Contacts of the helix formed by residues 107 - 114 (chain B) in PDB entry 1JZO
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 GLN 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LYS* 3.0 31.1 + - + +
104B LEU 3.0 5.8 + - - +
106B GLU* 1.3 78.8 - - + +
108B MET* 1.3 64.6 + - - +
109B ALA* 3.2 3.1 - - - -
110B ASP* 2.9 27.5 + - - +
111B TYR* 3.1 20.1 + - + -
196B TYR* 2.6 40.0 + - - -
198B PRO* 4.7 2.6 - - - +
199B PRO* 3.6 23.9 - - + +
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Residues in contact with MET 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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81B TYR* 3.7 35.0 - - + -
104B LEU* 3.2 12.3 + - + -
105B HIS* 3.0 25.9 + - + +
106B GLU 3.4 0.8 - - - -
107B GLN* 1.3 77.5 - - - +
109B ALA* 1.3 62.8 + - - +
111B TYR* 3.2 7.8 + - - +
112B ASN* 2.9 38.5 + - - +
118B VAL* 3.7 32.5 - - + -
120B TYR* 3.1 39.3 - - + +
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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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106B GLU 5.0 2.8 + - - +
107B GLN 3.1 1.7 + - - -
108B MET* 1.3 77.8 - - - +
110B ASP* 1.3 63.3 + - - +
112B ASN* 3.5 7.5 + - - +
113B ALA* 2.9 29.9 + - - +
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Residues in contact with ASP 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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106B GLU 5.2 0.3 - - - +
107B GLN* 2.9 24.1 + - - +
109B ALA* 1.3 80.2 - - - +
111B TYR* 1.3 65.5 + - - +
113B ALA* 3.3 7.3 + - - +
114B LEU* 3.0 30.6 + - + +
199B PRO* 3.6 20.8 - - + +
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Residues in contact with TYR 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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90B ILE* 5.9 0.9 - - + -
104B LEU* 3.3 45.0 - - + +
107B GLN* 3.1 36.1 + - + -
108B MET* 3.2 9.8 + - - +
110B ASP* 1.3 74.1 - - - +
112B ASN* 1.3 60.6 + - - +
114B LEU* 3.2 9.3 + - - +
115B GLY 3.4 0.3 + - - -
116B ILE* 2.9 55.6 + - + +
118B VAL* 4.4 11.9 - - + -
196B TYR* 3.2 19.9 - - - -
197B GLN 2.6 25.4 + - - -
198B PRO* 3.7 1.5 - - - +
199B PRO* 3.4 33.4 - - + +
202B MET* 4.0 13.0 - - + -
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Residues in contact with ASN 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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81B TYR* 3.2 25.3 + - - +
82B LYS 3.6 17.0 + - - +
83B ALA* 3.2 19.4 - - - +
84B PRO* 3.3 13.5 - - + +
108B MET* 2.9 40.4 + - - +
109B ALA* 3.7 7.2 - - - +
111B TYR* 1.3 78.9 - - - +
113B ALA* 1.3 56.5 + - - +
115B GLY* 3.0 15.9 + - - -
116B ILE 2.9 20.1 + - - -
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Residues in contact with ALA 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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84B PRO* 4.9 5.8 - - - -
85B GLN* 5.3 6.2 + - - -
109B ALA 2.9 18.9 + - - +
110B ASP* 3.7 10.3 - - - +
112B ASN* 1.3 76.3 - - - +
114B LEU* 1.3 63.3 + - + +
115B GLY 3.1 2.8 + - - -
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Residues in contact with LEU 114 (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 LYS* 4.5 1.0 - - - +
110B ASP* 3.0 14.8 + - + +
111B TYR* 3.7 5.2 - - - +
112B ASN 3.1 0.6 - - - -
113B ALA* 1.3 81.7 - - + +
115B GLY* 1.3 58.4 + - - +
116B ILE* 3.4 3.5 + - + -
199B PRO* 3.4 45.5 - - + +
200B LYS* 3.6 17.3 - - + +
203B LYS* 2.9 48.4 - - + +
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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