Contacts of the helix formed by residues 124 - 136 (chain A) in PDB entry 1TYG
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 SER 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.3 6.4 + - - +
123A PRO* 1.3 81.4 - - - +
125A PHE* 1.3 65.7 + - - +
126A ASP* 3.6 9.1 + - - +
127A ILE* 3.2 32.2 + - - +
128A GLN* 3.1 21.2 + - - +
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Residues in contact with PHE 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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122A TYR* 6.1 2.2 - - + -
124A SER* 1.3 71.3 - - - +
126A ASP* 1.3 61.8 + - - +
127A ILE 3.0 4.7 - - - -
128A GLN* 3.2 25.3 - - - +
129A LYS* 2.9 36.0 + - - +
155A PRO* 3.5 49.8 - - + -
156A ASN* 4.5 0.4 - - - -
157A PHE* 4.7 14.9 - + + -
160A GLN* 3.6 22.9 - - - +
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Residues in contact with ASP 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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124A SER* 3.3 9.7 + - - +
125A PHE* 1.3 80.4 - - - +
127A ILE* 1.3 58.3 + - + +
129A LYS* 4.4 4.3 - - - -
130A GLU* 3.1 28.6 - - - +
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Residues in contact with ILE 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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122A TYR* 5.2 0.7 - - + -
123A PRO* 3.6 27.6 - - + -
124A SER* 3.2 25.2 + - - +
125A PHE 3.0 0.4 - - - -
126A ASP* 1.3 78.9 - - + +
128A GLN* 1.3 58.2 + - - +
129A LYS 3.3 1.6 - - - -
130A GLU* 3.7 4.0 - - - +
131A ALA* 2.7 32.6 + - - +
315A ASP* 5.8 0.4 - - - +
316A PRO* 3.9 36.1 - - + -
317A VAL* 4.2 12.1 - - + -
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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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119A THR* 2.8 43.5 + - - -
122A TYR* 3.5 40.4 - - + +
124A SER 3.1 13.5 + - - +
125A PHE* 3.2 26.9 - - - +
127A ILE* 1.3 74.9 - - - +
129A LYS* 1.3 58.0 + - - +
131A ALA* 4.1 0.3 - - - +
132A VAL* 3.0 38.6 + - + +
157A PHE* 3.1 39.3 - - + +
64B GLY* 5.2 1.2 - - - -
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Residues in contact with LYS 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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125A PHE 2.9 16.7 + - - +
126A ASP* 4.7 4.9 - - - +
128A GLN* 1.3 77.6 - - - +
130A GLU* 1.3 64.9 + - + +
132A VAL* 3.9 2.9 - - - +
133A ALA* 3.3 20.3 + - - +
157A PHE* 3.7 19.2 - - + -
160A GLN* 5.6 6.5 - - + +
166A TYR* 5.4 0.5 + - - -
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Residues in contact with GLU 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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126A ASP 3.1 23.5 - - - +
127A ILE* 3.3 4.0 + - - +
128A GLN 3.2 0.4 - - - -
129A LYS* 1.3 81.3 - - + +
131A ALA* 1.3 63.7 + - - +
132A VAL 3.2 0.2 - - - -
133A ALA* 3.6 5.7 + - - +
134A VAL* 3.2 28.2 + - - +
317A VAL* 3.7 15.0 - - + +
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Residues in contact with ALA 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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117A LEU* 4.8 1.3 - - + -
122A TYR* 3.9 23.6 - - + -
127A ILE 2.7 22.4 + - - +
128A GLN 4.1 0.4 - - - +
130A GLU* 1.3 71.4 - - - +
132A VAL* 1.3 59.2 - - - +
134A VAL* 3.6 0.8 + - - -
135A SER* 3.0 28.9 + - - -
310A VAL* 4.5 1.3 - - + -
316A PRO* 4.2 4.9 - - + -
317A VAL* 3.5 29.1 - - + +
320A ALA* 3.4 12.2 - - + +
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Residues in contact with VAL 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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117A LEU* 3.5 20.6 - - + -
118A GLY 5.0 0.2 - - - +
119A THR* 4.7 4.0 - - + -
122A TYR* 4.9 3.4 - - - +
128A GLN* 3.0 30.6 + - + +
129A LYS 3.9 4.5 - - - +
130A GLU 3.2 0.2 - - - -
131A ALA* 1.3 75.8 - - - +
133A ALA* 1.3 62.5 + - - +
135A SER* 2.6 24.0 + - - -
136A GLU* 3.5 2.4 + - - -
137A SER 4.1 2.9 + - - -
140A LEU* 3.5 32.8 - - + -
157A PHE* 4.1 17.9 - - + -
161A LEU* 4.9 0.7 - - + -
166A TYR* 3.4 27.1 + - + +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LYS 3.3 12.0 + - - +
130A GLU* 3.7 9.2 - - - +
132A VAL* 1.3 76.0 - - - +
134A VAL* 1.3 69.4 + - + +
136A GLU* 2.9 22.3 + - - +
166A TYR* 4.0 10.9 + - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 3.2 18.4 + - - +
131A ALA 4.0 2.0 - - - +
132A VAL 3.4 0.2 - - - -
133A ALA* 1.3 82.1 - - + +
135A SER* 1.3 58.4 + - - +
136A GLU* 5.0 0.2 - - - -
317A VAL* 3.7 25.8 - - + +
320A ALA* 4.1 1.6 - - + -
321A ARG* 3.3 45.3 - - + +
324A LYS* 2.9 33.1 + - - +
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Residues in contact with SER 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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113A SER* 4.7 1.0 + - - -
115A LEU* 3.7 24.9 - - - +
117A LEU* 3.8 14.1 - - - +
131A ALA 3.0 15.9 + - - -
132A VAL 2.6 19.1 + - - -
133A ALA 3.0 1.0 + - - -
134A VAL* 1.3 76.1 - - - +
136A GLU* 1.3 68.1 + - - +
137A SER* 3.1 18.2 - - - -
320A ALA* 4.2 19.1 - - - -
324A LYS* 3.7 14.7 - - - +
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Residues in contact with GLU 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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113A SER* 3.0 24.8 + - - -
132A VAL 3.5 1.1 + - - -
133A ALA 2.9 16.8 + - - +
134A VAL 3.7 2.2 - - - +
135A SER* 1.3 77.6 + - - +
137A SER* 1.3 59.7 + - - +
138A ASP* 3.9 2.2 + - - +
324A LYS* 3.5 40.3 + - + +
328A GLU* 5.2 3.8 - - - +
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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