Contacts of the strand formed by residues 383 - 392 (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 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B THR* 4.6 0.9 - - - -
318B GLU* 3.8 33.7 + - - +
381B GLU 3.4 9.3 + - - +
382B GLU* 1.3 72.9 - - - +
384B CYS* 1.3 65.2 + - - +
409B PRO* 4.1 14.4 - - + -
410B LEU 3.4 8.5 - - - +
411B VAL* 4.5 2.5 - - + -
425B THR* 3.9 27.5 + - + +
426B ILE* 5.6 2.0 - - + +
428B TRP* 6.0 0.2 - - - -
429B ASP* 3.0 36.7 + - + +
440B PHE* 3.7 36.3 - - + -
442B VAL* 3.9 10.5 - - - +
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Residues in contact with CYS 384 (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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315B MET* 3.8 23.1 - - + -
316B VAL 3.0 18.6 - - - +
317B THR* 4.2 4.7 - - + -
318B GLU 4.6 1.1 - - - +
382B GLU 4.9 3.8 - - - -
383B LYS* 1.3 78.5 - - - +
385B ALA* 1.3 59.7 + - - +
409B PRO* 3.3 2.9 - - - +
410B LEU* 2.5 49.3 + - - -
412B VAL* 4.3 20.4 - - - -
440B PHE* 4.2 9.0 - - - -
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Residues in contact with ALA 385 (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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315B MET* 3.2 8.0 - - - +
316B VAL* 2.7 39.4 + - + -
384B CYS* 1.3 76.9 - - - +
386B VAL* 1.3 60.9 + - - +
406B LEU* 4.2 14.1 - - + -
407B SER* 3.8 16.2 - - - +
408B LEU 4.3 1.3 - - - +
410B LEU* 3.6 5.8 - - - -
440B PHE* 3.7 25.0 - - + -
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO* 4.5 13.2 - - + -
283B LEU* 6.0 0.2 - - + -
289B PHE* 5.2 9.6 - - + -
313B ALA* 4.2 3.4 - - + -
314B ASP 3.8 14.4 - - - +
315B MET* 4.3 13.7 - - + +
340B ILE* 4.1 15.0 - - + -
363B LEU* 6.0 1.3 - - + -
385B ALA* 1.3 76.6 - - - +
387B LEU* 1.3 69.4 + - - +
388B PHE* 3.5 33.2 - - + -
406B LEU* 4.5 0.2 - - - -
407B SER* 3.1 32.0 + - - +
410B LEU* 3.8 18.2 - - + -
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Residues in contact with LEU 387 (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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312B ARG 3.9 0.5 - - - +
313B ALA* 3.6 1.7 - - - -
314B ASP* 2.9 44.2 + - + +
316B VAL* 4.1 17.2 - - + +
323B GLU* 4.9 8.7 - - - +
385B ALA 3.9 1.8 - - - -
386B VAL* 1.3 73.3 - - - +
388B PHE* 1.3 63.5 + - - +
389B SER* 4.1 12.5 + - - +
404B GLN* 4.0 34.5 - - + +
405B ALA 3.5 10.3 - - - +
406B LEU* 3.4 28.0 - - + +
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Residues in contact with PHE 388 (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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273B PHE* 4.3 3.6 - - + -
275B VAL* 3.9 22.0 - - + -
279B PRO* 5.1 0.7 - - + -
291B ALA* 3.5 32.3 - - + -
293B VAL* 3.7 20.9 - - + -
311B VAL* 4.3 4.7 - - + -
312B ARG 3.3 8.1 - - - +
313B ALA* 4.3 9.0 - - + -
360B PHE* 4.0 32.8 - + - -
363B LEU* 5.2 2.0 - - + -
386B VAL* 3.5 34.8 - - + -
387B LEU* 1.3 75.7 - - - +
389B SER* 1.3 61.6 + - - +
404B GLN* 3.4 5.0 - - - -
405B ALA* 2.8 41.9 + - + +
407B SER* 3.9 16.8 - - - -
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Residues in contact with SER 389 (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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273B PHE* 4.9 0.4 - - - -
310B LEU 3.6 2.8 - - - +
311B VAL* 3.4 4.2 - - - +
312B ARG* 3.0 45.6 + - - +
314B ASP* 5.8 2.5 - - - -
387B LEU* 4.3 11.9 - - - +
388B PHE* 1.3 73.8 + - - +
390B ALA* 1.3 61.2 + - - +
402B GLN* 3.8 14.6 + - - -
403B LEU 3.3 2.9 - - - -
404B GLN* 3.5 22.3 - - - +
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Residues in contact with ALA 390 (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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273B PHE* 4.5 9.3 - - + -
309B PRO* 4.8 8.1 - - + -
310B LEU 3.8 11.4 - - - +
311B VAL* 3.5 26.2 - - + -
347B LEU* 5.3 2.7 - - + -
389B SER* 1.3 77.1 - - - +
391B SER* 1.3 58.1 + - - +
402B GLN* 3.6 6.4 + - - +
403B LEU* 2.5 50.2 + - + +
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Residues in contact with SER 391 (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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309B PRO* 3.5 15.1 - - - +
310B LEU 5.0 1.4 + - - +
390B ALA* 1.3 74.3 - - - +
392B PHE* 1.3 67.5 + - - +
400B PRO* 5.4 6.7 - - - -
401B ILE 3.2 8.1 - - - -
402B GLN* 3.3 30.4 + - - +
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Residues in contact with PHE 392 (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* 4.0 8.1 - - + -
295B PHE* 3.9 26.5 - + - -
301B PHE* 3.7 35.4 - + + -
302B LEU* 3.5 25.4 - - + -
309B PRO* 4.0 16.8 - - + -
347B LEU* 6.5 0.7 - - + -
390B ALA* 6.3 0.2 - - + -
391B SER* 1.3 78.8 - - - +
393B THR* 1.3 73.0 + - - +
394B LEU* 4.0 17.3 - - + -
400B PRO* 4.0 2.4 - - - +
401B ILE* 2.6 69.8 + - + +
403B LEU* 4.1 14.4 - - + -
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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