Contacts of the helix formed by residues 126 - 136 (chain A) in PDB entry 3UC5
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A THR* 4.3 5.6 - - - -
90A ARG* 3.2 12.8 - - - +
124A PHE 3.5 5.4 + - - -
125A VAL* 1.3 74.6 - - - +
127A SER* 1.3 62.2 + - - +
128A SER* 3.7 3.3 + - - -
129A LEU* 3.1 26.1 + - - +
130A ALA* 3.0 25.0 + - - +
1440A ATP 2.7 28.8 + - - -
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Residues in contact with SER 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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9A SER* 6.1 0.9 - - - -
11A ASP* 3.6 21.4 + - - -
12A PRO* 2.7 28.8 + - - +
14A THR* 3.8 9.7 - - - +
17A HIS* 3.4 18.4 - - - -
126A SER* 1.3 72.2 - - - +
128A SER* 1.3 59.1 + - - +
130A ALA* 3.8 2.6 - - - +
131A LYS* 2.9 38.1 + - - +
1440A ATP 3.6 16.9 + - - -
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Residues in contact with SER 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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126A SER* 4.1 2.2 - - - -
127A SER* 1.3 75.2 - - - +
129A LEU* 1.3 58.0 + - - +
131A LYS* 3.4 16.5 + - - +
132A GLU* 2.9 46.8 + - - +
1440A ATP 2.6 30.4 + - - -
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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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124A PHE* 4.2 20.9 - - + +
126A SER* 3.1 19.2 + - - +
128A SER* 1.3 76.3 - - - +
130A ALA* 1.3 62.0 + - - +
132A GLU* 3.2 19.9 + - + +
133A VAL* 2.9 51.0 + - + +
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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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12A PRO* 5.8 2.0 - - + -
14A THR* 5.3 0.4 - - + -
125A VAL* 5.3 1.8 - - + -
126A SER 3.0 19.7 + - - +
127A SER* 3.8 4.3 - - - +
129A LEU* 1.3 77.9 - - - +
131A LYS* 1.3 56.1 + - - +
133A VAL* 3.4 1.4 + - - +
134A ALA* 2.9 32.5 + - - +
140A VAL* 3.9 22.5 - - + +
143A LEU* 5.3 7.4 - - + -
144A LEU* 4.2 27.8 - - + -
152A LEU* 5.8 0.4 - - - -
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Residues in contact with LYS 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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11A ASP* 2.8 43.5 + - - +
12A PRO* 3.8 13.2 - - + -
43A GLY* 5.1 1.8 - - - -
44A MET* 3.5 47.2 - - + +
127A SER* 2.9 25.5 + - - +
128A SER* 3.6 12.7 + - - +
130A ALA* 1.3 77.4 - - - +
132A GLU* 1.3 57.2 + - + +
134A ALA* 3.4 5.3 + - - +
135A MET* 2.9 42.2 + - + +
152A LEU* 5.5 4.0 - - + -
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Residues in contact with GLU 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 SER* 2.9 34.9 + - - +
129A LEU* 3.7 20.1 - - + +
131A LYS* 1.3 78.0 - - + +
133A VAL* 1.3 64.3 + - + +
135A MET* 3.5 16.2 + - + +
136A LEU* 3.3 31.4 + - + +
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Residues in contact with VAL 133 (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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129A LEU* 2.9 39.6 + - + +
130A ALA* 3.9 2.9 - - - +
132A GLU* 1.3 75.6 - - + +
134A ALA* 1.3 65.5 + - - +
136A LEU* 3.0 14.7 + - + +
137A GLY 3.2 0.3 + - - -
138A GLY* 2.9 38.9 + - - -
139A ASP 4.7 0.4 - - - +
140A VAL* 3.8 19.1 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.6 + - - +
131A LYS* 3.8 5.6 - - - +
133A VAL* 1.3 76.3 - - - +
135A MET* 1.3 59.5 + - + +
137A GLY* 3.0 18.0 + - - -
138A GLY 3.7 12.3 - - - +
140A VAL* 4.0 8.7 - - + +
152A LEU* 3.8 31.9 - - + -
156A LEU* 4.8 14.6 - - - +
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Residues in contact with MET 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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44A MET* 3.5 30.3 - - + -
131A LYS* 2.9 33.4 + - + +
132A GLU* 3.8 17.0 - - + +
133A VAL 3.2 0.4 - - - -
134A ALA* 1.3 78.1 - - + +
136A LEU* 1.3 62.3 + - + +
137A GLY 3.3 1.0 + - - -
156A LEU* 6.3 1.6 - - - -
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Residues in contact with LEU 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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132A GLU* 3.3 17.8 + - + +
133A VAL* 3.0 11.5 + - - +
135A MET* 1.3 80.0 - - + +
137A GLY* 1.3 59.8 + - - +
138A GLY 3.5 1.7 + - - +
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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