Contacts of the helix formed by residues 108 - 124 (chain A) in PDB entry 6A69
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLU 5.1 2.9 - - - +
105A ALA* 3.9 17.4 + - - +
106A LEU 3.7 0.9 - - - -
107A GLN* 1.3 80.9 + - - +
109A VAL* 1.3 64.5 + - - +
110A THR* 4.5 4.0 - - - +
111A LEU* 3.3 30.0 + - + +
112A ILE* 3.2 19.8 + - - +
433A GLU* 4.8 10.4 - - - +
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Residues in contact with VAL 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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107A GLN 4.1 9.2 - - - +
108A ASP* 1.3 71.7 - - - +
110A THR* 1.3 65.2 + - - +
112A ILE* 3.3 14.9 - - + +
113A ILE* 3.0 41.6 + - + +
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Residues in contact with THR 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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108A ASP* 4.5 2.7 - - - +
109A VAL* 1.3 77.7 - - - +
111A LEU* 1.3 65.2 + - + +
113A ILE* 3.4 6.7 + - - +
114A LEU* 3.0 27.3 + - + +
424A VAL* 4.3 11.4 - - + +
427A LEU* 5.0 15.4 + - + +
428A VAL* 3.9 34.8 - - + +
433A GLU* 5.7 2.7 - - - +
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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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105A ALA 3.9 18.8 - - - +
106A LEU* 4.3 10.5 - - + -
108A ASP* 3.3 31.2 + - + +
110A THR* 1.3 86.0 - - + +
112A ILE* 1.3 58.0 + - - +
114A LEU* 3.3 9.8 + - + +
115A GLU* 2.9 32.6 + - - +
163A VAL* 4.3 24.1 - - + +
166A VAL* 5.1 8.5 - - + -
167A VAL* 4.3 20.6 - - + -
428A VAL* 6.4 0.9 - - + -
433A GLU* 4.0 21.8 - - - +
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Residues in contact with ILE 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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106A LEU* 5.3 11.2 - - + +
107A GLN* 5.7 2.7 - - - +
108A ASP 3.2 6.4 + - - +
109A VAL* 3.3 33.0 - - + +
111A LEU* 1.3 75.6 - - - +
113A ILE* 1.3 62.4 + - + +
115A GLU* 3.3 24.5 + - + +
116A ILE* 3.0 47.7 + - + +
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Residues in contact with ILE 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 VAL* 3.0 37.8 + - + +
110A THR* 3.8 5.6 - - - +
112A ILE* 1.3 77.6 - - + +
114A LEU* 1.3 58.4 + - - +
116A ILE* 3.3 11.5 + - + +
117A ALA* 3.0 28.4 + - - +
420A PHE* 4.2 17.9 - - + -
424A VAL* 4.0 25.1 - - + -
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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 THR 3.0 17.0 + - - +
111A LEU* 3.3 10.7 + - + +
113A ILE* 1.3 77.8 - - - +
115A GLU* 1.3 57.2 + - - +
117A ALA* 3.8 2.3 - - - -
118A ALA* 3.0 28.8 + - - +
159A ILE* 3.8 16.6 - - + +
163A VAL* 3.7 24.2 - - + -
421A ILE* 3.7 28.9 - - + -
424A VAL* 3.8 18.8 - - + +
425A THR* 5.2 8.1 - - - +
428A VAL* 4.5 12.1 - - + -
884A ALA* 6.0 0.9 - - + +
888A LEU* 4.1 25.8 - - + -
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Residues in contact with GLU 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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106A LEU* 4.0 17.8 - - - +
111A LEU 2.9 19.0 + - - +
112A ILE* 3.7 26.5 - - + +
114A LEU* 1.3 76.6 - - - +
116A ILE* 1.3 62.4 + - + +
118A ALA* 3.2 7.4 + - - +
119A ILE* 3.0 35.3 + - + +
159A ILE* 5.5 1.3 - - - -
160A LEU* 5.4 16.1 - - + +
163A VAL* 3.8 26.9 - - + +
164A VAL* 5.3 6.6 - - - +
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Residues in contact with ILE 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 ILE* 3.0 33.4 + - + +
