Contacts of the strand formed by residues 297 - 302 (chain B) in PDB entry 2PO5
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 TYR 297 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLN* 3.2 25.1 + - + -
279A GLU* 5.0 5.4 + - - +
398A GLN* 2.8 64.7 + - + +
401A LEU* 3.8 5.6 - - - +
258B ILE* 3.1 19.5 - - + +
260B PHE* 3.9 13.9 - + + -
284B VAL* 3.7 28.3 - - + -
285B GLN* 3.4 19.3 + - - -
288B MET* 3.5 41.7 - - + -
293B TYR* 4.4 8.9 - + - -
296B PRO* 1.3 75.4 - - - +
298B ARG* 1.3 86.5 + - - +
299B LEU 5.1 0.2 - - - -
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Residues in contact with ARG 298 (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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226A ARG* 5.7 0.2 - - - +
273A GLY* 3.0 32.9 + - - +
274A ASP 4.9 0.7 - - - -
275A PRO* 3.3 32.0 - - - +
398A GLN* 4.0 12.6 + - - +
401A LEU* 3.0 50.1 + - + +
402A SER 4.5 2.0 - - - -
403A CYS* 3.8 20.8 - - - +
404A PRO* 4.2 18.6 - - + -
258B ILE 3.1 4.8 + - - +
259B LEU* 3.6 19.2 - - + +
260B PHE* 3.0 25.0 + - - +
297B TYR* 1.3 90.9 + - - +
299B LEU* 1.3 69.1 + - - +
300B VAL* 3.7 5.9 + - + -
313B PRO* 5.2 0.7 - - + -
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Residues in contact with LEU 299 (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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278A GLN* 4.1 23.2 - - + +
260B PHE* 3.4 21.8 - - + +
262B ALA* 4.5 3.6 - - + -
280B VAL* 3.9 15.3 - - + -
281B SER* 3.6 36.8 - - - +
284B VAL* 3.8 22.9 - - + -
297B TYR* 4.6 2.0 - - - -
298B ARG* 1.3 77.1 - - - +
300B VAL* 1.3 68.3 + - - +
301B TRP* 3.6 34.6 + - + -
313B PRO* 4.2 8.7 - - - +
335B ILE* 4.4 3.1 - - + -
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Residues in contact with VAL 300 (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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404A PRO* 5.3 0.2 - - + -
259B LEU* 4.0 24.7 - - + -
260B PHE 2.7 26.6 + - - +
261B SER* 3.3 2.0 - - - -
262B ALA 3.0 22.7 + - - -
298B ARG* 4.5 7.2 - - + -
299B LEU* 1.3 81.2 - - - +
301B TRP* 1.3 68.9 + - - +
313B PRO* 3.6 19.3 - - + +
315B THR* 3.4 30.7 - - + +
318B SER* 3.3 29.8 - - - +
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Residues in contact with TRP 301 (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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262B ALA* 3.1 23.1 - - + +
263B CYS 3.6 16.6 - - - -
264B SER* 3.4 23.8 - - - -
276B TYR* 3.8 24.2 - + - -
277B PRO* 3.9 24.0 - - + -
280B VAL* 4.1 7.2 - - + -
281B SER* 5.0 1.3 - - - -
299B LEU* 3.6 41.3 + - + -
300B VAL* 1.3 76.5 - - - +
302B GLN* 1.3 60.3 + - - +
304B LYS* 6.0 0.5 - - - +
311B LEU* 3.5 34.7 - - + +
312B GLY 3.2 35.2 + - - -
313B PRO* 2.9 7.4 + - - +
314B GLN* 3.2 12.1 - - - +
315B THR* 2.9 25.3 + - - -
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Residues in contact with GLN 302 (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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261B SER* 2.5 30.1 + - - +
262B ALA 2.8 18.1 + - - +
263B CYS* 3.7 4.4 - - - -
264B SER* 2.8 25.6 + - - -
301B TRP* 1.3 73.4 - - - +
303B SER* 1.3 75.5 + - - +
304B LYS 3.4 2.5 - - - -
314B GLN* 6.0 0.2 - - - -
315B THR* 3.4 18.8 + - - +
334B PRO* 5.6 0.2 - - - +
337B PHE* 4.8 4.9 - - - -
343B GLU* 3.1 39.7 + - - +
347B GLU* 3.4 22.4 + - - +
348B LEU* 3.3 22.4 - - - +
352B TYR* 4.3 3.6 - - + -
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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