Contacts of the helix formed by residues 98 - 107 (chain A) 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 CYS 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASP* 3.1 15.4 + - + +
96A ILE 3.3 1.7 - - - +
97A THR* 1.3 77.6 + - - +
99A GLY* 1.3 66.3 + - - +
100A TYR* 3.5 10.8 - - - -
101A SER* 3.0 30.4 + - - +
102A HIS* 3.1 12.5 + - - +
125A ARG* 3.5 20.4 - - - +
153A MET* 4.8 1.0 - - - +
182A THR* 3.2 43.5 - - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR 3.9 3.4 + - - -
98A CYS* 1.3 72.1 - - - +
100A TYR* 1.3 56.8 + - - +
102A HIS* 3.1 10.7 + - - +
103A LYS* 3.0 27.3 + - - +
125A ARG* 5.6 0.2 - - - +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A CYS* 3.3 8.1 - - - -
99A GLY* 1.3 72.8 - - - +
101A SER* 1.3 65.2 + - - +
103A LYS* 3.3 15.7 + - + +
104A LEU* 3.0 23.4 + - - +
182A THR 4.2 3.8 - - - +
183A PRO* 3.6 21.2 - - + +
196A TYR* 3.7 42.2 - + + -
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.1 27.9 + - - -
95A ASP 3.3 25.5 + - - -
98A CYS* 3.0 17.3 + - - -
100A TYR* 1.3 78.5 - - - +
102A HIS* 1.3 57.5 + - - +
104A LEU* 3.4 5.9 + - - +
105A HIS* 3.0 24.8 + - - +
120A TYR* 4.7 1.9 + - - -
153A MET* 3.3 11.6 - - - +
182A THR* 3.8 5.0 + - - -
183A PRO* 3.8 16.1 - - - +
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Residues in contact with HIS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A CYS 3.1 11.6 + - - +
99A GLY* 3.1 12.8 + - - +
101A SER* 1.3 75.4 - - - +
103A LYS* 1.3 68.2 + - - +
105A HIS* 3.3 1.5 + - - +
106A GLU* 2.9 47.5 + - + +
153A MET* 3.1 55.1 + - + +
154A ALA* 4.7 3.8 - - - -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLY 3.0 14.2 + - - +
100A TYR* 3.3 21.2 + - + +
102A HIS* 1.3 82.7 - - - +
104A LEU* 1.3 60.6 + - - +
106A GLU* 3.6 14.7 + - - +
107A GLN* 2.9 29.7 + - - +
196A TYR* 3.7 33.7 - - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 4.5 13.9 - - + -
100A TYR 3.0 15.9 + - - +
101A SER* 3.7 5.4 - - - +
102A HIS 3.2 0.2 - - - -
103A LYS* 1.3 77.8 - - - +
105A HIS* 1.3 65.4 + - - +
107A GLN 3.0 11.3 + - - -
108A MET* 3.4 12.3 + - + -
111A TYR* 3.3 44.3 - - + +
118A VAL* 5.1 5.8 - - + -
120A TYR* 3.5 23.6 - - + +
183A PRO* 3.9 28.7 - - + -
185A VAL* 5.7 1.1 - - + -
196A TYR* 4.0 18.3 - - + -
202A MET* 5.0 12.8 - - + -
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Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.4 28.7 - + - -
101A SER 3.0 18.3 + - - +
102A HIS* 3.8 3.1 - - - +
104A LEU* 1.3 78.7 - - - +
106A GLU* 1.3 64.2 + - - +
108A MET* 3.0 27.9 + - + +
120A TYR* 2.9 26.3 + - - +
149A PHE* 3.5 22.2 - + - -
150A ASP* 2.6 35.0 + - - -
153A MET* 4.0 24.5 - - + -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A HIS* 2.9 39.6 + - + +
103A LYS* 3.7 16.4 - - - +
104A LEU 3.2 0.2 - - - -
105A HIS* 1.3 77.5 - - - +
107A GLN* 1.3 62.0 + - + +
108A MET 3.4 1.2 + - - -
109A ALA* 5.1 1.9 + - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.9 26.3 + - - +
104A LEU* 3.0 8.9 + - - +
106A GLU* 1.3 85.7 - - + +
108A MET* 1.3 62.5 + - - +
109A ALA* 3.2 3.6 - - - -
110A ASP* 2.8 28.5 + - - +
111A TYR* 3.1 13.7 + - + -
196A TYR* 2.7 32.9 + - - -
198A PRO* 4.6 2.6 - - - +
199A PRO* 3.3 31.0 - - + +
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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