Contacts of the strand formed by residues 389 - 394 (chain B) in PDB entry 4PBY
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 VAL 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.8 7.6 - - + -
49B TRP* 4.2 9.0 - - + -
86B LEU* 4.3 13.2 - - + -
382B TRP* 3.7 3.6 - - - -
383B ASN* 2.9 39.6 + - + +
386B GLU* 3.1 31.0 + - + +
387B PRO 3.1 0.2 - - - -
388B TRP* 1.3 77.8 + - - +
390B ILE* 1.3 66.4 + - - +
401B VAL* 4.0 25.8 - - + -
402B TRP 3.4 5.4 - - - +
403B GLN* 3.6 25.8 - - + +
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ALA* 4.7 1.3 - - + -
342B LEU* 4.2 14.4 - - + -
344B VAL* 4.6 2.5 - - + -
380B PHE* 4.2 13.5 - - + -
381B SER 3.4 8.5 - - - +
382B TRP* 3.6 46.4 - - + -
388B TRP 3.6 3.1 + - - +
389B VAL* 1.3 84.5 - - - +
391B CYS* 1.3 72.3 + - - +
401B VAL* 3.3 3.3 - - - +
402B TRP* 2.9 83.4 + - + +
404B MET* 6.4 0.2 - - + -
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Residues in contact with CYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.5 5.5 - - - +
49B TRP* 3.5 32.8 - - + +
66B LEU* 3.7 28.9 - - + -
68B LEU* 5.1 0.7 - - - -
380B PHE* 3.0 3.8 - - - +
381B SER 2.7 37.7 + - - +
390B ILE* 1.3 73.0 - - - +
392B SER* 1.3 60.8 + - - +
393B VAL* 4.2 12.6 - - - -
399B MET* 4.1 19.3 - - - -
400B GLN 3.2 9.9 - - - +
401B VAL* 4.2 2.5 - - + +
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.9 15.3 - - - -
370B HIS* 3.9 0.2 + - - -
373B HIS* 2.8 31.7 + - - -
377B ILE* 4.7 4.0 - - - -
379B ASP 3.6 6.1 - - - -
380B PHE* 3.8 13.9 - - - +
390B ILE* 4.5 0.2 - - - -
391B CYS* 1.3 73.7 - - - +
393B VAL* 1.3 60.8 + - - +
399B MET* 3.5 0.7 - - - -
400B GLN 2.7 37.0 + - - -
402B TRP* 3.0 21.7 + - - -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.7 6.1 - - + -
44B SER* 3.5 24.0 - - - +
46B THR 3.8 17.7 - - - +
47B ALA* 4.0 6.1 - - + -
68B LEU* 4.2 16.2 - - + -
373B HIS* 4.4 0.9 - - - -
377B ILE* 3.7 2.0 - - - -
378B SER* 2.9 29.5 + - - -
379B ASP* 3.1 22.3 + - + +
391B CYS* 4.2 11.0 - - - -
392B SER* 1.3 78.1 - - - +
394B SER* 1.3 55.7 + - - +
398B ILE 3.5 5.6 - - - +
399B MET* 4.0 24.2 - - + -
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 4.3 5.7 - - - +
44B SER 4.7 5.1 + - - +
373B HIS* 2.9 29.4 + - - +
375B ALA 3.7 13.0 - - - -
376B LYS 3.2 17.0 - - - -
377B ILE* 4.1 1.3 - - - +
378B SER* 4.2 3.8 - - - +
393B VAL* 1.3 73.1 - - - +
395B GLU* 1.3 58.8 + - - +
396B ASP* 2.7 30.7 + - - -
397B ASN* 3.2 13.2 + - - -
398B ILE* 2.9 14.2 + - - +
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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