Contacts of the helix formed by residues 124 - 134 (chain E) 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 LYS 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A HIS* 3.5 27.7 + - + +
118E ARG* 3.4 32.6 - - - +
122E PHE* 3.9 19.1 - - + -
123E PRO* 1.3 78.6 - - - +
125E ASP* 1.3 60.1 + - - +
126E VAL 3.4 0.2 - - - -
127E GLN* 4.0 6.9 - - - -
128E LEU* 3.3 29.9 + - + +
-2J C 4.8 5.1 + - - -
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Residues in contact with ASP 125 (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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115A HIS* 3.2 26.7 - - - -
109E ALA* 3.3 26.4 - - + +
112E LEU* 3.4 28.3 - - - +
113E THR* 3.2 23.3 + - - +
118E ARG* 5.4 1.1 + - - -
120E THR 4.0 2.9 - - - +
121E LEU* 3.5 9.5 - - + -
122E PHE* 3.2 38.3 + - - +
124E LYS* 1.3 79.3 - - - +
126E VAL* 1.3 62.2 + - + +
128E LEU 4.1 0.2 - - - -
129E ALA* 3.6 4.3 + - - +
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Residues in contact with VAL 126 (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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105E LEU* 3.8 30.7 - - + -
106E PHE* 4.7 17.9 - - + -
109E ALA* 4.8 7.0 - - + -
121E LEU* 5.9 1.6 - - + -
122E PHE 3.8 14.6 - - - +
123E PRO 3.7 3.5 + - - +
124E LYS 3.4 0.2 - - - -
125E ASP* 1.3 80.1 - - + +
127E GLN* 1.3 66.3 + - - +
128E LEU 3.5 0.4 - - - -
129E ALA* 4.3 3.8 - - - +
130E ARG* 3.3 25.3 + - - +
50F ILE* 4.3 11.4 - - + -
53F GLU* 3.8 36.6 - - + +
57F VAL* 5.1 5.8 - - + -
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Residues in contact with GLN 127 (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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123E PRO 3.4 19.6 + - - +
124E LYS* 3.7 6.0 + - - +
125E ASP 3.3 0.2 - - - -
126E VAL* 1.3 83.9 - - - +
128E LEU* 1.3 59.9 + - - +
129E ALA 3.6 0.2 - - - -
130E ARG* 4.3 21.9 + - - +
131E ARG* 3.7 16.5 + - - +
53F GLU* 3.1 27.9 - - - +
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Residues in contact with LEU 128 (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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111A LEU* 3.7 44.0 - - + +
112A LEU* 3.8 21.3 - - + -
115A HIS* 3.6 39.3 - - + +
112E LEU* 3.8 10.5 - - + -
124E LYS 3.3 16.0 + - - +
127E GLN* 1.3 79.9 - - - +
129E ALA* 1.3 63.1 + - - +
130E ARG 3.4 0.2 - - - -
131E ARG* 3.5 12.4 + - + +
132E ILE* 3.5 21.4 - - + +
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Residues in contact with ALA 129 (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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132A ILE* 3.9 22.3 - - + +
105E LEU* 4.0 21.3 - - + -
108E ASP* 4.7 0.9 - - + -
109E ALA* 4.3 11.0 - - + +
112E LEU* 3.5 14.6 - - + +
125E ASP 3.6 16.2 + - - +
126E VAL 4.9 0.4 - - - +
127E GLN 4.3 0.2 - - - +
128E LEU* 1.3 81.4 - - - +
130E ARG* 1.3 61.6 + - + +
131E ARG 3.4 0.9 + - - -
132E ILE* 3.6 1.4 + - - +
133E ARG* 3.3 26.4 + - - +
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Residues in contact with ARG 130 (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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101E PHE* 4.9 6.3 - - - -
105E LEU* 3.9 23.3 - - + -
126E VAL* 3.3 23.1 + - - +
127E GLN* 4.3 20.9 + - - +
128E LEU 3.4 0.2 - - - -
129E ALA* 1.3 75.1 - - - +
131E ARG* 1.3 58.2 + - - +
133E ARG* 3.8 11.0 - - - +
134E GLY* 3.2 20.8 + - - -
135E LEU* 3.5 49.2 + - + +
53F GLU* 5.4 0.8 + - - -
57F VAL* 4.1 27.4 - - - +
60F VAL* 4.5 21.9 - - - +
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Residues in contact with ARG 131 (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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104A HIS* 5.2 8.7 - - - -
107A GLU* 5.1 12.7 + - - +
108A ASP* 3.8 22.3 + - - +
111A LEU* 3.8 30.7 - - + +
127E GLN 3.7 16.9 + - - +
128E LEU* 3.5 19.1 + - + +
129E ALA 3.2 0.4 - - - -
130E ARG* 1.3 77.2 - - - +
132E ILE* 1.3 63.7 + - + +
133E ARG 3.6 0.2 + - - -
134E GLY* 3.6 10.3 + - - -
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Residues in contact with ILE 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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104A HIS* 5.5 1.9 + - - -
108A ASP* 3.7 36.8 - - + +
111A LEU* 5.9 0.7 - - + -
112A LEU* 3.8 28.3 - - + -
129A ALA* 4.3 10.1 - - - +
132A ILE* 3.8 35.9 - - + +
133A ARG* 3.6 40.0 + - + +
128E LEU* 3.5 17.7 - - + +
129E ALA 3.6 3.5 + - - +
130E ARG 3.5 0.2 - - - -
131E ARG* 1.3 76.4 - - + +
133E ARG* 1.3 63.1 + - - +
134E GLY* 4.6 0.3 - - - -
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Residues in contact with ARG 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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132A ILE* 3.5 27.4 + - + +
133A ARG* 5.6 1.8 - - - +
101E PHE* 3.6 26.0 - - - -
104E HIS* 3.4 23.4 + - - -
105E LEU* 3.5 27.5 - - - +
108E ASP* 2.4 37.0 + - - +
129E ALA 3.3 17.4 + - - +
130E ARG* 4.0 12.8 - - - +
131E ARG 3.3 0.4 - - - -
132E ILE* 1.3 78.9 - - - +
134E GLY* 1.3 61.3 + - - +
135E LEU* 4.6 9.4 - - + +
95F ARG* 4.5 14.4 - - - +
99G ARG* 5.9 3.5 - - - +
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Residues in contact with GLY 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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130E ARG 3.2 7.5 + - - -
131E ARG* 3.6 7.5 + - - -
132E ILE 3.4 3.0 - - - -
133E ARG* 1.3 80.0 - - - +
135E LEU* 1.3 60.0 + - - +
99G ARG* 6.5 0.9 - - - -
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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