Contacts of the helix formed by residues 119 - 132 (chain A) in PDB entry 1XZQ
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 ASP 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.8 7.3 - - - -
118A MET* 1.3 82.4 - - - +
120A LEU* 1.3 59.5 + - - +
121A THR* 2.3 48.0 + - - +
122A SER* 3.1 25.5 + - - -
123A ALA* 3.5 8.0 + - - +
144A ASN 5.0 0.2 - - - +
147A GLY* 5.3 0.5 - - - -
150A ARG* 3.6 34.9 + - + +
430A THR* 3.2 27.3 - - - +
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Residues in contact with LEU 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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113A PHE* 3.8 17.0 - - + -
119A ASP* 1.3 71.7 - - - +
121A THR* 1.3 64.4 + - - +
122A SER 3.3 0.7 - - - -
123A ALA* 3.7 9.2 - - + -
124A GLU* 3.0 34.8 + - + +
387A ARG* 3.1 33.4 - - - +
428A GLU 4.1 5.4 - - - +
429A VAL 3.5 7.4 - - - +
430A THR 2.8 20.3 + - - +
431A GLY* 4.0 6.5 - - - -
434A PHE* 5.8 2.5 - - + -
438A LEU* 6.0 1.3 - - + -
439A LEU* 4.6 14.8 - - + -
442A ILE* 4.0 23.8 - - + -
443A PHE* 5.1 4.3 - - + -
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Residues in contact with THR 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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119A ASP* 2.3 38.0 + - - +
120A LEU* 1.3 73.0 - - - +
122A SER* 1.3 58.2 + - - +
124A GLU* 3.4 12.8 + - - +
125A ALA* 3.4 18.2 + - - +
144A ASN* 4.0 14.2 + - - +
149A LEU* 3.6 33.0 - - + +
150A ARG* 3.9 14.0 + - - +
387A ARG* 4.5 1.3 - - - +
388A GLN* 3.9 14.7 + - + +
429A VAL* 3.5 25.6 - - + +
430A THR* 4.6 2.5 - - + -
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Residues in contact with SER 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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118A MET* 3.2 22.6 - - - +
119A ASP* 3.1 24.5 + - - -
121A THR* 1.3 78.5 + - - +
123A ALA* 1.3 70.1 + - - +
124A GLU 3.2 0.4 - - - -
125A ALA* 3.1 13.2 + - - +
126A VAL* 3.2 15.3 + - - +
144A ASN 3.5 22.0 - - - -
145A LEU* 4.1 16.3 - - - +
147A GLY* 5.3 1.8 - - - -
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Residues in contact with ALA 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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109A THR* 4.0 17.9 - - + -
113A PHE* 5.2 5.2 - - + -
118A MET* 4.0 13.5 - - + -
119A ASP 3.5 11.8 + - - +
120A LEU* 3.4 13.4 + - + +
121A THR 3.4 0.2 - - - -
122A SER* 1.3 81.7 + - - +
124A GLU* 1.3 61.8 + - - +
126A VAL* 3.1 23.5 + - - +
442A ILE* 6.3 0.4 - - + -
443A PHE* 4.2 16.8 - - + -
446A PHE* 3.6 12.4 - - - -
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Residues in contact with GLU 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 LEU* 3.0 30.6 + - + +
121A THR* 3.4 6.3 - - - +
122A SER 3.2 0.2 - - - -
123A ALA* 1.3 78.7 - - - +
125A ALA* 1.3 58.0 + - - +
127A ARG* 3.6 7.4 + - - +
128A ASP* 3.2 29.4 + - - +
385A ASN* 3.4 23.4 + - - +
387A ARG* 3.0 41.5 + - - +
388A GLN* 3.1 19.2 + - - +
442A ILE* 4.1 16.8 - - + +
446A PHE* 4.9 6.1 - - - -
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Residues in contact with ALA 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 THR 3.4 12.5 + - - +
122A SER 3.1 10.1 + - - +
124A GLU* 1.3 75.6 - - - +
126A VAL* 1.3 60.9 + - - +
128A ASP* 4.3 8.1 - - - -
129A LEU* 2.8 33.4 + - - +
141A SER* 3.4 28.8 - - - +
144A ASN* 4.0 6.7 - - + -
145A LEU* 3.8 18.4 - - + +
