Contacts of the helix formed by residues 126 - 136 (chain A) in PDB entry 1LE9
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 LEU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PRO* 4.3 17.9 - - + -
121A VAL* 4.3 11.7 - - + -
122A LYS 4.1 1.3 - - - +
123A LYS* 3.1 48.6 + - + +
124A ARG 3.2 1.8 + - - -
125A ASP* 1.3 71.0 - - - +
127A GLU* 1.3 72.2 + - - +
128A GLN 3.0 1.1 - - - -
129A ALA* 2.7 16.1 + - - +
130A ILE* 2.8 20.8 + - + +
150A GLY 5.0 11.2 - - - +
151A ASP* 6.3 0.4 - - - -
152A TYR* 5.2 11.9 - - + +
154A LEU* 3.8 29.6 - - + -
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Residues in contact with GLU 127 (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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124A ARG 4.7 3.1 + - - +
126A LEU* 1.3 81.0 - - - +
128A GLN* 1.3 59.1 + - + +
130A ILE* 3.2 9.4 - - - +
131A SER* 2.7 40.5 + - - -
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Residues in contact with GLN 128 (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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124A ARG* 3.8 13.1 - - - +
125A ASP* 3.0 38.9 - - + +
127A GLU* 1.3 84.6 - - + +
129A ALA* 1.3 52.0 + - - +
131A SER* 2.9 10.4 + - - -
132A GLN* 2.8 36.1 + - - +
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Residues in contact with ALA 129 (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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87A PRO* 4.3 10.3 - - + -
89A GLU* 5.4 1.3 - - - +
121A VAL* 4.3 17.5 - - + -
125A ASP 3.3 18.7 + - - +
126A LEU* 2.7 16.7 + - - +
128A GLN* 1.3 75.6 - - - +
130A ILE* 1.3 58.3 + - - +
132A GLN* 3.4 12.1 - - - +
133A ARG* 2.5 41.2 + - - +
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Residues in contact with ILE 130 (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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85A PRO 4.2 6.5 - - - +
87A PRO* 4.8 9.8 - - + +
126A LEU* 2.8 21.4 + - + +
127A GLU* 3.2 16.4 - - - +
129A ALA* 1.3 69.3 - - - +
131A SER* 1.3 58.0 - - - +
132A GLN 2.7 6.7 + - - -
133A ARG* 2.6 49.6 + - + +
134A ILE* 3.3 6.2 + - + +
148A GLN* 3.0 54.7 - - + +
149A ARG* 5.4 3.4 - - + -
152A TYR* 3.5 23.6 - - + +
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Residues in contact with SER 131 (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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127A GLU* 2.7 26.0 + - - -
128A GLN* 2.9 13.0 + - - -
130A ILE* 1.3 77.8 - - - +
132A GLN* 1.3 56.4 + - - +
134A ILE* 3.5 20.3 - - - +
135A GLN* 3.5 22.6 + - - +
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Residues in contact with GLN 132 (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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89A GLU* 3.8 17.2 + - - +
97A ASP* 2.4 43.9 - - - +
128A GLN 2.8 7.5 + - - +
129A ALA* 3.4 13.4 + - - +
130A ILE 2.8 0.4 - - - -
131A SER* 1.3 74.6 - - - +
133A ARG* 1.3 74.9 + - - +
134A ILE 2.8 2.3 + - - -
135A GLN* 3.1 12.9 + - + +
136A THR* 2.7 41.5 + - + +
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Residues in contact with ARG 133 (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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85A PRO* 4.0 25.1 - - + +
86A HIS 3.6 11.5 + - - +
87A PRO* 2.6 28.6 + - - -
88A HIS 3.2 13.9 + - - -
89A GLU* 3.3 36.2 + - - +
97A ASP 4.5 5.8 - - - -
98A GLY* 3.7 10.9 - - - -
129A ALA* 2.5 44.1 + - - +
130A ILE* 2.6 36.9 + - + +
132A GLN* 1.3 82.0 - - - +
134A ILE* 1.3 55.4 + - - +
136A THR* 3.5 2.8 - - - +
137A ASN 3.1 5.2 + - - -
138A ASN* 2.7 52.9 + - + +
148A GLN* 4.6 0.4 - - - +
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Residues in contact with ILE 134 (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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130A ILE* 3.3 6.3 + - + +
131A SER* 3.5 25.1 - - - +
132A GLN 2.8 3.6 + - - -
133A ARG* 1.3 71.1 - - - +
135A GLN* 1.3 67.5 + - + +
136A THR 2.5 5.9 + - - -
137A ASN* 2.4 36.8 + - - +
138A ASN 4.8 0.4 - - - +
145A ILE* 3.8 34.8 - - + -
148A GLN* 3.5 37.9 - - + +
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Residues in contact with GLN 135 (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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131A SER* 3.5 19.0 + - - +
132A GLN* 3.1 15.0 + - + +
134A ILE* 1.3 81.9 - - + +
136A THR* 1.3 60.2 + - - +
137A ASN* 5.5 1.3 - - - -
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Residues in contact with THR 136 (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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73A ARG* 4.6 1.9 + - - -
97A ASP* 3.7 32.5 + - + +
99A TYR* 4.6 9.3 - - + -
132A GLN* 2.7 43.7 + - + +
133A ARG* 3.5 12.1 - - - +
134A ILE 2.5 4.9 + - - -
135A GLN* 1.3 75.3 - - - +
137A ASN* 1.3 73.0 + - - +
138A ASN* 4.3 10.8 - - + +
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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