Contacts of the helix formed by residues 131 - 147 (chain E) in PDB entry 6AHU
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 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ILE* 3.6 22.9 - - - +
103B THR* 5.4 0.2 + - - -
129E CYS* 3.6 4.1 - - + +
130E THR* 1.3 78.0 - - - +
132E GLU* 1.3 69.4 + - - +
133E GLY* 3.5 11.8 + - - -
134E GLU* 3.8 24.9 + - + +
135E ARG* 3.1 33.5 + - - +
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E THR 6.2 0.2 - - - -
131E ASP* 1.3 76.8 + - - +
133E GLY* 1.3 64.0 + - - +
135E ARG* 3.6 6.4 + - - +
136E GLU* 3.5 29.1 + - - +
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Residues in contact with GLY 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR* 5.4 7.5 + - - +
131E ASP* 3.4 8.6 + - - -
132E GLU* 1.3 79.8 - - - +
134E GLU* 1.3 59.9 + - - +
136E GLU* 3.9 11.0 + - - +
137E ALA* 3.7 15.2 + - - +
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Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 3.2 49.9 - - + +
103B THR* 5.1 6.2 + - - +
106B THR* 3.8 15.4 + - - +
125E LEU* 3.4 32.9 - - + +
129E CYS* 3.7 23.2 - - + +
131E ASP* 3.6 23.2 + - + +
132E GLU 3.3 0.4 - - - -
133E GLY* 1.3 74.6 - - - +
135E ARG* 1.3 60.7 + - - +
136E GLU 3.2 0.7 - - - -
137E ALA* 3.1 7.1 + - + +
138E ILE* 3.0 27.5 + - + +
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Residues in contact with ARG 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LEU* 3.5 41.1 + - + +
127E GLN* 4.8 2.8 - - - +
130E THR* 4.4 19.6 + - - +
131E ASP 3.1 19.7 + - - +
132E GLU* 3.6 7.1 + - - +
133E GLY 3.5 0.2 - - - -
134E GLU* 1.3 73.1 - - - +
136E GLU* 1.3 62.2 + - + +
138E ILE* 3.3 10.3 + - + +
139E GLN* 3.1 30.0 + - - +
139G PRO* 3.4 52.3 + - + +
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Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLU* 3.5 17.5 + - - +
133E GLY* 4.1 10.4 - - - +
134E GLU 3.2 0.4 - - - -
135E ARG* 1.3 78.7 - - + +
137E ALA* 1.3 57.5 + - - +
139E GLN* 3.4 17.7 + - - +
140E LYS* 3.1 36.4 + - - +
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Residues in contact with ALA 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR* 5.3 10.1 - - + -
106B THR* 3.7 30.8 - - + +
107B PHE* 5.3 10.8 - - + -
110B ALA* 5.7 0.3 - - - +
133E GLY 3.7 9.7 + - - +
134E GLU* 3.1 14.5 + - + +
136E GLU* 1.3 77.7 - - - +
138E ILE* 1.3 62.1 + - - +
140E LYS* 3.4 16.2 + - + +
141E SER* 3.3 15.6 + - - -
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Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 3.8 17.9 - - + +
122E LEU* 3.8 34.8 - - + +
125E LEU* 4.1 21.8 - - + -
126E LEU* 3.8 30.1 - - + -
134E GLU* 3.0 16.0 + - + +
135E ARG* 3.6 11.7 - - + +
136E GLU 3.3 0.2 - - - -
137E ALA* 1.3 76.6 - - - +
139E GLN* 1.3 58.5 + - + +
141E SER* 2.4 31.3 + - - +
142E VAL* 3.0 18.4 + - + +
139G PRO* 5.3 7.2 - - + -
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Residues in contact with GLN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ARG* 3.1 17.0 + - - +
136E GLU* 3.6 19.8 - - - +
