Contacts of the strand formed by residues 126 - 134 (chain A) in PDB entry 5CEO
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 LEU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU 3.4 23.3 - - - +
124A GLU* 3.7 11.4 - - - +
125A ILE* 1.3 73.8 - - - +
127A ASP* 1.4 68.8 + - - +
128A LEU* 3.3 4.7 + - - +
142A GLY* 3.3 2.9 - - - -
143A ARG* 2.8 73.1 + - + +
144A PHE* 6.2 0.2 - - - -
145A HIS 6.3 0.2 - - - +
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Residues in contact with ASP 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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126A LEU* 1.4 73.1 - - - +
128A LEU* 1.3 63.8 + - - +
129A GLN* 3.3 17.8 + - - +
141A LEU 3.2 10.3 - - - +
142A GLY* 4.0 2.0 - - - -
143A ARG* 2.8 39.5 + - + +
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Residues in contact with LEU 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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122A PHE* 3.7 35.0 - - + -
125A ILE* 3.7 34.8 - - + +
126A LEU 3.3 1.3 + - - +
127A ASP* 1.3 73.1 - - - +
129A GLN* 1.3 61.2 + - - +
140A PHE* 3.8 29.5 - - + -
141A LEU 3.4 4.9 - - - +
142A GLY* 4.3 2.5 - - - -
151A VAL* 3.8 23.3 - - + -
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Residues in contact with GLN 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* 3.9 13.2 + - - +
128A LEU* 1.3 74.3 - - - +
130A TRP* 1.3 66.1 + - - +
131A VAL* 3.6 1.9 + - + +
140A PHE* 3.7 4.0 - - - -
141A LEU* 2.7 67.9 + - + +
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Residues in contact with TRP 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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129A GLN* 1.3 75.5 - - - +
131A VAL* 1.3 61.9 + - - +
132A GLY* 3.3 40.0 + - - -
133A SER* 3.5 19.4 + - - -
138A ALA* 4.5 3.3 - - + +
139A VAL 3.5 15.0 - - - +
140A PHE* 3.4 37.6 - + + -
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Residues in contact with VAL 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 GLN* 3.9 3.4 - - + +
130A TRP* 1.3 80.5 - - - +
132A GLY* 1.3 56.8 + - - +
139A VAL* 2.9 41.1 + - + +
140A PHE* 4.0 4.7 - - - +
141A LEU* 3.8 28.7 - - + -
192A PHE* 4.5 7.2 - - + -
501A 50D 3.9 59.7 - - + +
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Residues in contact with GLY 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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130A TRP* 3.3 30.0 + - - -
131A VAL* 1.3 81.4 - - - +
133A SER* 1.3 54.8 + - - -
139A VAL 2.9 30.8 + - - +
501A 50D 3.1 17.3 - - - -
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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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130A TRP* 3.5 25.7 + - - -
132A GLY* 1.3 70.7 + - - -
134A GLY* 1.3 59.5 + - - +
137A GLY 3.2 11.0 - - - -
138A ALA* 3.7 13.2 + - - +
501A 50D 3.9 3.6 - - - +
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Residues in contact with GLY 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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133A SER* 1.3 75.2 - - - +
135A ALA* 1.4 59.0 + - - -
136A GLN* 3.2 14.4 - - - +
137A GLY 3.5 6.7 + - - -
197A GLN* 4.5 2.5 - - - -
501A 50D 3.5 23.5 - - - -
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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