Contacts of the strand formed by residues 253 - 256 (chain C) in PDB entry 2UZ1
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 ARG 253 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C VAL 3.9 3.4 - - - -
242C LEU* 4.5 12.3 + - - +
245C LEU* 2.9 47.0 + - + +
246C SER* 4.8 0.6 + - - -
248C LEU* 3.4 22.0 - - + +
249C PRO 3.3 13.7 - - - +
250C ASP* 3.1 20.8 + - - +
251C ALA 3.4 1.4 - - - +
252C MET* 1.3 74.9 - - - +
254C GLY* 1.3 62.6 + - - +
255C GLY* 3.3 3.3 + - - +
349C VAL* 4.7 5.2 - - - +
350C THR* 5.4 2.8 + - - -
405C SER 2.9 25.5 + - - +
406C ARG* 4.3 6.9 + - - +
407C VAL 2.9 24.5 + - - -
408C LYS* 3.8 30.9 - - - +
409C PRO* 4.8 1.4 - - - +
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Residues in contact with GLY 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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234C PRO* 4.8 0.2 - - - +
235C VAL 2.7 16.9 + - - +
236C PHE* 3.3 37.1 - - - -
252C MET 3.4 2.8 + - - -
253C ARG* 1.3 75.0 - - - +
255C GLY* 1.3 62.8 + - - +
259C ASN* 3.7 14.6 + - - -
349C VAL* 3.8 12.7 - - - +
353C ALA* 5.3 4.2 - - - +
405C SER* 4.8 0.7 - - - -
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Residues in contact with GLY 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C VAL 3.5 4.4 + - - -
236C PHE* 3.1 5.9 - - - +
237C ALA 2.9 23.6 + - - -
242C LEU* 4.3 7.0 - - - -
245C LEU* 3.7 16.6 - - - +
253C ARG* 3.3 5.2 - - - -
254C GLY* 1.3 77.5 - - - +
256C LEU* 1.3 63.5 + - - -
405C SER* 3.6 20.0 - - - -
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Residues in contact with LEU 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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236C PHE* 3.8 2.1 - - - -
237C ALA 3.3 11.9 - - - +
238C ASP* 3.8 20.2 - - - +
239C TYR* 3.9 20.6 - - + +
242C LEU* 4.0 22.6 - - + +
255C GLY* 1.3 72.5 - - - -
257C VAL* 1.3 59.7 + - - +
258C GLN* 3.1 29.2 - - + +
259C ASN* 2.9 30.1 + - - +
401C SER* 3.6 34.5 - - - +
404C MET* 4.4 9.2 - - + -
405C SER* 2.9 17.4 + - - +
412C PHE* 5.0 1.6 - - + -
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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
------------------------------------------------------------
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