Contacts of the helix formed by residues 109 - 114 (chain A) in PDB entry 6L49
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 ALA 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU 3.2 17.6 + - - +
106A PHE* 3.2 5.3 + - - +
108A ASP* 1.3 78.5 - - - +
110A TYR* 1.3 59.3 + - - +
111A LEU 3.2 2.0 - - - -
112A LEU* 3.1 13.4 + - - +
113A THR* 2.9 28.0 + - - -
121A LEU* 4.1 10.3 - - + -
125A ASP* 3.4 32.7 - - + +
126A VAL* 4.4 7.2 - - + +
129A ALA* 4.5 0.9 - - + -
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Residues in contact with TYR 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 PHE 2.9 16.3 + - - +
107A GLU* 4.2 7.4 - - - +
108A ASP 3.7 0.2 - - - -
109A ALA* 1.3 77.1 - - - +
111A LEU* 1.3 59.6 + - - +
113A THR* 3.3 19.5 + - + -
114A LEU* 3.3 37.8 + - + +
119A VAL* 3.4 36.8 - - - +
121A LEU* 4.6 3.5 - - + +
41B GLY 5.0 0.7 - - - +
42B GLY 3.2 20.6 - - - +
43B VAL* 3.7 36.3 - - + -
44B LYS* 3.4 23.9 - - + +
112G GLN* 3.9 28.1 + - - +
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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
----------------------------------------------------------
107A GLU 3.4 21.5 - - - +
108A ASP* 4.5 11.9 - - - +
109A ALA 3.2 0.6 - - - -
110A TYR* 1.3 77.2 - - - +
112A LEU* 1.3 60.9 + - - +
113A THR 3.3 0.2 - - - -
114A LEU* 3.9 5.0 + - - +
115A HIS* 3.5 18.7 + - - +
128E LEU* 3.7 24.6 - - + +
131E ARG* 3.8 42.2 - - + +
132E ILE* 5.9 1.3 - - + -
112G GLN* 3.4 31.6 - - - +
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Residues in contact with LEU 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 3.5 17.9 - - - +
109A ALA* 3.1 6.9 + - - +
111A LEU* 1.3 75.0 - - - +
113A THR* 1.3 64.7 + - - +
115A HIS* 3.5 13.8 + - + +
116A ALA* 3.8 2.4 + - - +
125A ASP* 3.2 43.1 - - - +
128A LEU* 4.0 22.7 - - + -
129A ALA* 4.0 9.4 - - + +
112E LEU* 3.8 25.6 - - + -
115E HIS* 3.5 19.1 + - + +
128E LEU* 3.8 16.8 - - + -
132E ILE* 3.8 18.4 - - + -
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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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109A ALA 2.9 15.3 + - - -
110A TYR* 3.3 24.4 - - + -
112A LEU* 1.3 77.6 - - - +
114A LEU* 1.3 61.1 + - + +
115A HIS 3.4 0.9 + - - -
116A ALA* 3.5 5.2 + - - +
118A ARG* 3.1 45.1 + - + +
119A VAL* 3.9 3.6 - - - -
120A THR 3.3 37.5 - - - +
121A LEU* 3.4 17.3 - - - +
125A ASP* 3.8 9.1 + - - +
115E HIS* 5.4 0.2 - - - -
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Residues in contact with LEU 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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110A TYR* 3.3 46.9 + - + +
111A LEU* 3.9 5.3 + - - +
113A THR* 1.3 79.0 - - - +
115A HIS* 1.3 63.2 + - - +
116A ALA 3.3 0.4 - - - -
117A GLY* 3.4 11.9 + - - -
118A ARG 3.6 19.3 - - - +
119A VAL* 4.9 2.7 - - + -
112G GLN* 5.2 10.1 - - + +
113G ALA 4.1 9.4 - - - +
114G VAL* 3.8 42.8 - - + -
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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