Contacts of the helix formed by residues 126 - 137 (chain A) in PDB entry 5UP8
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN* 3.3 14.3 + - - +
12A TYR* 3.5 14.7 - - - -
16A SER* 4.4 6.3 + - - +
76A ARG* 2.6 38.7 + - - -
121A ALA* 2.6 27.3 + - - +
124A LYS* 4.2 4.3 - - + +
125A ASN* 1.3 70.1 - - - +
127A PRO* 1.3 68.0 - - - +
128A HIS* 3.7 3.5 + - - +
129A LEU* 3.3 27.8 + - + +
130A ALA* 3.0 17.0 + - - +
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Residues in contact with PRO 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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11A ASN* 4.3 5.6 - - - +
125A ASN 3.4 12.1 - - - +
126A ASP* 1.3 84.4 - - - +
128A HIS* 1.3 66.7 + - + +
130A ALA* 2.8 19.5 + - + +
131A ASP* 2.9 17.3 + - - +
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Residues in contact with HIS 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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72A LEU* 4.7 10.8 - - + -
75A GLN* 4.8 10.3 + - + -
76A ARG* 3.4 41.6 - - + +
126A ASP* 3.9 7.2 - - - +
127A PRO* 1.3 83.3 - - + +
129A LEU* 1.3 61.3 + - - +
131A ASP* 3.5 3.2 + - - +
132A PHE* 2.9 45.4 + + + +
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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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12A TYR* 4.2 5.8 - - + -
16A SER* 3.8 29.6 - - - +
20A ILE* 4.4 14.4 - - + -
72A LEU* 3.6 38.4 - - + -
76A ARG* 5.2 0.9 - - + +
117A LEU* 4.2 13.9 - - + -
121A ALA* 3.6 21.8 - - + -
126A ASP* 3.3 23.2 + - - +
127A PRO 3.3 0.6 - - - -
128A HIS* 1.3 83.3 + - - +
130A ALA* 1.3 63.5 + - - +
132A PHE* 3.6 1.7 - - - +
133A ILE* 3.0 40.0 + - + +
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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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118A HIS* 3.2 32.8 - - + +
121A ALA* 3.9 12.9 - - + +
122A HIS* 5.0 4.7 - - + +
126A ASP 3.0 12.7 + - - +
127A PRO* 2.8 15.9 + - + +
129A LEU* 1.3 78.4 - - - +
131A ASP* 1.3 57.7 + - + +
133A ILE 3.3 0.2 + - - -
134A GLU* 2.9 32.5 + - - +
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Residues in contact with ASP 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 PRO 2.9 16.0 + - - +
128A HIS* 4.3 2.7 - - - +
130A ALA* 1.3 70.4 - - - +
132A PHE* 1.3 61.4 + - - +
134A GLU* 3.6 12.1 - - - +
135A THR* 2.9 47.3 + - - +
204A NA 2.4 25.1 - - - -
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Residues in contact with PHE 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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68A LYS* 4.1 20.6 - - + -
69A LEU* 4.1 11.0 - - + -
72A LEU* 3.1 41.5 - - + -
75A GLN* 5.1 6.5 - - - -
128A HIS* 2.9 30.7 + + + +
129A LEU* 3.6 6.7 - - - +
131A ASP* 1.3 75.6 + - - +
133A ILE* 1.3 78.2 + - + +
134A GLU 3.1 0.2 + - - -
135A THR* 4.4 0.2 - - - -
136A HIS* 3.0 48.1 + + - +
137A TYR* 3.4 32.1 - + - -
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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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20A ILE* 5.0 1.8 - - + -
23A GLN* 6.6 0.2 - - + -
69A LEU* 4.8 10.5 - - + -
114A LEU* 3.9 34.3 - - + +
117A LEU* 4.6 18.2 - - + -
118A HIS* 4.2 17.9 - - + -
129A LEU* 3.0 30.7 + - + +
130A ALA* 3.5 7.9 - - - +
132A PHE* 1.3 92.7 - - + +
134A GLU* 1.3 63.8 + - - +
137A TYR* 3.1 28.7 + - + -
138A LEU* 3.1 22.7 + - + -
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Residues in contact with GLU 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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118A HIS* 2.9 32.2 + - + +
130A ALA* 2.9 25.2 + - - +
131A ASP* 3.4 12.7 + - - +
132A PHE 3.1 0.4 - - - -
133A ILE* 1.3 79.7 - - - +
135A THR* 1.3 65.3 + - + +
138A LEU* 3.5 31.3 + - + +
139A ASN* 3.9 7.4 + - - +
204A NA 2.3 31.8 - - - -
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Residues in contact with THR 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 ASP* 2.9 45.6 + - - +
132A PHE* 4.4 0.3 - - - -
134A GLU* 1.3 76.3 - - + +
136A HIS* 1.3 84.2 + - - +
139A ASN* 5.3 7.1 - - - +
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Residues in contact with HIS 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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65A HIS* 5.3 5.9 + - - -
68A LYS* 3.0 37.4 + - - +
132A PHE* 3.0 39.5 + + - +
135A THR* 1.3 100.0 + - - +
137A TYR* 1.3 84.7 + - + +
140A GLU* 4.4 11.4 - - - +
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Residues in contact with TYR 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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27A GLU* 4.5 4.0 - - - -
65A HIS* 2.8 52.9 + + + -
68A LYS* 3.0 21.9 - - + +
69A LEU* 3.1 26.6 + - + +
114A LEU* 4.0 34.8 - - + -
132A PHE* 3.4 29.2 - + - -
133A ILE* 3.1 19.8 + - + +
135A THR 3.6 0.6 - - - -
136A HIS* 1.3 99.4 - - + +
138A LEU* 1.3 67.8 + - - +
139A ASN 3.4 1.6 - - - -
140A GLU* 3.2 7.1 + - - +
141A GLN* 2.8 28.6 + - - +
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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