113A ILE* 3.7 11.7 - - + +
115A GLU* 1.3 77.7 - - + +
117A ALA* 1.3 59.5 + - + +
119A ILE* 3.2 13.1 + - + +
120A VAL* 3.0 36.2 + - + +
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Residues in contact with ALA 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 ILE* 3.0 17.2 + - + +
114A LEU* 4.1 0.4 - - - +
116A ILE* 1.3 76.2 - - + +
118A ALA* 1.3 55.5 + - - +
120A VAL* 3.8 8.2 - - - +
121A SER* 2.5 38.6 + - - +
417A VAL* 4.3 7.0 - - + +
420A PHE* 4.6 21.1 - - + -
421A ILE* 3.7 23.8 - - + -
424A VAL* 5.9 0.9 - - + -
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Residues in contact with ALA 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 LEU 3.0 18.5 + - - +
115A GLU* 3.2 7.6 + - - +
117A ALA* 1.3 74.4 - - - +
119A ILE* 1.3 65.5 + - - +
121A SER* 3.4 7.9 - - - -
122A LEU* 3.0 28.0 + - - +
156A GLY* 3.9 14.3 - - - +
159A ILE* 3.7 31.0 - - + -
160A LEU* 4.5 7.6 - - + +
421A ILE* 4.7 3.0 - - - +
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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 GLU* 3.0 22.6 + - + +
116A ILE* 3.2 13.2 + - + +
118A ALA* 1.3 78.0 - - - +
120A VAL* 1.3 58.9 + - + +
122A LEU* 3.4 17.2 + - + +
123A GLY* 2.8 24.8 + - - -
160A LEU* 4.3 22.2 - - + -
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Residues in contact with VAL 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 ILE* 3.0 26.0 + - + +
117A ALA* 3.8 8.1 - - - +
119A ILE* 1.3 80.0 - - + +
121A SER* 1.3 56.1 + - - +
123A GLY* 2.9 16.5 + - - +
124A LEU* 2.9 25.0 + - + +
413A ILE* 6.2 0.4 - - + -
417A VAL* 3.8 25.1 - - + -
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Residues in contact with SER 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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117A ALA 2.5 24.2 + - - -
118A ALA* 3.4 9.4 - - - -
120A VAL* 1.3 76.7 - - - +
122A LEU* 1.3 61.0 + - - +
124A LEU* 3.8 8.4 + - - +
125A SER* 3.8 8.5 + - - -
155A GLU* 5.8 4.9 - - - -
156A GLY* 4.9 9.6 - - - -
414A GLN* 5.3 6.5 - - - +
417A VAL* 3.3 23.4 + - - +
421A ILE* 4.9 9.2 - - - +
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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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118A ALA 3.0 17.7 + - - +
119A ILE* 3.4 21.3 - - + +
121A SER* 1.3 76.6 - - - +
123A GLY* 1.3 66.8 + - - +
125A SER* 2.3 32.8 + - - +
126A PHE* 3.6 13.8 + - + +
152A GLY 5.7 0.4 - - - -
153A TRP* 4.8 21.1 - - + +
156A GLY* 4.3 25.2 - - - +
157A ALA* 4.3 6.5 - - + +
160A LEU* 5.4 9.6 - - + -
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Residues in contact with GLY 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 2.8 15.8 + - - -
120A VAL* 2.9 7.9 + - - -
122A LEU* 1.3 81.2 - - - +
124A LEU* 1.3 64.1 + - - +
125A SER 3.1 0.2 - - - -
126A PHE* 3.2 27.6 + - - +
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Residues in contact with LEU 124 (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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120A VAL* 2.9 21.1 + - + +
121A SER* 3.8 4.7 + - - +
122A LEU 3.3 0.4 - - - -
123A GLY* 1.3 79.0 - - - +
125A SER* 1.3 59.8 + - - +
127A TYR 4.4 7.4 - - - +
128A GLN* 4.3 14.7 - - - +
410A PRO* 3.8 22.9 - - + +
413A ILE* 3.8 29.8 - - + +
414A GLN* 3.8 41.2 - - + +
417A VAL* 4.4 10.1 - - + -
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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