Contacts of the strand formed by residues 301 - 305 (chain B) in PDB entry 1PE0
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 LEU 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ASP 3.4 18.0 + - - +
269B VAL* 3.3 15.2 - - + -
270B VAL 3.2 11.4 + - - -
295B GLN* 2.9 20.4 + - - +
300B GLY* 1.3 71.2 - - - -
302B ILE* 1.3 71.3 + - - +
348B LYS* 4.7 8.1 - - - -
350B GLY 4.5 3.8 - - - +
351B LEU* 3.6 38.6 - - + +
352B ILE 4.3 0.4 - - - +
353B LEU* 4.1 23.6 - - + -
368B ILE* 4.7 4.7 - - + -
371B ALA* 3.9 16.6 - - + -
372B LEU* 3.6 27.4 - - + -
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.6 9.4 - - + +
272B LEU* 4.9 2.9 - - + -
292B LEU* 3.8 35.4 - - + +
295B GLN* 3.5 26.5 - - + -
296B GLU* 4.3 8.3 - - + +
300B GLY 3.9 3.4 - - - +
301B LEU* 1.3 73.8 - - - +
303B ALA* 1.3 67.3 + - - +
312B LEU* 3.7 27.9 - - + +
317B ILE* 3.8 25.8 - - + -
351B LEU 3.0 13.1 + - - +
352B ILE* 3.7 9.0 - - + +
353B LEU* 2.9 26.3 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B VAL* 4.2 10.7 - - + +
270B VAL 3.0 8.4 + - - +
271B VAL* 3.3 5.0 - - + +
272B LEU* 2.8 26.9 + - - +
301B LEU* 4.2 1.1 - - + -
302B ILE* 1.3 76.2 - - - +
304B ALA* 1.3 60.7 + - - +
353B LEU* 3.1 11.9 - - + +
364B PHE* 3.6 22.9 - - + -
368B ILE* 3.8 23.6 - - + -
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.4 17.9 - - + +
302B ILE 4.3 0.2 - - - -
303B ALA* 1.3 74.1 - - - +
305B ILE* 1.3 61.5 + - - +
308B GLY 3.8 5.4 - - - +
309B PRO* 3.6 32.1 - - + +
312B LEU* 4.2 15.7 - - + -
353B LEU 2.9 7.3 + - - +
354B THR* 3.1 28.4 - - + -
355B SER 3.1 2.1 + - - -
364B PHE* 3.6 3.6 - - - -
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLU* 3.9 21.1 - - + +
272B LEU 3.2 11.9 + - - +
273B PRO* 4.0 8.7 - - + -
274B GLY* 3.3 6.6 - - - -
304B ALA* 1.3 76.5 - - - +
306B CYS* 1.3 70.7 + - + +
308B GLY* 2.9 17.8 + - - -
309B PRO* 3.6 2.7 - - - -
355B SER* 3.6 28.9 - - - +
357B GLY 3.4 27.4 - - - +
360B THR* 3.8 2.0 - - - +
361B SER* 3.7 20.0 - - - +
364B PHE* 3.7 32.5 - - + -
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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