Contacts of the helix formed by residues 115 - 126 (chain A) in PDB entry 1LTQ
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 PRO 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASP 4.2 3.8 - - - +
114A VAL* 1.3 92.0 - - + +
116A TRP* 1.3 57.3 + - - +
117A THR* 4.3 15.7 - - + -
118A GLU* 2.7 35.4 + - + +
119A LEU* 2.9 9.6 + - - +
140A TYR* 5.0 3.6 - - - +
253A LYS* 6.5 0.4 - - + -
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Residues in contact with TRP 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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114A VAL 3.5 2.8 + - - -
115A PRO* 1.3 69.4 - - - +
117A THR* 1.3 62.9 + - - +
119A LEU* 2.9 11.2 + - + +
120A VAL* 2.9 50.8 + - + +
133A ILE* 4.5 12.8 - - + -
136A LEU* 3.7 21.8 - - + -
137A ARG* 3.4 42.8 - - + -
140A TYR* 3.6 47.6 + + + +
255A ASP* 5.0 9.2 + - - +
280A THR* 6.1 1.8 - - - +
281A GLN* 5.1 9.0 - - + +
284A GLU* 3.3 37.1 + - + +
288A ARG* 3.2 30.1 - - - +
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Residues in contact with THR 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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115A PRO* 3.0 13.9 + - + -
116A TRP* 1.3 85.6 - - - +
118A GLU* 1.3 64.9 + - + +
120A VAL* 4.0 5.2 - - - +
121A LYS* 3.1 27.5 + - - +
253A LYS* 4.1 34.2 + - + +
255A ASP* 4.4 15.9 + - - +
281A GLN* 4.5 15.7 + - - +
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Residues in contact with GLU 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 VAL* 3.3 17.5 - - + -
115A PRO* 2.7 25.8 + - + +
117A THR* 1.3 79.8 - - + +
119A LEU* 1.3 64.5 + - - +
121A LYS* 3.7 15.6 + - - +
122A ARG* 2.6 74.8 + - - +
900A ADP 4.9 4.3 - - - -
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Residues in contact with LEU 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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10A CYS* 3.6 36.6 - - + -
11A PRO 3.8 21.3 - - - +
12A GLY* 4.4 2.6 - - - +
13A SER* 4.3 13.0 - - - +
114A VAL* 3.9 28.3 - - + +
115A PRO 2.9 13.6 + - - +
116A TRP* 3.4 12.6 - - + +
118A GLU* 1.3 77.5 - - - +
120A VAL* 1.3 58.0 + - - +
122A ARG* 3.9 3.5 - - - +
123A ASN* 2.8 32.7 + - - +
136A LEU* 4.3 15.7 - - + +
140A TYR* 3.7 22.7 - - + -
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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 TRP* 2.9 57.6 + - + +
117A THR* 4.0 5.4 - - - +
119A LEU* 1.3 72.8 - - - +
121A LYS* 1.3 67.7 + - - +
123A ASN* 3.2 2.8 + - - +
124A SER* 2.9 27.3 + - - -
133A ILE* 5.7 9.4 - - + -
136A LEU* 4.2 14.1 - - + -
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Residues in contact with LYS 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 THR 3.1 17.0 + - - +
118A GLU* 3.7 20.6 - - - +
119A LEU 3.4 0.2 - - - -
120A VAL* 1.3 80.6 - - - +
122A ARG* 1.3 64.5 + - + +
124A SER* 2.7 27.1 + - - +
125A LYS* 3.1 44.8 + - - +
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Residues in contact with ARG 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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12A GLY* 2.9 31.8 + - - +
13A SER* 3.7 17.4 + - - +
114A VAL* 3.9 20.4 - - - +
118A GLU* 2.6 48.6 + - - +
119A LEU* 3.9 3.4 - - - +
121A LYS* 1.3 79.8 - - + +
123A ASN* 1.3 64.0 + - - +
125A LYS* 3.0 19.0 + - - +
126A ARG* 3.2 15.0 + - - +
900A ADP 3.2 74.2 + - + +
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Residues in contact with ASN 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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11A PRO* 5.6 5.2 + - - +
12A GLY* 6.0 2.0 - - - -
119A LEU 2.8 22.6 + - - +
120A VAL* 3.6 3.8 - - - +
122A ARG* 1.3 72.6 - - - +
124A SER* 1.3 63.1 + - - +
125A LYS 3.1 1.1 + - - -
126A ARG* 3.2 20.9 + - - +
129A LYS 4.7 0.6 + - - -
130A ALA* 3.3 19.5 - - - +
131A VAL* 2.8 53.5 + - - +
132A PRO 5.1 0.3 - - - -
133A ILE* 5.2 1.7 + - - -
136A LEU* 4.2 25.6 - - + +
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Residues in contact with SER 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 16.2 + - - -
121A LYS* 2.7 25.2 + - - +
123A ASN* 1.3 77.7 + - - +
125A LYS* 1.3 63.2 + - - +
126A ARG 3.5 0.4 - - - -
127A GLY 4.9 1.8 + - - -
130A ALA* 5.5 1.3 - - - -
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Residues in contact with LYS 125 (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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121A LYS* 3.1 41.3 - - - +
122A ARG* 3.0 11.2 + - - +
124A SER* 1.3 86.5 - - - +
126A ARG* 1.3 58.2 + - - +
127A GLY* 2.9 13.5 + - - -
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Residues in contact with ARG 126 (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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11A PRO* 4.5 9.7 - - - +
12A GLY* 3.3 13.2 - - - +
122A ARG 3.2 16.8 + - - +
123A ASN* 3.2 23.8 + - - +
125A LYS* 1.3 76.2 - - - +
127A GLY* 1.3 62.2 + - - +
128A THR* 3.4 0.9 + - - +
129A LYS* 3.2 55.8 + - - +
130A ALA* 3.5 16.8 - - - +
131A VAL* 6.2 0.2 - - - +
900A ADP 2.6 84.6 + - - -
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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