Contacts of the helix formed by residues 121 - 135 (chain A) in PDB entry 4JGH
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.7 7.6 - - - +
42A GLU* 2.8 40.6 + - - +
104A PHE* 3.7 2.4 - - - -
119A PHE* 3.9 3.1 - - - +
120A ASP* 1.3 80.2 - - - +
122A VAL* 1.3 66.6 + - - +
123A VAL* 3.2 8.8 + - - +
124A HIS* 2.9 28.4 + - - +
125A LEU* 3.0 12.8 + - - +
196A PHE* 5.3 2.0 - - - -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 3.1 28.9 - - + +
40A LEU* 4.8 0.9 - - - +
43A LEU* 3.8 26.2 - - + -
72A ILE* 4.7 3.4 - - + -
82A LEU* 4.0 20.2 - - + -
97A ILE* 4.0 32.3 - - + -
104A PHE* 3.5 25.7 - - + -
121A SER* 1.3 72.3 + - - +
123A VAL* 1.3 62.2 + - - +
125A LEU* 3.4 7.4 - - + +
126A ILE* 3.2 24.5 + - + +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.9 18.2 - - + +
43A LEU* 3.7 39.7 - - + -
46A THR* 3.8 14.8 - - + -
48A TRP* 3.6 23.2 - - + -
121A SER* 3.0 6.7 - - - +
122A VAL* 1.3 77.1 - - + +
124A HIS* 1.3 63.9 + - - +
125A LEU 3.2 0.4 - - - -
126A ILE* 3.6 1.4 + - - +
127A ASP* 3.1 22.2 + - - +
194A TYR* 4.0 1.3 - - + +
196A PHE* 3.3 30.7 - - + -
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Residues in contact with HIS 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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116A LEU* 5.0 8.2 - - + +
119A PHE* 3.3 38.2 - + + -
120A ASP* 4.8 5.6 - - + -
121A SER* 2.9 26.5 + - - +
123A VAL* 1.3 76.2 - - - +
125A LEU* 1.3 67.9 + - - +
127A ASP* 3.5 3.7 + - + +
128A TYR* 3.1 23.6 + + + +
196A PHE* 3.8 27.1 - + + -
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Residues in contact with LEU 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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84A ILE* 5.1 1.1 - - + -
97A ILE* 4.6 12.1 - - + -
104A PHE* 3.8 34.3 - - + +
105A ARG* 3.9 16.8 - - - +
106A LEU* 4.1 12.8 - - + +
119A PHE* 3.5 30.0 - - + -
121A SER 3.0 10.1 + - - +
122A VAL* 3.4 10.3 - - + +
124A HIS* 1.3 74.1 - - - +
126A ILE* 1.3 86.6 + - + +
127A ASP 3.0 1.0 + - - -
128A TYR* 3.1 13.3 + - - +
129A TYR* 3.2 33.0 + - + -
152A LEU* 4.9 0.2 - - + -
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Residues in contact with ILE 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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48A TRP* 3.6 34.5 - - + -
70A PHE* 3.4 34.1 - - + -
72A ILE* 3.9 15.3 - - + -
84A ILE* 3.5 31.4 - - + -
97A ILE* 5.2 0.9 - - + -
122A VAL* 3.2 16.9 + - + +
123A VAL 4.0 0.4 - - - +
124A HIS 3.5 0.2 - - - -
125A LEU* 1.3 89.0 - - + +
127A ASP* 1.3 61.6 + - - +
129A TYR* 3.7 1.0 + - - +
130A VAL* 2.9 34.4 + - + +
152A LEU* 4.1 12.5 - - + +
198A VAL* 4.9 1.3 - - + -
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 5.2 0.6 - - + -
123A VAL 3.1 18.4 + - - +
124A HIS* 3.7 5.8 + - + +
125A LEU 3.0 1.0 + - - -
126A ILE* 1.3 73.6 - - - +
128A TYR* 1.3 68.2 + - - +
130A VAL* 3.0 6.6 + - - +
131A GLN* 2.9 43.9 + - - +
195A LYS 4.9 0.3 - - - +
196A PHE* 3.4 42.8 - - + -
197A GLN* 3.6 14.4 + - - +
198A VAL* 3.9 14.7 - - + +
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Residues in contact with TYR 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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114A SER* 4.2 5.7 - - - -
115A LYS* 3.7 17.1 + - + +
116A LEU* 3.6 48.6 + - + -
119A PHE* 3.5 34.1 - + + -
124A HIS* 3.1 13.3 + + + +
125A LEU 3.1 4.3 + - - +
127A ASP* 1.3 81.1 - - - +
129A TYR* 1.3 78.5 + + - +
131A GLN* 3.1 9.0 + - - +
132A MET* 3.1 59.5 + - + +
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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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106A LEU* 3.4 39.4 + - + +
112A VAL* 3.7 19.2 - - + +
114A SER* 3.9 17.9 - - - -
116A LEU 3.6 12.0 + - - -
117A LYS* 3.8 12.5 + - - +
119A PHE* 3.7 17.9 - + - -
125A LEU* 3.2 36.7 + - + +
126A ILE 4.1 0.2 - - - +
128A TYR* 1.3 92.7 - + - +
130A VAL* 1.3 56.5 + - - +
132A MET* 4.4 5.6 - - + -
133A CYS* 2.7 40.8 + - + +
152A LEU* 3.6 23.1 - - + -
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Residues in contact with VAL 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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70A PHE* 3.7 30.1 - - + -
126A ILE* 2.9 30.1 + - + +
127A ASP* 3.0 9.5 + - - +
129A TYR* 1.3 75.5 - - - +
131A GLN* 1.3 59.8 + - + +
134A LYS* 2.8 35.0 + - + +
152A LEU* 3.0 19.3 - - + +
153A THR* 3.4 22.0 - - - +
198A VAL* 4.4 20.0 - - + -
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Residues in contact with GLN 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 ASP* 2.9 35.5 + - - +
128A TYR* 3.4 9.2 - - - +
130A VAL* 1.3 76.9 - - + +
132A MET* 1.3 84.5 + - + +
134A LYS* 4.4 0.6 - - - +
135A ASP* 3.1 24.8 + - - +
197A GLN* 3.1 44.2 + - + +
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Residues in contact with MET 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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114A SER* 6.2 0.4 - - - -
128A TYR* 3.1 56.0 + - + +
129A TYR* 3.8 7.4 - - + +
131A GLN* 1.3 99.5 - - + +
133A CYS* 1.3 69.0 + - - +
135A ASP* 3.0 26.1 + - - +
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Residues in contact with CYS 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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129A TYR* 2.7 24.5 + - + +
132A MET* 1.3 74.8 - - - +
134A LYS* 1.3 60.7 + - - +
135A ASP 4.2 3.8 - - - +
150A LEU 5.0 2.5 - - - +
151A TYR* 4.1 25.5 - - + -
152A LEU* 3.5 28.7 - - + +
153A THR* 4.4 3.2 - - - +
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Residues in contact with LYS 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 VAL* 2.8 25.8 + - + +
131A GLN* 4.4 0.9 - - - +
133A CYS* 1.3 78.7 - - - +
135A ASP* 1.3 64.0 + - - +
153A THR* 3.6 31.9 - - + +
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Residues in contact with ASP 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 GLN 3.1 18.4 + - - +
132A MET* 3.0 15.1 + - - +
133A CYS 4.2 3.4 - - - +
134A LYS* 1.3 85.1 - - - +
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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