Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 3TR6
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A VAL* 4.4 13.9 - - + -
120A SER* 1.3 92.4 + - - +
122A ALA* 1.3 60.7 + - - +
123A LYS* 4.3 8.1 - - + +
124A ASP* 2.9 43.1 + - - +
125A THR* 3.2 9.2 + - - -
224A SAH 3.6 20.0 - - - +
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Residues in contact with ALA 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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68A ILE* 3.8 23.6 - - + -
92A CYS* 4.2 11.2 - - + -
120A SER 3.1 3.0 + - - -
121A PRO* 1.3 71.4 - - - +
123A LYS* 1.3 63.5 - - - +
125A THR* 3.7 7.4 - - - -
126A LEU* 2.9 32.8 + - + +
153A TYR* 3.7 25.6 - - + +
224A SAH 3.0 20.2 + - + +
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Residues in contact with LYS 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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121A PRO* 4.6 8.5 - - + -
122A ALA* 1.3 78.4 - - - +
124A ASP* 1.3 69.6 + - - +
126A LEU* 4.0 4.0 - - - +
127A ALA* 3.3 23.0 + - - +
149A ASN* 5.4 7.0 - - - +
152A LEU* 3.7 30.3 - - + -
153A TYR* 3.7 15.4 + - + +
156A GLU* 5.0 3.5 - - - +
224A SAH 6.1 0.4 - - - +
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Residues in contact with ASP 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 SER* 3.9 8.4 - - - +
121A PRO* 2.9 36.0 + - - +
123A LYS* 1.3 89.1 - - - +
125A THR* 1.3 60.2 + - - +
127A ALA* 3.2 5.3 + - - +
128A GLU* 2.9 43.9 + - + +
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Residues in contact with THR 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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90A ILE* 4.9 1.8 - - + -
92A CYS* 3.9 19.9 - - - -
118A ARG* 3.8 38.9 + - + +
120A SER* 3.4 21.0 + - - -
121A PRO 3.2 4.9 + - - -
122A ALA* 3.2 7.1 + - - -
124A ASP* 1.3 77.4 - - - +
126A LEU* 1.3 58.5 + - + +
128A GLU* 3.5 14.4 + - - +
129A LEU* 3.1 41.7 + - + +
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Residues in contact with LEU 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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66A ILE* 4.4 19.7 - - + -
68A ILE* 4.0 30.3 - - + -
92A CYS* 5.3 2.0 - - - -
122A ALA* 2.9 18.0 + - + +
123A LYS* 4.0 4.5 - - - +
125A THR* 1.3 81.5 - - + +
127A ALA* 1.3 61.9 + - - +
129A LEU* 3.5 8.2 + - + +
130A ILE* 3.2 28.6 + - - +
141A ILE* 5.8 0.4 - - + -
153A TYR* 4.0 24.0 - - + +
156A GLU* 3.7 35.7 - - + +
157A SER* 4.7 3.6 - - - +
160A LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 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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123A LYS 3.3 16.8 + - - +
124A ASP* 3.2 7.4 + - - +
126A LEU* 1.3 76.5 - - - +
128A GLU* 1.3 60.8 + - + +
130A ILE* 3.8 3.5 - - - +
131A HIS* 2.8 51.8 + - + +
156A GLU* 4.2 11.4 + - - +
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Residues in contact with GLU 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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118A ARG* 6.2 0.2 - - - -
124A ASP* 2.9 32.9 + - + +
125A THR* 3.7 12.5 + - - +
127A ALA* 1.3 76.5 - - - +
129A LEU* 1.3 65.0 + - + +
131A HIS* 3.5 4.4 - - - -
132A ALA* 2.9 30.0 + - + +
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Residues in contact with LEU 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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66A ILE* 3.8 19.1 - - + -
90A ILE* 3.7 28.5 - - + -
118A ARG* 6.2 1.6 - - - +
125A THR* 3.1 24.2 + - + +
126A LEU* 3.6 14.8 - - + +
127A ALA 3.3 0.2 - - - -
128A GLU* 1.3 80.7 - - + +
130A ILE* 1.3 60.0 + - - +
132A ALA* 3.4 5.3 + - + -
134A GLN* 3.0 42.2 + - + +
138A TYR* 3.5 23.1 - - + +
160A LEU* 3.8 10.5 - - + -
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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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126A LEU 3.2 13.7 + - - +
127A ALA* 3.8 4.5 - - - +
129A LEU* 1.3 72.8 - - - +
131A HIS* 1.3 65.3 + - + +
132A ALA 2.7 15.2 + - - -
133A GLY* 2.8 15.9 + - - -
134A GLN 4.0 3.3 + - - +
135A ALA* 4.8 14.8 + - + +
156A GLU* 3.4 32.5 - - - +
159A LYS* 3.8 36.3 - - + -
160A LEU* 3.9 18.8 - - + -
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Residues in contact with HIS 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 ALA* 2.8 37.2 + - + +
128A GLU* 3.5 4.0 - - - +
130A ILE* 1.3 81.8 - - + +
132A ALA* 1.3 56.8 + - - +
133A GLY 3.6 0.4 - - - -
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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