Contacts of the strand formed by residues 129 - 134 (chain B) in PDB entry 5DO7
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B TYR* 3.5 6.0 + - - -
41B SER* 2.9 12.9 + - - -
42B GLY* 2.8 37.6 + - - +
90B ASN* 5.4 1.0 + - - -
127B ILE* 4.2 15.4 - - - +
128B LYS* 1.3 75.8 - - - +
130B GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR 3.4 3.4 - - - -
40B TYR 2.8 27.3 + - - -
41B SER* 3.8 6.5 - - - -
129B SER* 1.3 74.9 - - - +
131B GLN* 1.3 76.7 + - - +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.8 6.6 - - - -
39B THR* 3.2 40.0 + - - +
41B SER* 4.7 1.4 + - - -
130B GLY* 1.3 90.4 - - - +
132B ILE* 1.3 67.0 + - - +
133B TRP* 3.6 31.7 - - + +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 4.6 5.8 - - + -
37B TYR 3.9 2.7 - - - +
38B PHE* 3.3 44.6 - - + -
41B SER* 5.4 1.3 - - - +
117B VAL* 4.6 8.1 - - + +
118B ILE* 4.1 28.7 - - + +
131B GLN* 1.3 78.3 - - - +
133B TRP* 1.3 72.0 + - - +
134B ILE* 5.3 3.4 - - + -
138B PRO* 3.2 3.6 - - - +
139B SER* 2.8 48.9 + - - +
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Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.5 5.6 - - - +
37B TYR* 2.9 78.6 + + + +
38B PHE 5.2 0.7 - - - -
39B THR* 5.2 5.1 + - - -
131B GLN* 3.6 31.9 - - + +
132B ILE* 1.3 87.6 + - - +
134B ILE* 1.3 63.4 + - - +
136B GLY* 4.9 3.1 - - - -
137B GLN* 2.9 38.8 - - - +
138B PRO* 3.8 15.0 - - + -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 4.1 9.6 - - - +
35B SER 3.2 2.7 - - - -
36B LEU* 4.0 17.5 - - + -
37B TYR* 5.7 0.7 - - - -
132B ILE* 5.3 4.9 - - + -
133B TRP* 1.3 75.8 - - - +
135B ASN* 1.3 85.1 - - - +
136B GLY* 2.1 24.2 + - - -
137B GLN* 2.6 43.6 + - + +
138B PRO 3.5 9.5 + - - +
139B SER* 5.3 2.2 - - - -
143B LEU* 3.3 35.4 - - + -
144B VAL* 5.3 6.7 - - + -
147B CYS* 4.9 2.0 - - + -
148B VAL* 4.9 9.0 - - + -
233B ILE* 4.5 15.0 - - + -
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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