Contacts of the helix formed by residues 107 - 125 (chain D) in PDB entry 6AH0
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 LYS 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D GLU* 1.3 61.1 + - - +
109D THR* 3.5 3.4 - - - +
110D ARG* 3.4 6.0 + - - +
111D GLU* 2.8 24.6 + - - -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS* 1.3 71.9 - - - +
109D THR* 1.3 66.3 - - - +
111D GLU* 3.0 12.3 + - - +
112D THR* 3.1 10.6 + - - -
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Residues in contact with THR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS 3.5 2.8 - - - +
108D GLU* 1.3 76.1 - - - +
110D ARG* 1.3 55.3 + - - +
112D THR* 3.3 1.7 + - - -
113D TYR* 2.9 22.7 + - - -
179D ILE* 5.6 11.0 - - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS* 3.4 9.2 + - - +
108D GLU 3.2 0.4 - - - -
109D THR* 1.3 72.1 - - - +
111D GLU* 1.3 67.0 + - - +
112D THR 3.1 1.6 - - - -
113D TYR* 2.9 13.6 + - - +
114D GLU* 3.0 13.0 + - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS 2.8 16.0 + - - -
108D GLU* 3.0 6.7 + - - +
110D ARG* 1.3 76.1 - - - +
112D THR* 1.3 57.5 + - - +
114D GLU* 4.3 0.7 + - - -
115D VAL 4.2 8.3 + - - -
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLU 3.1 12.4 + - - -
109D THR 3.7 2.2 - - - -
111D GLU* 1.3 75.6 - - - +
113D TYR* 1.3 64.6 + - - +
114D GLU 3.4 0.9 - - - -
115D VAL* 3.5 3.9 + - - +
116D LEU* 3.0 18.7 + - - -
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D THR 2.9 16.4 + - - -
110D ARG* 2.9 5.9 + - - +
112D THR* 1.3 74.6 - - - +
114D GLU* 1.3 70.4 + - - +
116D LEU* 3.1 4.3 + - - +
117D LEU 3.0 13.0 + - - -
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ARG 3.0 13.4 + - - -
111D GLU 4.8 0.7 - - - -
113D TYR* 1.3 73.7 - - - +
115D VAL* 1.3 53.1 + - - +
117D LEU* 2.4 28.8 + - - +
118D SER 2.9 8.7 + - - -
1031D GLU* 5.8 8.2 - - - +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLU 4.2 5.8 + - - -
112D THR* 3.5 7.9 + - - +
113D TYR 3.3 0.8 - - - -
114D GLU* 1.3 73.6 - - - +
116D LEU* 1.3 61.6 + - - +
118D SER* 3.1 5.8 + - - +
119D PHE* 3.0 18.7 + - - -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D THR 3.0 14.6 + - - -
113D TYR* 3.5 5.4 - - - +
114D GLU 3.1 0.4 - - - -
115D VAL* 1.3 75.9 - - - +
117D LEU* 1.3 62.1 + - - +
119D PHE* 3.1 4.7 + - - +
120D ILE* 3.0 17.2 + - - -
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR 3.0 7.9 + - - -
114D GLU 2.4 20.5 + - - -
116D LEU* 1.3 68.8 - - - +
118D SER* 1.3 60.3 + - - +
120D ILE* 3.2 3.8 + - - +
121D GLN* 3.0 18.9 + - - -
136D ALA* 6.5 1.8 - - - +
1032D GLU* 4.9 5.1 - - - -
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Residues in contact with SER 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D GLU 2.9 9.9 + - - -
115D VAL* 3.1 7.2 + - - +
117D LEU* 1.3 75.9 - - - +
119D PHE* 1.3 64.7 + - - +
121D GLN* 3.0 2.9 + - - -
122D ALA* 2.9 20.8 + - - -
1031D GLU 5.5 0.4 - - - -
1032D GLU* 4.0 25.4 - - - +
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL 3.0 13.7 + - - -
116D LEU* 3.1 4.4 + - - +
118D SER* 1.3 73.5 - - - +
120D ILE* 1.3 66.9 + - - +
122D ALA* 3.2 3.3 + - - +
123D ALA* 3.0 16.3 + - - -
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU 3.0 12.4 + - - -
117D LEU* 3.5 4.7 - - - +
118D SER 3.1 0.6 - - - -
119D PHE* 1.3 73.3 - - - +
121D GLN* 1.3 64.8 + - - +
123D ALA* 2.8 13.0 + - - -
124D LEU* 2.9 12.7 + - - -
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Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU 3.0 9.3 + - - -
118D SER* 3.0 6.4 + - - +
120D ILE* 1.3 72.0 - - - +
122D ALA* 1.3 62.0 + - - +
124D LEU 5.0 0.2 - - - -
125D GLY* 2.4 49.2 + - - -
1032D GLU* 6.2 2.5 - - - +
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D SER 2.9 13.2 + - - -
119D PHE* 3.6 4.7 - - - +
121D GLN* 1.3 74.5 - - - +
123D ALA* 1.3 62.1 + - - +
125D GLY* 4.6 0.9 + - - -
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Residues in contact with ALA 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PHE 3.0 8.2 + - - -
120D ILE 2.8 14.2 + - - -
122D ALA* 1.3 75.4 - - - +
124D LEU* 1.3 61.0 + - - +
125D GLY* 4.8 0.2 - - - -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ILE 2.9 13.2 + - - -
123D ALA* 1.3 73.0 - - - +
125D GLY* 1.3 61.0 + - - +
127D GLN* 5.3 1.6 + - - -
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Residues in contact with GLY 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLN* 2.4 42.5 + - - +
122D ALA 5.2 1.1 - - - -
123D ALA 3.5 0.8 - - - -
124D LEU* 1.3 71.3 - - - +
126D ASP* 1.3 60.3 + - - -
127D GLN* 2.9 8.9 + - - -
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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