Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 6UPX
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ILE* 3.6 10.5 - - + +
129A LYS* 1.3 74.9 - - - +
131A SER* 1.3 61.8 + - - +
132A LYS* 3.4 18.1 + - - +
133A LYS* 3.3 38.2 - - + +
134A ARG* 3.0 30.4 + - - +
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Residues in contact with SER 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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129A LYS 3.2 8.3 + - - -
130A ASP* 1.3 74.3 + - - +
132A LYS* 1.3 61.0 + - - +
134A ARG* 4.0 9.4 + - - +
135A PHE* 2.9 35.0 + - - +
222A LEU 4.1 0.5 - - - +
223A GLY* 3.5 38.7 + - - -
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Residues in contact with LYS 132 (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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98A LYS* 6.2 2.0 - - - +
130A ASP* 3.4 16.0 + - - +
131A SER* 1.3 82.5 - - - +
133A LYS* 1.3 76.0 + - - +
135A PHE* 4.5 4.1 - - - +
136A ALA* 3.9 17.2 + - - +
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Residues in contact with LYS 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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128A ILE* 5.6 2.9 - - + -
130A ASP* 3.3 35.1 + - + +
132A LYS* 1.3 94.4 - - - +
134A ARG* 1.3 60.6 + - - +
135A PHE 3.3 1.8 - - - -
136A ALA* 3.4 4.0 + - - +
137A ALA* 2.9 30.4 + - - +
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Residues in contact with ARG 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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125A ALA 3.6 16.2 - - - +
126A LEU 3.9 11.1 + - - -
128A ILE* 2.5 43.0 + - + +
129A LYS* 3.0 28.4 + - - +
130A ASP 3.0 16.4 + - - +
131A SER* 4.0 12.0 + - - +
133A LYS* 1.3 76.7 - - - +
135A PHE* 1.3 58.4 + - - +
137A ALA* 3.4 5.0 + - - +
138A ILE* 2.9 38.7 + - + +
220A THR 3.6 6.2 + - - -
221A SER* 2.5 49.0 + - - +
222A LEU 4.4 1.3 - - - +
223A GLY* 3.4 16.6 - - - +
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Residues in contact with PHE 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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98A LYS* 4.2 35.7 - - + +
101A LYS* 4.2 38.1 - - + -
102A VAL* 4.4 18.4 - - + -
131A SER 2.9 19.1 + - - +
132A LYS* 4.5 5.2 - - - +
134A ARG* 1.3 77.4 - - - +
136A ALA* 1.3 61.6 + - + +
138A ILE* 3.4 5.9 + - - +
139A TRP* 2.9 32.0 + - + +
222A LEU* 3.3 53.8 - - + +
224A PHE* 4.8 13.7 - + - -
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Residues in contact with ALA 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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101A LYS* 5.2 11.2 - - - +
132A LYS 3.9 15.9 + - - +
133A LYS* 3.4 5.7 + - - +
134A ARG 3.4 0.2 - - - -
135A PHE* 1.3 82.6 - - + +
137A ALA* 1.3 57.9 + - - +
139A TRP* 3.8 8.0 - - + +
140A THR* 2.8 37.1 + - + +
7N A 5.5 4.5 - - - +
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Residues in contact with ALA 137 (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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125A ALA* 4.8 12.8 - - + +
128A ILE* 6.1 1.3 - - + -
133A LYS 2.9 17.9 + - - +
134A ARG* 3.7 7.2 - - - +
136A ALA* 1.3 74.9 - - - +
138A ILE* 1.3 59.4 + - - +
140A THR* 2.8 19.1 + - - -
141A LEU* 2.9 27.8 + - + +
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Residues in contact with ILE 138 (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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105A CYS* 5.2 2.0 - - + -
113A LEU* 4.3 10.1 - - + -
122A MET* 4.0 19.5 - - - +
125A ALA* 4.3 11.2 - - + -
126A LEU* 3.7 25.4 - - + -
134A ARG* 2.9 28.9 + - + +
135A PHE* 3.6 4.5 - - - +
137A ALA* 1.3 73.9 - - - +
139A TRP* 1.3 60.3 + - + +
141A LEU* 3.2 5.1 + - - +
142A CYS* 2.9 50.1 + - - -
221A SER 3.8 16.2 - - - +
222A LEU* 4.0 29.4 - - + -
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Residues in contact with TRP 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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100A LYS* 5.4 3.1 - - + +
101A LYS* 3.2 72.2 - - + +
104A GLU* 3.5 14.5 - - + +
105A CYS* 3.4 18.2 - - - -
135A PHE* 2.9 22.6 + + + +
136A ALA* 3.8 6.7 - - + +
138A ILE* 1.3 78.7 - - + +
140A THR* 1.3 75.1 + - + +
143A LYS* 3.0 60.4 + - + +
7N A 3.6 32.3 - - + -
8N G 3.1 30.1 - - - -
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Residues in contact with THR 140 (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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136A ALA* 2.8 24.4 + - + +
137A ALA* 2.8 17.2 + - - -
139A TRP* 1.3 97.6 - - + +
141A LEU* 1.3 64.0 + - - +
143A LYS* 4.0 18.0 + - - +
7N A 5.7 2.7 - - - +
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Residues in contact with LEU 141 (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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121A LEU* 3.8 33.0 - - + +
122A MET* 3.9 13.5 - - + -
125A ALA* 3.8 29.4 - - + -
137A ALA* 2.9 20.9 + - + +
138A ILE 3.2 3.6 + - - +
140A THR* 1.3 83.7 - - - +
142A CYS* 1.3 56.8 + - - +
143A LYS 3.4 2.3 + - - -
144A THR* 4.6 5.9 + - - +
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Residues in contact with CYS 142 (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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104A GLU 3.7 5.4 - - - +
105A CYS* 3.4 26.7 - - - -
113A LEU* 4.3 6.3 - - - -
114A LEU* 3.7 30.0 - - + +
115A LEU* 4.7 9.4 - - + -
122A MET* 4.2 15.0 - - + -
138A ILE* 2.9 37.5 + - - -
139A TRP 3.6 2.0 - - - -
141A LEU* 1.3 74.0 - - - +
143A LYS* 1.3 62.2 + - - +
144A THR* 3.3 7.2 - - - +
145A LYS* 4.4 6.4 - - + +
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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