Contacts of the helix formed by residues 100 - 111 (chain A) in PDB entry 2JAJ
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 GLU 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.0 12.3 + - - +
70A LEU* 4.0 29.9 - - + +
72A ASP* 3.5 15.2 + - - +
73A CYS* 3.6 21.1 + - + +
75A PHE 4.4 0.9 - - - +
76A VAL* 5.5 0.2 - - - -
79A VAL* 3.5 20.1 - - + +
97A ARG* 2.7 70.9 + - - +
99A LYS* 1.3 78.1 - - - +
101A VAL* 1.3 60.7 + - - +
102A ASP 3.1 1.1 + - - -
103A MET 3.9 2.3 + - - -
104A MET* 3.8 15.4 + - - +
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Residues in contact with VAL 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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79A VAL* 4.3 13.0 - - + -
89A ILE* 3.5 21.4 - - + +
90A THR 3.5 25.4 - - - +
92A PRO* 4.1 13.2 - - + -
98A ARG 3.2 17.7 - - - +
99A LYS 3.1 1.8 - - - -
100A GLU* 1.3 76.2 - - - +
102A ASP* 1.3 71.9 + - - +
104A MET* 3.8 6.9 - - - +
105A LYS* 2.8 33.1 + - + +
117A GLU* 5.3 6.1 - - - +
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Residues in contact with ASP 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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99A LYS* 3.6 35.8 - - - +
100A GLU 3.1 2.0 - - - -
101A VAL* 1.3 91.5 - - - +
103A MET* 1.3 63.6 + - - +
105A LYS* 3.4 7.2 + - - +
106A GLU* 3.4 22.6 + - - +
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Residues in contact with MET 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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18A ARG* 3.6 41.1 - - - +
64A LEU* 3.8 18.8 - - + -
65A PRO* 3.5 39.0 - - + -
99A LYS 4.7 0.6 + - - -
100A GLU 3.9 1.4 + - - -
102A ASP* 1.3 81.5 - - - +
104A MET* 1.3 61.7 + - - +
106A GLU* 3.5 7.5 + - + +
107A ALA* 3.1 21.1 + - - +
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Residues in contact with MET 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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16A VAL* 3.7 27.4 - - + -
64A LEU* 4.3 7.5 - - + +
76A VAL* 3.5 36.3 - - + -
79A VAL* 3.8 22.4 - - + +
80A ALA* 3.7 20.9 - - + -
89A ILE* 4.3 4.3 - - + -
100A GLU 3.8 6.6 + - - +
101A VAL* 3.4 8.0 + - - +
102A ASP 3.3 0.6 - - - -
103A MET* 1.3 76.2 - - - +
105A LYS* 1.3 66.8 + - - +
107A ALA* 3.2 2.0 + - - +
108A LEU* 2.9 47.2 + - + +
276A VAL* 3.9 11.9 - - + -
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Residues in contact with LYS 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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89A ILE* 4.0 17.2 - - + +
101A VAL* 2.8 19.3 + - + +
102A ASP* 3.6 7.0 - - - +
104A MET* 1.3 77.2 - - - +
106A GLU* 1.3 61.0 + - - +
108A LEU* 3.8 1.5 - - - +
109A GLU* 2.8 61.6 + - - +
115A ILE* 4.3 17.9 - - + +
117A GLU* 3.7 36.6 + - + +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ASP 3.4 12.0 + - - +
103A MET* 3.8 9.4 - - + +
104A MET 3.2 0.2 - - - -
105A LYS* 1.3 82.6 - - + +
107A ALA* 1.3 64.6 + - - +
109A GLU* 3.5 17.5 + - - +
110A LYS* 3.1 43.2 + - - +
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Residues in contact with ALA 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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16A VAL* 4.7 9.6 - - + -
62A VAL* 4.3 15.4 - - + +
64A LEU* 3.9 24.2 - - + -
103A MET 3.1 17.2 + - - +
104A MET* 3.2 6.9 + - - +
106A GLU* 1.3 75.5 - - - +
108A LEU* 1.3 62.5 + - - +
110A LYS* 3.3 11.5 + - - +
111A LEU* 3.2 26.5 + - - +
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Residues in contact with LEU 108 (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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16A VAL* 4.1 7.6 - - + -
80A ALA* 3.8 20.0 - - + -
82A VAL* 4.2 5.4 - - + -
87A ALA* 3.5 24.7 - - + -
89A ILE* 3.8 18.8 - - + -
104A MET* 2.9 31.3 + - - +
105A LYS* 4.0 1.6 - - - +
107A ALA* 1.3 73.5 - - - +
109A GLU* 1.3 66.3 + - - +
111A LEU* 3.1 13.2 + - + +
112A GLN 3.3 7.1 + - - -
113A LEU* 3.4 31.3 + - + +
115A ILE* 3.7 15.9 - - + -
276A VAL* 5.0 1.6 - - + -
278A ILE* 3.7 22.4 - - + -
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Residues in contact with GLU 109 (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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105A LYS* 2.8 59.8 + - - +
106A GLU* 3.5 22.5 - - - +
108A LEU* 1.3 75.3 - - - +
110A LYS* 1.3 59.5 + - + +
112A GLN* 2.9 23.9 + - - +
113A LEU 4.9 2.9 - - - +
115A ILE* 4.0 20.8 - - + +
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Residues in contact with LYS 110 (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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106A GLU* 3.1 31.0 + - - +
107A ALA* 3.7 8.7 - - - +
108A LEU 3.3 0.2 - - - -
109A GLU* 1.3 76.1 - - + +
111A LEU* 1.3 59.5 + - + +
112A GLN* 3.2 11.7 + - - +
280A LYS* 4.4 6.1 + - - -
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Residues in contact with LEU 111 (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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14A HIS* 3.8 37.5 - - + +
16A VAL* 4.0 14.4 - - + -
62A VAL* 4.5 16.6 - - + -
107A ALA 3.2 12.5 + - - +
108A LEU* 3.1 12.0 + - + +
109A GLU 3.1 1.0 - - - -
110A LYS* 1.3 77.1 - - + +
112A GLN* 1.3 68.3 + - - +
113A LEU* 3.3 14.6 + - + +
278A ILE* 3.6 34.9 - - + +
280A LYS* 3.5 30.9 - - + +
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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