137E ALA 3.3 0.4 - - - -
138E ILE* 1.3 75.7 - - + +
140E LYS* 1.3 59.3 + - - +
142E VAL* 3.9 7.5 - - - +
143E THR* 2.8 31.8 + - - +
138G THR* 3.6 33.8 + - + -
139G PRO* 3.2 32.2 + - + -
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Residues in contact with LYS 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PHE* 5.4 16.6 - - + -
110B ALA* 5.8 0.2 - - - -
136E GLU* 3.1 20.2 + - - +
137E ALA* 3.6 15.5 - - + +
138E ILE 3.2 0.6 - - - -
139E GLN* 1.3 76.1 - - - +
141E SER* 1.3 61.3 + - - +
142E VAL 3.5 0.2 - - - -
143E THR* 4.1 3.1 - - - -
144E ARG* 3.3 52.3 + - - +
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Residues in contact with SER 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 5.2 2.0 - - - -
110B ALA* 3.8 31.5 - - - -
114B GLU* 5.9 0.4 - - - +
122E LEU* 3.6 22.8 - - - +
137E ALA 3.3 9.8 + - - -
138E ILE* 2.4 32.8 + - - +
140E LYS* 1.3 77.2 - - - +
142E VAL* 1.3 64.2 + - - +
144E ARG* 4.2 2.8 - - - +
145E SER* 3.2 23.7 + - - -
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E LEU* 6.2 0.4 - - + -
138E ILE* 3.0 25.9 + - + +
139E GLN* 4.3 4.3 - - - +
140E LYS 3.5 0.2 - - - -
141E SER* 1.3 80.4 - - - +
143E THR* 1.3 63.1 + - - +
145E SER* 2.6 22.6 + - - +
146E CYS* 3.2 21.1 + - - -
136G ARG* 4.8 18.6 - - + -
138G THR* 4.2 22.2 - - + -
139G PRO* 5.3 10.1 - - + -
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Residues in contact with THR 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E GLN* 2.8 22.2 + - - +
140E LYS* 4.5 3.4 - - - -
142E VAL* 1.3 78.4 - - - +
144E ARG* 1.3 62.5 + - + +
146E CYS* 3.3 16.3 + - - +
147E LEU* 3.3 24.8 + - + +
138G THR* 4.7 10.0 - - - +
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Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PHE* 5.5 10.5 - - - -
110B ALA* 6.4 1.5 - - - +
111B ARG* 5.9 5.3 - - - +
114B GLU* 3.3 28.3 + - - +
140E LYS* 3.3 38.7 + - - +
141E SER* 4.5 2.7 - - - +
143E THR* 1.3 79.7 - - + +
145E SER* 1.3 60.2 + - - +
147E LEU* 3.4 25.7 + - + +
148E LEU* 3.4 18.1 + - - +
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Residues in contact with SER 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA* 5.6 9.6 - - - -
114B GLU* 5.5 2.6 - - - +
119E ARG* 6.0 4.9 - - - -
141E SER 3.2 17.4 + - - -
142E VAL* 2.6 26.3 + - - +
144E ARG* 1.3 75.0 - - - +
146E CYS* 1.3 63.7 + - - +
147E LEU 3.2 0.2 - - - -
148E LEU* 3.4 32.5 + - - +
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Residues in contact with CYS 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL* 3.2 24.9 + - - -
143E THR* 3.3 10.3 + - + +
145E SER* 1.3 84.7 + - - +
147E LEU* 1.3 63.0 + - + +
148E LEU 3.2 3.7 + - - +
66G CYS 5.2 3.6 - - - -
67G SER* 6.1 2.5 - - - -
136G ARG* 5.0 18.2 - - - -
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E THR* 3.3 24.6 + - + +
144E ARG* 3.7 20.0 - - + +
145E SER 3.2 0.8 - - - -
146E CYS* 1.3 79.6 - - + +
148E LEU* 1.3 62.2 + - - +
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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