Contacts of the strand formed by residues 127 - 133 (chain B) in PDB entry 2R92
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 GLY 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TYR 3.1 14.4 - - - +
97B VAL* 3.6 2.3 - - - +
98B THR* 2.6 38.1 + - - +
101B MET* 3.9 13.1 - - - +
126B SER* 1.3 71.7 + - - +
128B LEU* 1.3 68.2 + - - +
129B PHE* 4.0 2.0 - - - -
166B PHE* 4.2 10.5 - - - -
168B GLY 4.0 3.6 - - - -
169B ARG* 4.8 0.7 - - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 5.5 7.0 - - + -
95B ILE* 4.5 15.0 - - + -
96B TYR 3.6 2.7 - - - +
97B VAL* 5.6 4.7 - - + -
126B SER* 3.8 1.1 - - - +
127B GLY* 1.3 78.1 - - - +
129B PHE* 1.3 65.3 + - - +
130B VAL 4.3 0.2 - - - -
166B PHE* 3.2 1.5 - - - -
167B ILE* 2.6 60.2 + - + +
168B GLY 2.9 10.1 + - - +
170B LEU* 3.3 47.8 - - + +
417B PHE* 4.1 31.2 - - + -
453B ILE* 4.3 9.4 - - + -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.0 3.6 - - - +
96B TYR* 2.4 61.4 + + + -
98B THR* 4.0 26.9 - - + -
101B MET* 5.0 10.5 - - + -
127B GLY 5.1 0.2 - - - -
128B LEU* 1.3 85.1 - - - +
130B VAL* 1.3 61.2 + - - +
164B LYS 4.5 10.1 - - - +
165B VAL 2.9 6.5 - - - +
166B PHE* 3.3 44.0 - + + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.3 14.1 - - + -
92B PHE* 4.1 24.5 - - + -
93B GLY 3.2 29.4 - - - +
94B LYS 3.2 3.6 - - - +
95B ILE* 3.2 36.1 - - + -
129B PHE* 1.3 73.2 - - - +
131B ASP* 1.3 61.4 + - - +
132B VAL* 3.2 9.7 + - - +
165B VAL* 2.8 34.7 + - - +
167B ILE* 3.3 23.8 - - + +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.0 0.3 - - - -
93B GLY* 3.0 26.2 + - - -
94B LYS* 3.1 24.5 + - - +
96B TYR* 2.9 35.3 + - - -
130B VAL* 1.3 68.7 - - - +
132B VAL* 1.3 64.0 + - - +
133B LYS* 4.4 9.3 - - + +
164B LYS* 3.0 33.7 + - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.3 30.1 - - + -
91B SER 3.6 9.6 - - - +
92B PHE* 4.1 23.6 - - + -
130B VAL 3.2 14.1 + - - +
131B ASP* 1.3 74.8 - - - +
133B LYS* 1.3 68.3 - - - +
164B LYS* 3.6 28.6 + - + +
165B VAL* 3.6 26.7 - - + -
167B ILE* 5.2 2.7 - - + -
448B ILE* 5.3 5.8 - - + -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.3 35.0 - - - +
91B SER* 3.6 27.0 + - - +
93B GLY* 4.8 16.0 - - - +
131B ASP* 4.4 14.1 - - - +
132B VAL* 1.3 84.0 - - - +
164B LYS* 5.4 1.3 - - - +
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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