Contacts of the helix formed by residues 126 - 139 (chain A) in PDB entry 3RS9
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 THR 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.6 12.8 + - + +
125A ILE* 1.3 77.9 - - - +
127A GLY* 1.3 70.5 + - - +
128A GLU 3.6 0.2 + - - -
129A TYR* 3.5 20.3 + - - +
130A ALA* 3.6 5.0 + - - -
161A ARG* 3.7 31.2 - - - +
493A BA3 5.2 4.2 + - - -
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Residues in contact with GLY 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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126A THR* 1.3 78.7 - - - +
128A GLU* 1.3 63.2 + - - -
130A ALA* 3.1 14.2 + - - +
131A GLU* 3.2 21.3 + - - +
161A ARG* 4.8 1.4 - - - +
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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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126A THR 3.6 0.4 + - - -
127A GLY* 1.3 70.9 - - - -
129A TYR* 1.3 66.2 - - + +
131A GLU* 3.8 18.0 - - + +
132A ILE* 3.0 38.3 + - + +
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Residues in contact with TYR 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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48A GLY* 5.6 2.2 - - - -
75A LEU* 3.1 45.7 + - + -
76A GLY* 3.6 13.1 - - - -
77A LYS* 4.6 6.1 + - + +
116A ILE* 3.9 15.8 - - + +
117A PHE* 3.4 28.6 - + + -
125A ILE* 3.6 19.7 - - + -
126A THR 3.5 8.4 + - - +
127A GLY 3.2 0.8 - - - -
128A GLU* 1.3 79.9 - - + +
130A ALA* 1.3 57.1 + - - +
132A ILE* 3.4 7.3 + - + +
133A ILE* 3.0 32.9 + - + +
493A BA3 3.6 32.8 + + - -
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Residues in contact with ALA 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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125A ILE* 3.6 4.0 - - - +
126A THR 3.6 9.4 + - - -
127A GLY 3.1 11.7 + - - +
129A TYR* 1.3 78.1 - - - +
131A GLU* 1.3 58.9 + - + +
133A ILE* 3.2 2.1 + - - +
134A ASN* 2.9 40.7 + - - +
161A ARG* 3.4 28.9 - - - +
162A THR* 3.8 20.6 - - + +
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Residues in contact with GLU 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 GLY* 3.2 17.9 + - - +
128A GLU* 3.4 18.8 + - - +
130A ALA* 1.3 72.2 - - + +
132A ILE* 1.3 62.1 + - + +
134A ASN* 3.4 8.6 + - - +
135A LEU* 2.9 44.5 + - + +
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Residues in contact with ILE 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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46A LEU* 4.1 17.9 - - + -
75A LEU* 3.3 42.8 - - + -
101A PHE* 3.3 48.2 - - + -
116A ILE* 4.6 4.7 - - + -
128A GLU* 3.0 25.0 + - + +
129A TYR* 3.7 7.0 - - + +
131A GLU* 1.3 78.8 - - + +
133A ILE* 1.3 58.1 + - - +
135A LEU* 3.3 9.7 + - + +
136A VAL* 2.8 34.3 + - - +
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Residues in contact with ILE 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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116A ILE* 4.2 16.6 - - + -
117A PHE* 4.9 3.6 - - + -
125A ILE* 3.7 35.7 - - + -
129A TYR 3.0 20.5 + - - +
130A ALA 3.2 4.0 + - - +
132A ILE* 1.3 75.2 - - - +
134A ASN* 1.3 57.5 + - - +
136A VAL* 3.3 7.6 + - - +
137A ASN* 3.0 32.4 + - - +
150A SER* 4.1 17.7 - - - +
162A THR* 4.0 13.7 - - + +
163A ALA 3.5 31.9 - - - +
164A VAL* 3.6 16.4 - - + +
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Residues in contact with ASN 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 ALA* 2.9 29.4 + - - +
131A GLU* 3.8 7.7 - - - +
133A ILE* 1.3 77.9 - - - +
135A LEU* 1.3 61.3 + - + +
137A ASN* 3.4 10.3 + - - +
138A LYS* 3.0 44.0 + - - +
161A ARG* 5.6 1.6 - - - +
162A THR* 2.9 28.0 + - - +
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Residues in contact with LEU 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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101A PHE* 3.8 25.6 - - + -
103A PRO* 4.3 29.2 - - + +
106A LEU* 3.4 23.8 - - + +
131A GLU* 2.9 33.8 + - + +
132A ILE* 3.5 4.7 - - + +
134A ASN* 1.3 72.9 - - + +
136A VAL* 1.3 64.8 + - - +
138A LYS* 3.2 22.5 + - + +
139A SER* 3.3 8.3 + - - -
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Residues in contact with VAL 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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46A LEU* 3.7 29.4 - - + -
101A PHE* 4.7 3.4 - - + -
106A LEU* 4.1 14.6 - - + -
112A VAL* 4.2 18.6 - - + -
114A ASP* 6.2 0.7 - - + -
132A ILE* 2.8 27.4 + - + +
133A ILE* 3.3 7.4 + - - +
135A LEU* 1.3 71.7 - - - +
137A ASN* 1.3 63.1 + - - +
139A SER* 2.6 31.3 + - - -
140A GLY 4.4 0.5 + - - -
143A VAL* 3.9 32.5 - - + +
164A VAL* 4.9 8.7 - - + -
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Residues in contact with ASN 137 (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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133A ILE* 3.0 24.9 + - - +
134A ASN* 3.7 11.6 + - - +
135A LEU 3.4 0.2 - - - -
136A VAL* 1.3 77.4 - - - +
138A LYS* 1.3 59.9 + - + +
139A SER 3.3 0.6 + - - -
140A GLY 4.7 2.1 + - - -
143A VAL* 6.1 0.9 - - - -
162A THR* 4.7 2.0 + - - -
163A ALA 2.9 24.9 + - - -
164A VAL* 3.6 6.8 - - - +
165A LYS* 2.9 36.8 + - + +
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Residues in contact with LYS 138 (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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134A ASN* 3.0 34.7 + - - +
135A LEU* 3.2 15.6 + - + +
137A ASN* 1.3 76.7 - - + +
139A SER* 1.3 62.0 + - - +
140A GLY 3.4 2.6 + - - -
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Residues in contact with SER 139 (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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106A LEU* 3.7 22.9 - - - +
135A LEU 3.3 10.3 + - - -
136A VAL* 2.6 24.4 + - - +
137A ASN 3.3 0.2 - - - -
138A LYS* 1.3 78.8 - - - +
140A GLY* 1.3 61.9 + - - +
141A LYS* 3.2 39.6 + - - +
143A VAL* 5.3 0.5 - - - +
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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