Contacts of the helix formed by residues 121 - 134 (chain A) in PDB entry 1UXI
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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88A ARG* 3.5 30.0 - - + +
89A GLU* 4.2 13.7 - - + +
92A ILE* 3.7 43.5 - - + +
119A ASN 3.7 0.2 - - - -
120A ASN* 1.4 81.8 - - + +
122A LEU* 1.3 60.8 + - - +
123A ASP 3.5 1.3 - - - +
124A ALA* 3.4 15.4 + - + +
125A MET* 2.9 34.2 + - + +
175A HIS 5.8 1.1 - - - +
302A THR* 5.0 6.1 - - + -
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Residues in contact with LEU 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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117A MET* 3.5 23.1 - - + +
118A VAL 3.6 14.1 - - - +
119A ASN 3.4 7.6 - - - +
120A ASN* 3.1 18.9 + - - +
121A PRO* 1.3 70.9 - - - +
123A ASP* 1.3 63.3 + - - +
125A MET* 3.5 0.7 + - - +
126A THR* 2.6 42.2 + - - +
142A GLY* 3.9 4.0 - - - -
143A GLN 3.3 24.5 - - - +
144A ALA* 3.9 13.7 - - + -
175A HIS* 3.8 17.4 + - + +
251A ALA* 3.4 30.7 - - + -
1310A NAD 3.8 1.8 - - - +
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Residues in contact with ASP 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* 3.5 0.8 - - - +
122A LEU* 1.3 81.5 + - - +
124A ALA* 1.3 63.1 + - - +
126A THR* 3.4 3.1 + - - -
127A TYR* 3.1 18.5 + - - +
144A ALA* 5.6 0.7 - - - +
173A GLY 4.1 0.5 - - - +
174A GLY* 3.3 18.5 - - - -
175A HIS* 2.7 30.9 + - - +
251A ALA* 3.7 17.3 - - - +
264A TYR* 3.6 35.5 - - - +
266A GLY* 3.8 7.6 + - - -
299A VAL* 4.1 16.0 - - + +
302A THR* 5.4 1.1 - - - +
303A LEU* 4.7 1.9 - - - +
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Residues in contact with ALA 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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92A ILE* 4.2 10.3 - - + -
121A PRO* 3.4 21.6 + - + +
122A LEU 3.3 0.4 - - - -
123A ASP* 1.3 79.6 - - - +
125A MET* 1.3 58.7 + - + +
127A TYR* 3.0 5.7 + - - +
128A LEU* 2.9 28.4 + - - +
302A THR* 3.5 25.8 + - - +
303A LEU* 3.8 18.8 - - + +
306A LEU* 4.0 10.2 - - + +
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Residues in contact with MET 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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92A ILE* 3.7 14.1 - - + +
95A ASN* 3.1 20.4 - - + +
96A ALA* 3.1 33.9 - - + +
99A THR* 3.2 28.2 - - - +
117A MET* 3.9 15.6 - - + +
119A ASN* 3.6 22.2 - - + +
120A ASN 3.9 4.3 - - - +
121A PRO* 2.9 35.6 + - + +
122A LEU 4.0 0.2 - - - +
124A ALA* 1.3 76.2 - - + +
126A THR* 1.3 56.9 + - - +
128A LEU* 3.4 10.0 + - - +
129A ALA* 2.9 28.4 + - - +
306A LEU* 6.1 0.7 - - - -
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Residues in contact with THR 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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117A MET* 3.4 14.3 - - + +
122A LEU* 2.6 25.2 + - - +
123A ASP* 3.7 5.4 - - - -
124A ALA 3.2 0.4 - - - -
125A MET* 1.3 73.2 - - - +
127A TYR* 1.3 65.8 + - - +
129A ALA* 3.4 3.8 + - - +
130A ALA* 3.1 21.8 + - - +
140A VAL* 3.8 4.0 - - + +
141A ILE* 3.4 12.3 - - - +
142A GLY* 3.4 39.0 - - - +
251A ALA* 4.8 0.4 - - - -
264A TYR* 3.6 28.4 - - + -
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Residues in contact with TYR 127 (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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123A ASP 3.1 12.2 + - - +
