Contacts of the helix formed by residues 105 - 114 (chain A) in PDB entry 2JAM
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 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLY* 1.3 75.1 - - - +
106A LEU* 1.3 66.9 + - - +
107A PHE* 3.4 3.6 - - + +
108A ASP* 3.3 28.8 + - - +
109A ARG* 3.1 22.5 + - - +
147A PRO 5.3 0.7 - - - +
148A GLU* 4.0 37.3 - - - +
150A LEU 3.9 0.7 - - - +
151A LEU* 3.4 24.2 - - + +
152A TYR* 4.5 0.2 - - - -
1305A J60 4.5 24.1 + - - +
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Residues in contact with LEU 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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104A GLY 3.8 0.6 + - - -
105A GLU* 1.3 72.2 - - - +
107A PHE* 1.3 74.5 + - + +
109A ARG* 3.3 3.8 + - - +
110A ILE* 3.2 34.5 + - + +
124A VAL* 3.9 26.7 - - + -
147A PRO* 4.4 8.2 + - + +
150A LEU* 3.2 47.9 + - + +
152A TYR* 3.4 33.7 - - + +
161A ILE* 4.2 4.5 - - + -
209A ILE* 4.3 7.2 - - + -
213A LEU* 3.9 24.0 - - + -
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Residues in contact with PHE 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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105A GLU* 3.4 2.6 - - + +
106A LEU* 1.3 87.6 - - + +
108A ASP* 1.3 65.6 + - - +
110A ILE* 3.3 10.4 + - + +
111A LEU* 3.2 25.2 + - - +
147A PRO* 4.1 26.9 - - + -
209A ILE* 4.6 5.2 - - + -
212A ILE* 3.4 41.5 - - + -
213A LEU* 3.5 37.5 - - + -
292A VAL* 5.5 0.9 - - + -
296A ILE* 3.7 31.7 - - + +
300A PHE* 3.6 35.2 - + + -
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Residues in contact with ASP 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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104A GLY* 5.7 0.9 - - - -
105A GLU* 3.3 38.2 + - - +
107A PHE* 1.3 76.9 - - - +
109A ARG* 1.3 65.5 + - + +
111A LEU* 3.3 15.7 + - - +
112A GLU* 3.2 35.2 + - - +
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Residues in contact with ARG 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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103A GLY 2.9 31.0 + - - +
104A GLY* 4.3 2.2 - - - -
105A GLU 3.1 15.6 + - - +
107A PHE 3.3 0.2 - - - -
108A ASP* 1.3 78.5 - - + +
110A ILE* 1.3 61.7 + - - +
112A GLU* 3.3 27.7 + - - +
113A ARG* 3.2 18.0 + - - +
152A TYR* 3.4 43.5 - - + +
154A THR 2.8 24.2 + - - -
155A PRO* 3.7 15.7 + - - +
156A GLU 2.9 25.5 + - - -
157A GLU* 4.0 12.7 + - - +
159A SER* 4.2 4.6 - - - -
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Residues in contact with ILE 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 LEU* 3.2 24.6 + - + +
107A PHE* 3.7 17.5 - - + +
108A ASP 3.3 0.4 - - - -
109A ARG* 1.3 76.4 - - - +
111A LEU* 1.3 62.9 + - - +
113A ARG* 3.2 27.7 + - - +
116A TYR* 3.8 47.8 - - + +
124A VAL* 6.2 0.9 - - + -
152A TYR* 5.0 5.4 - - - +
213A LEU* 3.2 35.0 - - + -
289A TYR* 3.3 11.5 - - + -
292A VAL* 4.7 1.6 - - + -
293A SER 6.1 0.4 - - - +
296A ILE* 4.0 17.0 - - + -
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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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107A PHE 3.2 9.8 + - - +
108A ASP* 3.5 17.7 - - - +
110A ILE* 1.3 77.8 - - - +
112A GLU* 1.3 60.2 + - + +
289A TYR* 2.6 28.0 + - - +
293A SER* 3.6 41.1 - - - +
296A ILE* 3.7 28.7 - - + +
297A GLN* 3.8 22.4 - - + +
303A SER* 5.7 6.1 - - - -
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Residues in contact with GLU 112 (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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108A ASP* 3.2 25.9 + - - +
109A ARG* 3.8 26.8 - - - +
110A ILE 3.2 0.8 - - - -
111A LEU* 1.3 77.9 - - + +
113A ARG* 1.3 63.0 + - - +
114A GLY 3.6 0.4 + - - -
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Residues in contact with ARG 113 (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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109A ARG 3.2 16.8 + - - +
110A ILE* 3.2 23.0 + - - +
112A GLU* 1.3 78.4 - - - +
114A GLY* 1.3 60.0 + - - +
115A VAL* 2.7 46.2 + - + +
116A TYR* 3.7 23.1 - - - -
120A ASP* 3.2 35.0 + - - +
152A TYR* 5.6 4.2 + - - -
157A GLU* 5.0 23.1 + - - +
289A TYR* 4.5 0.9 - - + -
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Residues in contact with GLY 114 (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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112A GLU 3.6 2.8 + - - -
113A ARG* 1.3 75.8 - - - +
115A VAL* 1.3 56.6 + - - +
287A ASP* 4.5 5.0 - - - +
289A TYR* 3.3 41.7 + - - +
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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