Contacts of the helix formed by residues 112 - 119 (chain A) in PDB entry 4ILG
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LYS* 5.5 0.9 + - - -
110A GLU 3.4 11.0 + - - +
111A ASP* 1.3 77.2 + - - +
113A THR* 1.3 62.2 + - - +
114A TRP 3.3 2.0 - - - -
115A TYR* 3.2 19.6 + - + +
116A ASN* 2.8 42.0 + - - +
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Residues in contact with THR 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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19A GLN* 3.3 20.0 - - - +
111A ASP* 2.2 33.3 + - - -
112A ASP* 1.3 76.3 - - - +
114A TRP* 1.3 64.2 + - - +
116A ASN* 3.0 19.9 + - + +
117A LEU* 3.0 33.6 + - + +
270A TYR* 5.5 8.5 - - + +
273A LYS* 5.7 5.9 + - + +
274A THR* 4.6 12.8 - - - +
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Residues in contact with TRP 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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18A ASP* 3.3 42.8 + - + -
19A GLN* 3.4 24.2 + - + +
39A GLY* 6.4 1.6 - - - -
40A HIS* 6.1 0.9 - + - -
41A VAL 2.9 26.4 + - - -
42A HIS* 4.1 5.1 + + - -
43A VAL* 3.7 23.1 - - + -
59A TRP* 4.0 17.3 - + - -
105A TYR* 4.7 4.5 - - - +
111A ASP 5.4 0.2 + - - -
112A ASP 3.3 0.8 - - - -
113A THR* 1.3 77.9 - - - +
115A TYR* 1.3 59.4 + - - +
117A LEU* 3.2 13.9 + - + +
118A THR* 2.7 60.7 + - + +
229A LEU* 4.4 9.2 - - + -
233A PHE* 3.9 24.9 - + - -
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Residues in contact with TYR 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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40A HIS* 4.2 20.2 - + - -
112A ASP* 3.2 23.3 + - + +
114A TRP* 1.3 81.7 - - - +
116A ASN* 1.3 68.1 + - - +
118A THR* 3.7 4.0 - - - -
119A GLU* 2.7 76.8 + - + +
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Residues in contact with ASN 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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112A ASP* 2.8 36.9 + - - +
113A THR* 3.0 9.4 + - - +
115A TYR* 1.3 88.7 - - - +
117A LEU* 1.3 58.7 + - - +
119A GLU* 4.2 9.1 + - - +
225A GLN* 3.2 17.7 + - - -
266A GLU* 5.6 1.8 + - - -
267A ILE* 5.4 3.5 - - - +
270A TYR* 3.4 60.5 + - + +
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Residues in contact with LEU 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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19A GLN* 4.6 5.2 - - + +
113A THR* 3.0 35.0 + - + +
114A TRP* 3.6 21.3 - - + +
116A ASN* 1.3 78.9 - - - +
118A THR* 1.3 62.4 + - + +
225A GLN* 3.4 26.9 + - - +
228A PHE* 4.6 4.3 - - + -
229A LEU* 3.8 23.9 - - + +
232A MET* 5.3 2.5 - - + -
270A TYR* 3.5 36.8 - - + +
271A GLN* 3.9 19.6 + - + +
274A THR* 4.1 19.5 - - + +
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Residues in contact with THR 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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40A HIS* 2.8 38.1 + - - -
41A VAL* 4.0 13.7 - - + -
59A TRP* 4.9 0.7 - - + -
114A TRP* 2.7 60.9 + - + +
115A TYR* 3.7 1.7 - - - -
117A LEU* 1.3 82.5 - - - +
119A GLU* 1.3 65.0 + - - +
120A PHE 3.1 3.4 - - - -
121A VAL* 2.9 18.5 + - + -
225A GLN* 3.7 0.4 - - - -
229A LEU* 3.8 17.5 - - + -
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Residues in contact with GLU 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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40A HIS* 4.3 3.6 + - - -
115A TYR* 2.7 59.1 + - + +
116A ASN* 4.5 10.1 + - - +
117A LEU 3.7 0.2 - - - -
118A THR* 1.3 73.6 - - - +
120A PHE* 1.3 87.7 + - + +
122A GLN* 3.9 12.5 + - - -
225A GLN* 3.6 2.7 + - - +
263A LYS* 3.1 32.5 + - - -
266A GLU* 5.1 0.3 - - - +
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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