Contacts of the strand formed by residues 288 - 295 (chain B) in PDB entry 4Y5U
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 LYS 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287B THR* 1.3 81.2 - - + +
289B PHE* 1.3 64.6 + - - +
290B GLN* 4.8 8.2 - - - +
361B LYS* 3.1 18.2 + - - +
362B ASN* 2.5 39.4 + - + +
363B LEU 3.3 10.3 - - - +
364B LEU* 4.0 10.7 - - + +
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Residues in contact with PHE 289 (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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279B PRO* 4.4 8.5 - - + -
280B PRO* 4.0 21.8 - - + -
283B LEU* 3.4 42.0 - - + -
287B THR 3.5 10.3 - - - -
288B LYS* 1.3 75.0 - - - +
290B GLN* 1.3 74.7 + - - +
291B ALA* 5.8 0.2 - - + -
315B MET* 5.3 2.2 - - + -
340B ILE* 3.8 26.2 - - + -
360B PHE 3.8 0.2 - - - +
361B LYS 3.8 1.2 - - - +
363B LEU* 2.5 62.8 + - + +
364B LEU* 3.7 22.4 - - - -
365B LEU* 3.7 13.7 - - + -
386B VAL* 5.2 9.2 - - + -
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Residues in contact with GLN 290 (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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277B LYS* 3.5 34.8 + - + +
279B PRO* 3.4 21.3 - - - +
280B PRO* 4.0 3.4 - - - +
288B LYS* 4.8 8.8 - - + +
289B PHE* 1.3 84.0 - - - +
291B ALA* 1.3 63.4 + - - +
359B LEU* 4.0 13.8 - - + +
360B PHE 3.3 8.7 - - - +
361B LYS* 3.4 36.1 + - - +
363B LEU* 4.3 4.3 - - - -
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Residues in contact with ALA 291 (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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277B LYS* 3.2 20.2 - - - +
279B PRO* 4.1 14.1 - - + -
289B PHE* 5.8 0.2 - - + -
290B GLN* 1.3 75.3 - - - +
292B GLY* 1.3 58.3 + - - +
359B LEU* 3.7 5.3 - - - +
360B PHE* 2.9 31.0 + - - +
363B LEU* 4.0 10.2 - - + +
386B VAL* 6.3 0.2 - - + -
388B PHE* 3.5 33.0 - - + -
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Residues in contact with GLY 292 (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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275B VAL* 3.6 5.7 - - - +
276B GLU* 2.7 33.1 + - - -
277B LYS* 3.0 18.7 + - - +
291B ALA* 1.3 76.1 - - - +
293B VAL* 1.3 57.9 + - - -
357B SER* 6.5 0.2 - - - -
358B ALA 3.5 10.5 - - - -
359B LEU* 4.2 7.9 - - - -
360B PHE* 4.5 2.2 - - - -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 4.2 14.1 - - + -
274B LEU 3.3 14.8 - - - +
275B VAL* 4.1 6.3 - - - -
276B GLU* 4.9 0.2 - - - -
292B GLY* 1.3 76.2 - - - -
294B ARG* 1.3 62.4 + - - +
311B VAL* 3.8 28.0 - - + -
347B LEU* 4.9 1.6 - - + -
357B SER* 3.3 4.7 - - - -
358B ALA* 2.9 41.8 + - + +
360B PHE* 3.8 9.9 - - + -
388B PHE* 3.7 34.3 - - + -
405B ALA* 4.1 7.2 - - + -
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Residues in contact with ARG 294 (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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220B SER* 5.0 1.0 + - - -
221B LEU* 3.5 38.1 - - + +
222B ALA* 4.0 6.9 - - - +
225B GLN* 3.0 26.1 + - - -
272B CYS 3.4 2.3 - - - +
273B PHE* 3.7 4.3 - - - -
274B LEU* 3.0 31.2 + - + +
276B GLU* 3.6 40.0 + - + +
292B GLY 4.4 0.2 + - - -
293B VAL* 1.3 76.6 - - - +
295B PHE* 1.3 62.5 + - - +
296B LEU* 4.0 18.6 - - + +
347B LEU* 5.0 0.7 - - - -
354B ASN 3.8 3.8 + - - -
355B CYS* 3.1 30.1 - - - +
356B CYS 3.2 16.6 - - - +
357B SER* 4.1 5.2 - - - +
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Residues in contact with PHE 295 (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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225B GLN* 4.6 0.3 - - - +
269B VAL* 3.5 30.3 - - + -
272B CYS* 3.5 20.2 - - + -
273B PHE* 4.2 6.1 - + + -
294B ARG* 1.3 76.1 - - - +
296B LEU* 1.3 64.4 + - - +
297B LEU* 3.4 14.5 + - + -
298B GLY* 3.3 33.2 - - - -
301B PHE* 5.0 1.1 - + + -
302B LEU* 4.4 14.4 - - + -
347B LEU* 4.1 20.1 - - + +
356B CYS* 2.7 35.2 + - - +
392B PHE* 3.9 35.9 - + - -
403B LEU* 4.0 15.7 - - + -
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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