Contacts of the helix formed by residues 127 - 134 (chain A) in PDB entry 2YYU
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A SER 3.7 4.6 + - - +
126A THR* 1.3 76.2 - - - +
128A GLU* 1.3 64.5 + - - +
129A ARG* 3.1 19.0 + - - +
130A MET* 2.8 28.3 + - - +
131A LEU* 3.2 19.4 + - - +
141A LEU* 4.0 8.3 - - - -
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Residues in contact with GLU 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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127A ASP* 1.3 73.5 - - - +
129A ARG* 1.3 66.6 + - - +
131A LEU* 3.4 4.3 + - - +
132A HIS* 3.0 53.5 + - + +
140A PRO* 3.7 9.7 - - - +
141A LEU* 3.3 38.4 + - + +
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Residues in contact with ARG 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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127A ASP* 3.1 17.1 + - - +
128A GLU* 1.3 77.6 - - - +
130A MET* 1.3 73.7 + - - +
132A HIS* 5.0 1.1 - - - -
133A GLU* 2.8 56.1 + - + +
134A GLU* 2.8 39.2 + - - +
95B ARG* 6.2 1.6 - - - +
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Residues in contact with MET 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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123A LEU* 5.7 1.6 - - + -
125A SER 4.6 4.9 - - - +
126A THR* 3.1 41.3 - - + +
127A ASP* 2.8 24.6 + - - +
129A ARG* 1.3 89.7 - - - +
131A LEU* 1.3 58.3 + - - +
134A GLU* 2.9 46.7 + - - +
135A LEU* 3.0 17.4 + - + -
91B ALA 3.8 11.2 - - - +
92B GLY* 3.5 29.2 - - - +
93B GLY* 3.9 10.5 - - - -
95B ARG* 6.1 4.0 - - - -
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Residues in contact with LEU 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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122A GLN* 3.6 24.9 - - - +
126A THR* 4.3 4.2 - - + +
127A ASP 3.2 14.9 + - - +
128A GLU* 3.6 3.6 - - + +
130A MET* 1.3 79.3 - - - +
132A HIS* 1.3 62.0 + - + +
135A LEU* 3.3 13.9 - - + +
136A TRP 3.2 8.1 + - - -
137A ILE* 3.0 61.4 + - + -
139A ARG 3.9 13.0 - - - +
141A LEU* 3.5 44.2 - - + +
144A THR* 4.1 8.3 - - + +
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Residues in contact with HIS 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 GLU* 3.0 48.8 + - + +
129A ARG* 4.1 1.3 - - - +
131A LEU* 1.3 82.6 - - + +
133A GLU* 1.3 75.6 + - + +
136A TRP* 3.3 24.9 - - - -
137A ILE 2.8 28.0 - - - +
138A SER* 5.4 1.3 - - - -
139A ARG 2.7 31.3 + - - -
140A PRO* 4.7 1.1 - - + -
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Residues in contact with GLU 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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129A ARG* 2.8 47.3 + - + +
132A HIS* 1.3 84.0 - - + +
134A GLU* 1.3 58.2 + - + +
136A TRP* 3.8 3.8 + - - +
147B HIS* 3.1 23.0 + - - -
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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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129A ARG* 2.8 40.8 + - - +
130A MET* 2.9 26.4 + - - +
133A GLU* 1.3 76.4 - - + +
135A LEU* 1.3 63.9 + - + +
136A TRP 3.3 1.6 - - - -
93B GLY* 3.3 8.0 - - - -
94B ARG* 2.7 45.2 + - - +
95B ARG 4.6 0.5 + - - -
147B HIS* 3.2 24.3 + - - -
148B TYR* 3.7 9.2 - - - -
151B LEU* 3.8 26.7 - - + +
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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