Contacts of the helix formed by residues 111 - 118 (chain A) in PDB entry 1QL6
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 LEU 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLU* 1.4 74.4 - - - +
112A PHE* 1.3 51.6 + - - +
114A TYR* 3.3 17.1 + - + -
115A LEU* 2.7 34.3 + - + +
121A LEU* 4.4 8.3 - - + -
129A ILE* 3.5 47.6 - - + -
152A PRO* 3.6 14.8 - - + +
155A ILE* 2.9 44.5 + - + +
157A LEU* 4.2 15.5 - - + +
163A ILE* 5.3 0.4 - - + -
218A ILE* 4.9 3.4 - - + -
222A LEU* 3.9 22.7 - - + -
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Residues in contact with PHE 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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110A GLU* 3.0 21.7 - - - +
111A LEU* 1.3 77.7 - - - +
113A ASP* 1.3 71.4 + - - +
115A LEU* 3.1 10.8 + - + +
116A THR* 3.0 42.8 + - - -
152A PRO* 3.2 18.2 + - + -
153A GLU* 3.7 38.4 - - + +
189A TYR* 5.9 1.1 - - - -
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Residues in contact with ASP 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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108A LYS 5.6 1.6 - - - +
109A GLY* 3.9 6.4 - - - -
110A GLU* 2.9 44.9 + - - +
112A PHE* 1.3 87.3 - - - +
114A TYR* 1.3 62.7 - - - +
116A THR* 3.5 10.0 + - - +
117A GLU* 3.4 23.9 + - - +
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Residues in contact with TYR 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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108A LYS 5.4 1.1 - - - +
110A GLU 2.9 15.9 + - - +
111A LEU* 3.7 19.5 - - + +
113A ASP* 1.3 76.1 - - - +
115A LEU* 1.3 64.5 + - - +
117A GLU* 3.5 7.8 + - + +
118A LYS* 3.2 52.7 + - + +
121A LEU* 3.8 19.5 - - + -
125A GLU* 2.5 38.1 + - - -
129A ILE* 5.1 3.4 - - + -
157A LEU* 3.7 12.8 - - + -
161A MET* 3.5 30.8 - - + +
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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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111A LEU* 2.7 22.4 + - + +
112A PHE* 3.1 10.1 + - + +
114A TYR* 1.3 74.1 - - - +
116A THR* 1.3 56.0 + - - +
118A LYS* 4.9 1.8 - - - -
119A VAL* 2.9 57.1 + - - +
120A THR* 4.0 3.1 - - - -
121A LEU* 4.2 14.6 - - + -
152A PRO* 5.4 7.4 - - + -
221A THR* 3.8 32.5 - - + +
222A LEU* 3.9 39.9 - - + +
225A GLY* 5.2 3.4 - - - +
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Residues in contact with THR 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 PHE* 3.0 37.2 + - - -
113A ASP* 3.5 12.8 - - - +
114A TYR 3.4 0.2 - - - -
115A LEU* 1.3 75.0 - - - +
117A GLU* 1.3 60.1 + - + +
119A VAL* 4.0 9.6 + - - +
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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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113A ASP 3.4 13.2 + - - +
114A TYR* 4.0 9.2 - - + +
115A LEU 3.2 0.6 - - - -
116A THR* 1.3 81.1 - - + +
118A LYS* 1.3 61.6 + - + +
119A VAL* 3.5 4.0 - - - +
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Residues in contact with LYS 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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114A TYR* 3.2 56.7 + - + +
115A LEU 3.2 2.7 + - - +
117A GLU* 1.3 79.6 - - + +
119A VAL* 1.3 61.4 + - - +
120A THR* 2.8 30.5 + - - +
121A LEU* 3.8 12.6 - - + +
122A SER 6.1 0.2 - - - +
125A GLU* 3.2 16.3 + - - -
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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