Contacts of the helix formed by residues 114 - 123 (chain A) in PDB entry 2JG0
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 SER 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLY 3.2 4.2 + - - -
113A GLN* 1.3 77.5 - - - +
115A LEU* 1.3 60.5 + - - +
116A ARG 3.7 0.2 + - - -
117A GLU* 3.0 39.8 + - - +
118A HIS* 2.9 29.1 + - - +
488A TYR* 3.9 0.7 - - - -
540A ASP* 3.5 26.7 - - - +
541A ASN* 3.5 22.4 - - - +
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Residues in contact with LEU 115 (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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114A SER* 1.3 72.2 - - - +
116A ARG* 1.3 64.4 + - - +
118A HIS* 3.3 1.7 + - - +
119A ILE* 3.0 34.2 + - + +
484A VAL* 4.3 9.4 - - + -
485A GLN* 3.3 30.5 - - - +
488A TYR* 3.8 27.1 - - + -
494A LEU* 3.9 31.6 - - + -
525A THR* 3.7 25.1 - - + -
529A LEU* 4.4 9.0 - - + -
540A ASP 3.5 7.2 - - - +
541A ASN* 3.0 9.4 + - - +
542A VAL* 4.0 15.5 - - + -
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Residues in contact with ARG 116 (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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114A SER 3.3 0.2 - - - -
115A LEU* 1.3 75.9 - - - +
117A GLU* 1.3 58.8 + - + +
119A ILE* 3.3 7.3 + - - +
120A ASP* 2.9 43.8 + - - +
170A GLU* 3.2 29.3 + - - -
526A LEU* 4.2 16.8 + - + +
529A LEU* 3.9 25.7 + - + +
530A ASP* 3.3 16.4 + - - +
538A PRO* 4.4 10.2 - - - +
539A CYS 2.9 25.2 + - - +
540A ASP* 2.9 47.8 + - + +
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Residues in contact with GLU 117 (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 GLY 4.4 1.7 - - - +
113A GLN* 3.5 26.8 - - + +
114A SER* 3.0 38.0 + - - +
116A ARG* 1.3 80.8 - - + +
118A HIS* 1.3 58.8 + - - +
120A ASP* 3.3 8.4 + - - +
121A GLY* 2.9 27.4 + - - -
540A ASP* 5.2 6.1 - - - +
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Residues in contact with HIS 118 (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 TYR* 5.9 2.7 - - + -
109A PRO* 3.7 26.9 - - + +
113A GLN* 3.4 15.5 + - - +
114A SER 2.9 17.0 + - - +
115A LEU 3.5 3.6 - - - +
117A GLU* 1.3 76.2 - - - +
119A ILE* 1.3 63.4 + - - +
121A GLY* 3.2 2.6 + - - -
122A LEU* 3.0 57.7 + - + +
488A TYR* 3.5 22.0 - + + +
492A LYS 4.2 6.7 - - - -
493A LYS* 4.2 9.6 - - + -
494A LEU* 3.4 33.9 + - + +
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Residues in contact with ILE 119 (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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115A LEU* 3.0 23.9 + - + +
116A ARG* 3.6 7.0 - - - +
118A HIS* 1.3 78.3 - - - +
120A ASP* 1.3 63.6 + - - +
122A LEU* 3.1 15.8 + - - +
123A TRP* 3.6 25.2 + - + -
494A LEU* 4.0 24.2 - - + -
522A ASN* 3.8 26.1 + - + +
525A THR* 3.7 31.2 - - + -
526A LEU* 3.6 38.4 - - + -
529A LEU* 5.3 0.2 - - + -
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Residues in contact with ASP 120 (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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116A ARG* 2.9 36.2 + - - +
117A GLU* 3.7 7.8 - - - +
119A ILE* 1.3 77.0 - - - +
121A GLY* 1.3 63.8 + - - +
122A LEU 3.3 0.3 + - - -
123A TRP* 3.4 26.3 + - + -
124A PRO* 3.9 5.9 - - - +
171A SER* 4.0 22.9 - - - -
173A HIS* 5.2 6.1 + - - +
526A LEU* 4.3 10.6 - - - +
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Residues in contact with GLY 121 (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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113A GLN* 5.5 2.2 - - - -
117A GLU 2.9 15.0 + - - -
118A HIS* 3.2 4.0 + - - -
120A ASP* 1.3 77.9 - - - +
122A LEU* 1.3 60.3 + - - +
123A TRP 3.4 0.2 - - - -
124A PRO* 3.3 16.6 - - - +
125A VAL* 4.2 8.8 - - - +
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Residues in contact with LEU 122 (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 TYR* 4.9 10.5 - - + -
118A HIS* 3.0 45.5 + - + +
119A ILE 3.1 6.4 + - - +
121A GLY* 1.3 77.6 - - - +
123A TRP* 1.3 65.7 + - - +
124A PRO 3.3 1.3 - - - -
125A VAL* 3.0 42.9 + - + +
126A LEU* 3.0 21.1 + - + +
517A GLY* 3.1 32.1 - - - +
522A ASN* 3.7 13.0 - - - +
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Residues in contact with TRP 123 (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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119A ILE* 3.6 18.3 + - + +
120A ASP* 3.4 26.4 + - - +
121A GLY 3.4 0.4 - - - -
122A LEU* 1.3 77.6 - - - +
124A PRO* 1.3 64.8 - - + +
126A LEU* 3.1 20.2 + - + +
127A THR* 2.6 25.0 + - - -
147A VAL* 4.1 17.2 - - + +
164A THR* 3.6 34.8 - - + -
167A GLY* 4.3 9.9 - - - -
168A LEU* 3.7 23.5 - - + +
171A SER* 3.9 14.1 + - - -
173A HIS* 4.0 19.5 - - + +
176A LYS* 4.6 9.4 - - + -
519A GLY* 4.4 2.0 - - - -
522A ASN* 3.9 24.2 - - + -
523A GLY 4.0 9.0 - - - -
526A LEU* 3.8 21.1 - - + -
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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