Contacts of the strand formed by residues 270 - 274 (chain C) in PDB entry 2PI8
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 THR 270 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C PHE* 3.6 29.2 - - + -
60C VAL* 3.4 24.9 - - - +
61C TYR* 3.3 27.4 - - - -
64C VAL* 4.2 6.7 - - + -
268C GLY 3.6 1.0 + - - -
269C THR* 1.3 74.4 - - - +
271C LEU* 1.3 66.3 + - - +
292C LEU* 4.5 4.3 - - + -
293C MSE 3.7 2.9 - - - -
294C VAL* 4.7 2.5 - - - -
333C LEU* 2.9 52.7 + - + +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C VAL* 3.8 22.0 - - + -
265C ILE* 4.3 7.4 - - + -
269C THR* 3.8 20.4 - - + +
270C THR* 1.3 83.8 - - - +
272C ILE* 1.3 60.4 + - - +
273C ALA* 3.9 1.7 + - + -
291C ARG 3.5 1.7 - - - +
292C LEU* 3.5 4.3 - - - -
293C MSE 2.6 49.8 + - + +
295C ALA* 4.7 2.9 - - + -
307C PHE* 3.6 39.3 - - + -
330C VAL* 4.1 13.0 - - + -
331C TRP 3.6 3.1 - - - +
332C VAL* 3.7 30.7 - - + -
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Residues in contact with ILE 272 (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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27C PRO* 6.2 3.8 - - + -
33C PRO* 4.3 12.8 - - + -
67C TRP* 4.3 13.2 - - + -
74C THR* 4.4 8.1 - - + -
77C MSE 4.5 9.0 - - + -
271C LEU* 1.3 73.6 - - - +
273C ALA* 1.3 61.3 + - - +
290C LEU* 3.7 35.0 - - + -
291C ARG 3.4 7.9 - - - +
292C LEU* 3.7 17.7 - - + -
330C VAL* 3.5 0.6 - - - +
331C TRP* 2.8 57.6 + - + +
333C LEU* 3.6 21.4 - - + +
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Residues in contact with ALA 273 (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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98C PHE* 3.7 19.3 - - + -
271C LEU 3.9 0.4 + - - +
272C ILE* 1.3 77.3 - - - +
274C GLU* 1.3 59.8 + - - +
275C VAL* 3.4 2.7 + - + +
289C GLU 3.1 4.2 - - - +
290C LEU* 3.4 9.0 - - - +
291C ARG 2.9 32.7 + - - +
293C MSE 3.8 15.7 - - + -
329C ARG 3.3 12.1 - - - +
330C VAL* 3.6 18.2 - - + +
331C TRP* 4.6 1.8 - - - -
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Residues in contact with GLU 274 (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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29C ALA* 3.5 21.8 - - + +
30C VAL* 4.6 10.9 + - - +
98C PHE* 4.1 1.5 - - - -
273C ALA* 1.3 69.8 - - - +
275C VAL* 1.3 64.2 + - - +
276C PRO* 3.3 9.4 - - - +
288C TYR* 3.4 27.0 - - + +
289C GLU* 3.4 2.0 + - - -
290C LEU* 3.5 32.3 + - + +
328C GLY* 3.3 14.9 - - - -
329C ARG* 2.7 57.5 + - - +
331C TRP* 4.1 5.8 - - + -
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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