Contacts of the strand formed by residues 131 - 136 (chain A) in PDB entry 5ONS
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 ILE 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.7 14.6 - - - +
33A PHE* 4.5 4.7 - - + -
77A PRO* 4.0 13.0 - - + -
78A PHE 3.4 24.7 - - - +
79A TYR* 3.8 35.4 - - + -
80A PRO* 4.5 4.7 - - + -
92A LEU* 3.4 33.2 - - + +
93A PRO* 3.6 14.2 - - - +
129A ASP 3.5 5.8 + - - +
130A THR* 1.3 73.8 - - - +
132A VAL* 1.3 62.5 + - - +
145A VAL* 3.9 11.7 - - + -
146A GLY 3.4 8.1 - - - +
147A VAL* 4.3 5.6 - - + +
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Residues in contact with VAL 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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92A LEU* 3.7 7.3 - - - +
93A PRO* 3.4 15.7 - - + +
95A GLN* 4.0 26.5 - - + +
126A ALA* 4.8 1.3 - - + -
130A THR* 3.8 23.3 - - + +
131A ILE* 1.3 80.4 - - - +
133A ALA* 1.3 58.7 + - - +
134A ILE* 3.7 22.7 - - + -
145A VAL* 3.7 4.0 - - - +
146A GLY 2.9 46.5 + - - +
148A MET* 4.0 14.4 - - + -
164A ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 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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85A LEU* 3.7 26.9 - - + -
92A LEU* 3.7 11.7 - - + +
93A PRO 2.8 10.2 + - - +
94A HIS* 3.3 27.2 - - + +
95A GLN 2.9 27.9 + - - +
132A VAL* 1.3 71.4 - - - +
134A ILE* 1.3 62.1 + - - +
135A MET* 3.5 1.8 + - - +
142A ALA* 4.4 8.1 - - + -
144A CYS 3.9 4.5 - - - -
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Residues in contact with ILE 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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95A GLN* 3.3 7.9 - - + +
97A VAL* 3.8 23.1 - - + -
105A VAL* 5.6 1.8 - - + -
111A ILE* 3.8 24.7 - - + -
132A VAL* 3.7 27.1 - - + -
133A ALA* 1.3 72.9 - - - +
135A MET* 1.3 67.5 + - - +
142A ALA* 3.3 5.0 - - - +
143A LEU* 3.1 41.5 + - + +
144A CYS* 2.8 40.7 + - + +
146A GLY* 4.2 5.4 - - - +
164A ILE* 3.9 16.8 - - + -
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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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89A PRO* 6.1 3.1 - - + -
94A HIS* 3.9 48.2 - - + +
95A GLN 2.7 17.0 + - - +
96A GLN* 3.2 16.8 - - + +
97A VAL* 3.0 30.5 + - - +
133A ALA* 4.1 2.2 - - - +
134A ILE* 1.3 75.2 - - - +
136A ALA* 1.3 62.6 + - - +
139A LYS 4.7 4.0 - - - +
140A GLN 3.4 27.1 - - - +
141A HIS* 3.9 2.5 - - - +
142A ALA* 3.6 34.3 - - - +
143A LEU* 4.2 2.2 - - - -
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Residues in contact with ALA 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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96A GLN* 3.8 6.6 - - - +
97A VAL* 3.8 5.6 - - + -
102A ILE* 3.5 36.1 - - + -
135A MET* 1.3 77.3 - - - +
137A GLU* 1.3 55.1 + - - +
138A GLY 3.1 0.5 + - - -
139A LYS* 2.7 40.0 + - + +
141A HIS 4.8 0.4 + - - -
143A LEU* 4.4 7.4 - - + +
43B TYR* 3.7 21.6 + - - +
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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