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Residues in contact with VAL 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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71A TYR* 4.4 12.8 - - + +
109A THR* 4.1 11.4 - - + +
118A MET* 4.8 6.7 - - - -
122A SER 3.2 15.1 + - - +
123A ALA* 3.1 14.1 + - - +
125A ALA* 1.3 77.5 - - - +
127A ARG* 1.3 64.2 + - - +
129A LEU* 3.8 3.7 - - - +
130A ILE* 3.2 26.8 + - + +
145A LEU* 5.1 11.7 - - + -
446A PHE* 4.6 4.3 - - + -
450A LYS* 3.5 38.1 - - + -
82B HIS* 4.6 13.5 - - + +
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Residues in contact with ARG 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 ALA 3.7 0.8 + - - -
124A GLU* 3.6 7.7 + - - +
125A ALA 3.2 0.2 - - - -
126A VAL* 1.3 85.9 - - - +
128A ASP* 1.3 78.4 + - - +
130A ILE* 3.3 4.9 + - - +
131A GLU* 3.0 45.2 + - - +
442A ILE 5.3 0.2 - - - -
445A ASN* 2.9 51.4 + - - +
446A PHE* 3.8 36.6 - - + -
447A CYS* 6.2 4.5 - - - -
450A LYS* 6.2 0.2 - - - -
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Residues in contact with ASP 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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124A GLU* 3.2 20.5 + - - +
125A ALA* 4.0 2.8 - - - +
127A ARG* 1.3 94.1 + - - +
129A LEU* 1.3 66.4 + - - +
131A GLU* 3.2 6.9 + - - +
132A ALA* 3.0 22.7 + - - +
137A SER* 4.9 3.6 + - - +
141A SER* 3.4 20.3 + - - +
209A ASN* 3.5 29.6 + - - +
384A THR* 4.4 10.0 + - - -
385A ASN* 4.8 7.8 + - - -
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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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125A ALA 2.8 20.9 + - - +
126A VAL 3.8 3.1 - - - +
128A ASP* 1.3 71.9 - - - +
130A ILE* 1.3 68.2 + - - +
132A ALA* 2.8 25.2 + - - +
138A LEU* 3.6 11.6 - - + +
141A SER* 4.0 13.8 - - - -
142A LEU* 4.2 12.3 - - + +
145A LEU* 3.4 31.4 - - + -
58B ASP* 3.7 17.0 - - - +
82B HIS* 3.9 18.4 - - + +
84B GLY* 5.0 2.9 - - - -
86B LEU* 5.9 0.3 - - - +
87B VAL* 3.4 34.1 - - + -
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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 VAL* 3.2 18.4 + - + +
127A ARG* 3.8 5.4 - - - +
129A LEU* 1.3 79.5 - - - +
131A GLU* 1.3 59.9 + - + +
132A ALA 3.7 0.7 + - - +
240A THR* 4.2 2.3 - - - +
447A CYS* 5.1 6.3 - - - -
450A LYS* 3.7 34.3 - - + -
13B LYS* 3.6 19.7 - - + +
14B GLY 3.3 28.9 - - - +
15B ALA* 4.0 1.6 - - - +
82B HIS* 3.8 21.1 - - + -
83B GLY 3.4 20.2 - - - +
84B GLY* 3.7 17.1 - - - +
85B PRO* 4.0 9.5 - - - +
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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 ARG* 3.0 50.6 + - + +
128A ASP* 3.2 7.6 + - - +
129A LEU 3.0 1.4 - - - -
130A ILE* 1.3 81.4 - - + +
132A ALA* 1.3 64.2 + - - +
133A LYS* 3.3 19.3 + - - +
240A THR* 3.7 13.6 + - - +
241A ASP* 4.8 3.3 - - - +
445A ASN 4.8 2.4 - - - +
446A PHE 5.7 1.6 - - - +
447A CYS* 6.3 1.1 - - - -
13B LYS* 3.1 40.4 + - + -
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Residues in contact with ALA 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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128A ASP 3.0 9.6 + - - +
129A LEU* 2.8 16.9 + - - +
130A ILE 3.4 1.5 - - - +
131A GLU* 1.3 76.0 - - - +
133A LYS* 1.3 60.5 + - - +
134A SER 3.6 2.2 - - - +
137A SER* 4.5 8.5 - - - +
138A LEU* 3.7 41.1 - - + +
238A ILE* 4.8 1.4 - - - +
240A THR* 4.3 6.6 - - - +
86B LEU* 3.2 26.5 + - + +
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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