Contacts of the strand formed by residues 389 - 394 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.8 8.5 - - + -
49A TRP* 4.2 6.5 - - + -
86A LEU* 4.6 7.4 - - + -
382A TRP* 3.6 4.5 - - - +
383A ASN* 2.7 50.1 + - + +
386A GLU* 3.2 31.3 + - + +
387A PRO 3.1 0.8 - - - -
388A TRP* 1.3 78.6 - - - +
390A ILE* 1.3 56.4 + - - +
401A VAL* 3.9 24.0 - - + -
402A TRP 3.3 9.6 - - - +
403A GLN* 3.6 26.9 - - + +
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Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TRP* 4.4 1.8 - - - -
334A ALA* 4.8 1.1 - - + -
342A LEU* 4.3 12.3 - - + -
344A VAL* 4.7 3.6 - - + -
380A PHE* 4.2 17.9 - - + -
381A SER 3.5 5.4 - - - +
382A TRP* 3.6 55.0 - - + +
388A TRP 4.4 3.1 - - - +
389A VAL* 1.3 76.3 - - - +
391A CYS* 1.3 74.8 + - - +
392A SER 4.1 0.4 - - - +
401A VAL* 3.4 4.3 - - - +
402A TRP* 2.9 76.5 + - + +
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Residues in contact with CYS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.4 6.1 - - - +
49A TRP* 3.5 30.2 - - + +
66A LEU* 3.8 28.3 - - + -
68A LEU* 5.1 0.7 - - - -
380A PHE* 3.0 4.2 - - - -
381A SER* 2.9 37.2 + - - +
390A ILE* 1.3 73.2 - - - +
392A SER* 1.3 61.4 + - - +
393A VAL* 4.2 11.0 - - - -
399A MET* 3.8 23.8 - - - -
400A GLN 3.3 5.6 - - - +
401A VAL* 4.2 3.8 - - + +
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU* 4.1 13.9 - - - -
370A HIS* 4.1 0.5 + - - -
373A HIS* 2.8 31.1 + - - -
377A ILE* 4.5 5.2 - - - -
379A ASP 3.7 4.9 - - - -
380A PHE* 3.9 14.1 - - - -
390A ILE 4.0 0.6 - - - -
391A CYS* 1.3 72.7 - - - +
393A VAL* 1.3 64.5 + - - +
399A MET* 3.5 1.9 - - - -
400A GLN 2.8 35.3 + - - -
402A TRP* 3.0 22.3 + - - -
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 5.2 1.8 - - + -
44A SER* 3.3 29.6 - - - +
46A THR 3.8 16.8 - - - +
47A ALA* 4.2 8.7 - - + -
68A LEU* 4.1 20.6 - - + -
373A HIS* 4.3 2.0 - - - -
377A ILE* 3.6 3.9 - - - +
378A SER* 2.9 23.6 + - - -
379A ASP* 3.1 22.7 + - + +
391A CYS* 4.2 1.8 - - - -
392A SER* 1.3 79.9 - - - +
394A SER* 1.3 60.1 + - - +
398A ILE 3.4 6.7 - - - +
399A MET* 4.0 23.1 - - + -
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 4.0 5.4 - - - +
44A SER 4.5 5.3 + - - +
373A HIS* 2.8 29.3 + - - +
375A ALA* 3.7 13.9 - - - -
376A LYS 3.2 15.9 - - - -
377A ILE* 4.3 0.7 - - - -
378A SER* 4.2 3.6 - - - +
393A VAL* 1.3 73.9 - - - +
395A GLU* 1.3 66.1 + - - +
396A ASP* 2.8 23.3 + - - -
397A ASN* 3.2 14.7 + - - -
398A ILE* 3.0 12.3 + - - +
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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