Contacts of the strand formed by residues 252 - 257 (chain C) in PDB entry 2QC8
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 CYS 252 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C MET* 3.7 30.7 - - - -
134C GLU 3.2 13.7 - - - -
135C GLN* 3.9 20.2 - - - +
218C LEU* 4.0 8.7 - - - -
251C GLY* 1.3 74.5 - - - +
253C HIS* 1.3 67.6 + - - +
254C THR* 3.1 14.0 + - - -
342C PRO* 2.8 19.6 + - - +
343C SER 3.2 20.6 - - - +
344C ALA* 3.9 3.8 - - - -
346C CYS* 3.8 9.9 - - - -
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Residues in contact with HIS 253 (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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132C GLY 3.4 2.3 - - - +
133C MET* 3.4 3.3 - - - -
134C GLU* 2.9 50.1 + - + +
136C GLU* 4.4 3.9 + - - -
251C GLY 4.8 1.3 - - - -
252C CYS* 1.3 76.7 - - - +
254C THR* 1.3 59.0 + - - +
255C ASN* 3.9 1.1 + - - -
299C ARG* 4.6 0.4 - - - -
338C GLU* 2.9 16.5 + - + +
339C ASP 3.4 6.5 - - - +
340C ARG* 3.4 39.0 + - - +
342C PRO* 4.8 0.4 - - - -
401C MN 4.3 3.1 - - - -
402C MN 2.3 24.5 + - - -
601C P3S 2.6 60.6 + - + +
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Residues in contact with THR 254 (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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131C PHE* 4.1 10.1 - - + -
132C GLY 3.5 2.5 - - - -
133C MET* 3.4 31.3 - - + +
252C CYS 3.1 12.7 + - - -
253C HIS* 1.3 71.0 - - - +
255C ASN* 1.3 67.2 + - - +
256C PHE* 4.0 2.8 + - - +
337C PHE* 4.0 0.3 - - - +
338C GLU* 3.7 0.4 - - - -
339C ASP* 2.7 44.6 + - - +
342C PRO* 3.7 3.2 - - - +
351C VAL* 3.4 19.4 - - + +
352C THR* 5.1 0.2 - - + -
355C LEU* 3.6 27.8 - - + -
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Residues in contact with ASN 255 (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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131C PHE* 3.3 8.1 - - - +
132C GLY 2.6 49.5 + - - +
134C GLU* 3.3 20.2 + - - +
253C HIS 4.0 3.6 + - - -
254C THR* 1.3 75.4 - - - +
256C PHE* 1.3 60.6 + - - +
326C PRO* 5.2 0.3 - - - +
336C TYR* 3.5 20.0 - - + -
337C PHE 3.2 3.8 - - - -
338C GLU* 3.2 27.2 - - - +
501C ADP 3.2 47.6 + - - +
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Residues in contact with PHE 256 (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 PRO* 3.9 18.4 - - + -
130C TRP 3.5 7.4 - - - -
131C PHE* 3.5 24.2 - + + -
254C THR 4.7 1.6 - - - +
255C ASN* 1.3 75.6 - - - +
257C SER* 1.3 78.9 + - - +
258C THR* 4.0 17.5 - - + -
261C MET* 4.3 9.1 - - + +
336C TYR* 3.2 4.6 - - - +
337C PHE* 2.8 70.1 + + + +
355C LEU* 4.1 27.6 - - + -
356C ILE* 4.1 13.7 - - + -
359C CYS* 4.1 24.0 - - + -
360C LEU* 4.4 5.8 - - + -
501C ADP 3.9 0.8 - - - -
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Residues in contact with SER 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PRO* 3.4 4.2 - - - +
130C TRP* 2.9 32.0 + - - +
256C PHE* 1.3 78.6 - - - +
258C THR* 1.3 62.9 + - - +
261C MET* 3.8 7.4 - - - -
262C ARG* 3.0 19.4 + - - -
335C GLY 3.3 25.8 - - - -
336C TYR* 3.7 2.0 - - - -
501C ADP 2.8 33.1 + - - -
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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