Contacts of the strand formed by residues 385 - 388 (chain A) in PDB entry 4WB9
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 THR 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PHE* 3.8 3.5 - - - -
358A ILE* 3.9 9.9 - - + +
368A LEU* 3.7 17.9 - - + -
370A CYS 3.5 13.9 - - - +
372A GLY* 3.0 22.0 + - - +
383A GLN 2.6 20.9 + - - -
384A PRO* 1.3 72.3 - - - +
386A VAL* 1.3 67.0 + - - +
387A PHE* 3.7 23.1 - - + -
404A PRO 3.0 11.4 + - - +
405A VAL* 3.3 10.4 - - + -
406A GLN 2.8 26.2 + - - -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 4.3 1.6 - - + -
320A VAL* 5.5 0.4 - - + -
323A SER 4.8 0.9 - - - +
324A VAL* 4.1 19.1 - - + +
327A ALA* 3.7 28.0 - - + -
368A LEU* 3.8 9.2 - - - +
369A GLU* 3.0 32.1 + - + -
370A CYS* 3.4 17.9 + - - -
385A THR* 1.3 80.7 - - - +
387A PHE* 1.3 68.3 + - - +
388A SER 4.7 0.2 - - - +
406A GLN* 3.5 31.6 - - + +
408A ILE* 4.0 19.7 - - + -
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Residues in contact with PHE 387 (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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358A ILE* 3.5 35.4 - - + -
361A GLY* 4.1 4.5 - - - -
362A LYS* 4.0 19.7 - - + -
366A ALA* 3.5 17.0 - - + -
367A LYS 3.3 11.7 - - - +
368A LEU* 3.7 28.0 - - + -
385A THR* 3.7 14.1 - - + -
386A VAL* 1.3 76.1 - - - +
388A SER* 1.3 54.4 + - - +
390A VAL* 3.6 18.6 - - + +
396A ILE* 3.7 20.2 - - + -
405A VAL* 3.9 14.6 - - + -
406A GLN 2.8 11.0 + - - +
407A GLN* 3.9 11.2 - - - +
408A ILE* 2.8 35.3 + - - +
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Residues in contact with SER 388 (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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316A TYR* 3.5 11.4 - - - -
320A VAL* 4.0 22.4 - - - -
367A LYS* 2.9 41.1 + - - +
369A GLU* 2.4 31.8 + - - +
387A PHE* 1.3 73.3 - - - +
389A ASN* 1.3 70.4 + - - +
390A VAL* 3.1 5.9 + - - +
408A ILE* 3.4 8.1 - - - -
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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