Contacts of the strand formed by residues 128 - 132 (chain C) in PDB entry 6PUO
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 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C LEU* 5.7 2.9 - - - -
63C ILE* 5.5 0.8 - - - +
127C PHE* 1.3 91.8 - - - +
129C ASP* 1.3 59.8 + - - +
141C LYS* 3.7 6.9 - - - +
142C TYR* 2.9 36.4 + - - +
162C TRP* 5.2 2.1 + - - -
259C SER 4.6 7.4 - - - -
260C PHE* 4.8 7.9 - - - -
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLY* 1.3 73.9 - - - -
130C ILE* 1.3 84.5 + - - +
139C VAL* 3.3 24.5 - - - +
140C LYS 2.9 22.8 + - - +
141C LYS* 4.3 17.8 - - + +
142C TYR* 3.4 5.5 - - - -
259C SER 3.1 22.4 + - - +
260C PHE* 3.3 34.8 - - + +
262C ALA* 3.3 9.0 - - - +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ASP* 1.3 83.4 + - - +
131C VAL* 1.3 72.3 + - - +
132C PHE* 4.9 9.9 - - + -
139C VAL* 3.4 2.6 - - - +
140C LYS* 2.9 54.4 + - + +
142C TYR* 4.0 15.0 - - + -
253C LEU* 3.8 34.1 - - + -
260C PHE 5.4 0.7 - - - -
262C ALA* 3.5 16.2 - - + +
264C TYR* 3.9 25.6 - - + -
277C LEU* 4.9 11.2 - - + -
284C PHE* 5.0 10.1 - - + -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ILE* 1.3 80.5 - - - +
132C PHE* 1.3 76.4 + - - +
136C SER 4.3 10.1 - - - +
137C GLN* 4.7 6.1 - - - +
138C LYS 3.7 21.3 - - - +
139C VAL* 4.4 10.5 - - + -
140C LYS* 6.0 0.7 - - - -
260C PHE 5.6 0.7 - - - +
261C PRO* 5.0 5.8 - - + -
262C ALA 3.0 34.8 + - - +
263C GLU* 3.5 6.3 - - + +
264C TYR* 3.2 13.5 + - - +
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ILE* 4.9 8.7 - - + -
131C VAL* 1.3 81.0 - - - +
133C THR* 1.3 61.4 + - - +
134C GLY 3.0 8.7 + - - -
135C LEU* 3.8 20.8 + - + -
136C SER* 3.7 22.1 + - - +
138C LYS 5.0 0.6 + - - -
140C LYS* 3.6 28.7 - - + -
264C TYR* 3.5 42.4 - + - +
266C LEU* 5.0 13.0 - - + -
277C LEU* 4.9 6.5 - - + -
278C ASP 3.2 26.7 - - - -
279C SER* 3.6 35.0 - - - -
284C PHE* 4.5 9.6 - + - -
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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