124A ALA 3.0 9.5 + - - +
126A THR* 1.3 77.2 - - - +
128A LEU* 1.3 65.6 + - - +
130A ALA* 3.0 5.6 + - + +
131A GLU* 2.9 45.0 + - + -
137A LYS* 5.9 5.6 - - - -
253A TYR* 4.1 7.0 - + - -
262A ASP* 2.7 52.9 + - - -
263A ILE* 4.1 11.4 - - - -
264A TYR* 3.3 24.7 - + + -
303A LEU* 3.9 26.0 - - + -
306A LEU* 4.8 4.9 - - + -
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Residues in contact with LEU 128 (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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96A ALA* 3.5 44.2 - - + +
99A THR* 4.0 16.8 - - + -
100A ARG* 3.7 30.1 - - + +
124A ALA 2.9 12.0 + - - +
125A MET* 3.4 12.8 - - - +
127A TYR* 1.3 79.5 - - - +
129A ALA* 1.3 52.3 + - - +
131A GLU* 3.1 14.1 + - - +
132A VAL* 2.8 46.7 + - + +
306A LEU* 4.1 24.2 - - + +
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Residues in contact with ALA 129 (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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99A THR* 4.7 0.4 - - + -
103A ILE* 3.7 36.4 - - + +
115A ILE* 4.8 3.1 - - + +
117A MET* 3.8 13.5 - - + -
125A MET 2.9 17.2 + - - +
126A THR* 3.8 6.5 - - - +
127A TYR 3.2 0.2 - - - -
128A LEU* 1.3 73.8 - - - +
130A ALA* 1.3 54.5 + - - +
133A SER* 2.5 41.9 + - - -
140A VAL* 4.2 10.8 - - + -
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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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126A THR 3.1 5.7 + - - +
127A TYR* 3.0 10.4 + - + +
129A ALA* 1.3 77.4 - - - +
131A GLU* 1.3 58.6 + - - +
133A SER* 3.4 5.5 + - - -
134A GLY* 2.9 27.2 + - - -
135A PHE 4.0 4.3 + - - +
137A LYS* 3.9 22.8 + - + -
140A VAL* 3.8 12.1 - - + +
264A TYR* 3.6 35.4 - - + +
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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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100A ARG* 4.5 15.4 + - - -
127A TYR* 2.9 37.3 + - + +
128A LEU* 3.2 16.8 - - - +
130A ALA* 1.3 78.7 - - - +
132A VAL* 1.3 67.3 + - + +
133A SER 3.3 0.7 + - - -
134A GLY* 3.4 7.4 + - - -
137A LYS* 6.1 1.3 - - - +
306A LEU* 5.2 5.1 - - - +
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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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100A ARG* 3.4 42.6 - - + +
103A ILE* 3.8 11.0 - - + -
104A SER* 3.7 40.7 - - - +
107A ALA* 5.4 0.2 - - - +
128A LEU* 2.8 34.8 + - + +
131A GLU* 1.3 74.1 - - + +
133A SER* 1.3 59.8 + - - +
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Residues in contact with SER 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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103A ILE* 3.6 16.4 - - - +
107A ALA* 3.7 13.8 - - - +
115A ILE* 4.0 6.5 - - - -
129A ALA 2.5 24.7 + - - -
130A ALA* 3.4 5.9 + - - -
132A VAL* 1.3 78.5 - - - +
134A GLY* 1.3 63.4 + - - +
135A PHE* 3.0 39.8 + - - +
140A VAL* 3.9 3.5 - - - +
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Residues in contact with GLY 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 ALA 2.9 15.4 + - - -
131A GLU 3.4 7.9 + - - -
133A SER* 1.3 76.8 - - - +
135A PHE* 1.3 64.6 + - - +
136A PRO* 3.9 1.9 - - - +
137A LYS* 6.3 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