Contacts of the helix formed by residues 105 - 114 (chain S) in PDB entry 1JJ2
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 ASP 105 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800 A 4.4 8.0 + - - +
950 A 3.8 20.4 + - - +
970 G 2.6 39.8 + - - +
102S ASP* 5.0 1.0 + - - +
103S LEU 3.0 4.0 - - - +
104S GLU* 1.3 78.4 - - - +
106S GLU* 1.3 66.7 + - - +
107S LYS* 2.7 29.2 + - - +
108S ARG* 3.6 27.6 + - + +
109S GLU* 3.1 23.0 + - - +
111S ARG* 4.6 0.2 + - - -
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Residues in contact with GLU 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970 G 4.0 15.8 + - - +
104S GLU 3.8 4.7 + - - +
105S ASP* 1.3 74.2 + - - +
107S LYS* 1.3 56.9 + - + +
109S GLU* 3.7 9.8 - - - +
110S ALA* 2.8 37.5 + - - +
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Residues in contact with LYS 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790 G 3.0 35.8 + - + +
970 G 3.5 55.3 + - + +
105S ASP* 2.7 20.3 + - - +
106S GLU* 1.3 70.9 - - + +
108S ARG* 1.3 64.8 + - - +
110S ALA* 3.3 6.5 + - - +
111S ARG* 2.9 40.0 + - - +
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Residues in contact with ARG 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800 A 4.2 14.7 + - - +
40S VAL* 3.7 14.8 - - - +
41S ARG 3.2 8.5 + - - -
43S ASN* 3.0 37.5 - - - +
46S ASP* 2.8 43.0 + - - -
101S LEU* 3.4 19.3 - - - +
102S ASP 2.9 28.3 + - - +
103S LEU* 4.1 10.1 - - + +
105S ASP* 3.3 24.3 + - + +
107S LYS* 1.3 76.9 - - - +
109S GLU* 1.3 64.5 + - - +
111S ARG* 3.1 21.2 + - - +
112S LEU* 2.9 24.3 + - + +
119S ALA* 3.9 7.6 - - + +
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Residues in contact with GLU 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S TYR* 5.6 0.2 - - + -
103S LEU* 4.1 40.9 - - + +
105S ASP 3.1 14.4 + - - +
106S GLU* 3.8 8.7 - - - +
108S ARG* 1.3 78.5 - - - +
110S ALA* 1.3 63.4 + - - +
112S LEU* 3.2 8.1 + - + +
113S GLU* 3.0 47.3 + - - +
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Residues in contact with ALA 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S GLU 2.8 23.2 + - - +
107S LYS* 3.4 8.5 - - - +
109S GLU* 1.3 74.2 + - - +
111S ARG* 1.3 63.3 + - - +
113S GLU* 3.2 5.8 + - - +
114S SER* 3.0 25.8 + - - -
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Residues in contact with ARG 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790 G 3.6 56.9 + - - +
800 A 2.9 34.1 + - - -
970 G 5.2 0.6 - - - +
37S GLN* 3.9 0.2 - - - +
105S ASP* 4.6 2.2 + - - -
107S LYS* 2.9 22.0 + - - +
108S ARG* 3.4 30.3 - - - +
110S ALA* 1.3 77.2 - - + +
112S LEU* 1.3 58.1 + - - +
114S SER* 3.1 10.3 + - - -
117S ASP* 3.0 32.6 - - + +
118S SER 4.4 3.6 - - - -
119S ALA* 3.6 34.2 - - + +
8073S MG 2.8 19.1 - - - -
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Residues in contact with LEU 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S LEU* 5.1 4.7 - - + -
35S TYR* 3.6 47.0 - - + +
37S GLN* 3.6 28.4 - - - +
40S VAL* 4.5 10.8 - - + -
101S LEU* 3.7 22.4 - - + -
103S LEU* 3.5 37.9 - - + -
108S ARG* 2.9 17.0 + - - +
109S GLU 3.2 8.5 + - - +
111S ARG* 1.3 76.1 - - - +
113S GLU* 1.3 58.9 + - - +
119S ALA* 3.9 9.1 - - + +
8073S MG 2.6 18.0 - - - -
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Residues in contact with GLU 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S TYR* 3.9 30.3 + - + +
109S GLU* 3.0 44.1 + - - +
110S ALA* 3.8 5.1 - - - +
112S LEU* 1.3 74.4 - - - +
114S SER* 1.3 70.4 + - - +
115S GLU* 3.5 2.4 + - - +
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Residues in contact with SER 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S TYR 4.8 1.9 - - - +
110S ALA 3.0 14.2 + - - -
111S ARG* 3.1 16.2 + - - -
112S LEU 3.5 0.2 - - - +
113S GLU* 1.3 82.9 - - - +
115S GLU* 1.3 57.2 + - - +
116S ASP* 4.2 5.4 - - - -
117S ASP* 3.5 21.2 + - - +
8073S MG 2.3 29.8 - - - -
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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