residues 105 - 113 (chain B) in PDB entry 6J7Z
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 GLY 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B HIS 4.2 0.2 - - - -
102B GLY 3.1 15.3 + - - -
103B LYS 3.2 1.8 + - - -
104B SER* 1.3 77.8 - - - +
106B LEU* 1.3 61.6 + - - +
107B THR 3.4 2.2 - - - -
108B LYS* 3.7 14.8 + - - +
109B ALA* 3.3 21.5 + - - +
195B ARG* 6.0 0.2 - - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.9 21.5 - - + -
61B ILE* 3.7 23.3 - - + -
62B GLU* 4.0 29.6 - - + +
82B ILE* 4.2 14.8 - - + -
101B HIS* 3.1 28.4 + - + +
104B SER* 3.2 16.2 + - - +
105B GLY* 1.3 77.2 - - - +
107B THR* 1.3 61.1 + - - +
109B ALA* 3.2 3.6 + - + -
110B VAL* 2.9 43.4 + - + +
194B HIS 4.3 5.6 - - - +
195B ARG* 4.6 8.5 - - - +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 6.2 0.9 - - - -
90B LEU* 4.3 21.1 - - + +
91B ASP* 6.0 0.2 - - - +
93B MET* 3.9 12.8 - - + +
98B LYS 4.7 0.7 + - - -
101B HIS* 2.7 39.4 + - - +
102B GLY* 3.8 6.8 + - - -
106B LEU* 1.3 73.5 - - - +
108B LYS* 1.3 57.1 + - - +
110B VAL* 3.2 7.5 + - - +
111B LYS* 2.9 51.4 + - - +
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Residues in contact with LYS 108 (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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105B GLY* 3.7 14.5 + - - +
106B LEU 3.3 0.2 - - - -
107B THR* 1.3 78.5 - - - +
109B ALA* 1.3 63.6 + - - +
111B LYS* 3.3 13.2 + - + +
112B GLU* 2.9 48.4 + - - +
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Residues in contact with ALA 109 (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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82B ILE* 3.8 30.8 - - + +
105B GLY 3.3 12.5 + - - +
106B LEU* 3.2 11.1 + - - +
108B LYS* 1.3 82.2 - - - +
110B VAL* 1.3 53.9 + - - +
112B GLU* 3.0 8.2 + - - +
113B SER* 2.7 36.6 + - - -
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Residues in contact with VAL 110 (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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61B ILE* 3.6 28.7 - - + +
82B ILE* 3.6 19.7 - - + -
83B ILE 3.5 15.3 - - - +
84B LYS* 3.7 15.4 - - - +
85B GLN* 3.7 17.3 - - + +
90B LEU* 3.7 26.5 - - + -
106B LEU* 2.9 27.9 + - + +
107B THR* 3.6 6.5 - - - +
109B ALA* 1.3 75.9 - - - +
111B LYS* 1.3 62.4 + - - +
112B GLU 3.3 0.3 + - - -
113B SER* 3.3 10.8 + - - -
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Residues in contact with LYS 111 (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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84B LYS* 3.8 19.0 + - - +
85B GLN 5.6 0.7 - - - -
87B ASP* 3.1 28.7 + - - +
90B LEU* 4.0 20.5 - - + +
91B ASP* 3.7 20.9 + - - -
107B THR* 2.9 32.5 + - - +
108B LYS* 3.5 14.4 - - + +
110B VAL* 1.3 76.4 - - - +
112B GLU* 1.3 59.5 + - - +
113B SER 3.7 1.2 + - - +
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Residues in contact with GLU 112 (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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108B LYS* 2.9 42.2 + - - +
109B ALA* 3.0 9.8 + - - +
111B LYS* 1.3 77.3 - - - +
113B SER* 1.3 63.6 + - - +
114B THR* 3.7 8.3 + - - +
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Residues in contact with SER 113 (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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82B ILE* 2.7 37.1 + - - -
84B LYS* 3.5 32.4 + - - +
109B ALA 2.7 18.7 + - - -
110B VAL 3.3 8.7 + - - -
111B LYS 4.3 0.7 - - - +
112B GLU* 1.3 76.0 - - - +
114B THR* 1.3 60.0 + - - +
115B ILE* 2.9 18.2 + - - +
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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