Contacts of the helix formed by residues 387 - 391 (chain B) in PDB entry 3A8X
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 ASP 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LYS* 5.0 12.2 + - - +
293B GLU* 4.6 3.1 - - - +
297B PHE* 6.1 1.8 - - - -
367B TYR* 3.6 9.7 + - - +
369B ASP* 3.9 21.6 - - - +
371B LYS* 6.0 0.3 - - - -
374B ASN* 3.7 16.6 - - - +
386B THR* 1.3 90.2 + - + +
388B TYR* 1.3 62.3 + - - +
389B GLY* 3.0 21.1 + - - -
390B MET 4.6 2.3 + - - -
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Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 5.3 0.2 - - - +
289B TRP* 5.4 0.5 - - - -
292B THR* 5.3 2.8 - - - +
293B GLU* 4.2 23.9 + - + +
296B VAL* 3.7 28.7 - - + +
297B PHE* 3.4 57.6 - + - -
300B ALA* 4.1 5.4 - - + +
306B LEU* 3.5 28.7 - - + +
307B VAL* 2.7 37.8 + - + -
360B LEU* 5.2 1.1 - - + -
367B TYR* 4.2 14.6 - + - -
385B LEU 4.0 9.9 - - - -
386B THR* 4.6 3.6 - - - -
387B ASP* 1.3 74.1 + - - +
389B GLY* 1.3 60.0 + - - +
390B MET 3.4 2.5 - - - -
391B CYS* 3.3 32.2 + - - +
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Residues in contact with GLY 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 6.2 3.1 - - - -
289B TRP* 3.7 36.1 + - - -
292B THR* 6.1 0.7 - - - +
293B GLU* 3.8 6.9 + - - -
387B ASP* 3.0 17.1 + - - -
388B TYR* 1.3 78.3 - - - +
390B MET* 1.3 60.3 + - - +
391B CYS 3.3 2.6 + - - +
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Residues in contact with MET 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TYR 3.7 5.6 + - - +
368B ARG* 2.8 42.9 + - + +
369B ASP* 3.8 32.0 + - + +
387B ASP* 4.6 2.2 + - - -
388B TYR 3.4 0.2 - - - -
389B GLY* 1.3 76.5 - - - +
391B CYS* 1.3 62.2 + - - +
403B TPO 6.2 0.4 - - + -
404B PHE 5.2 0.9 - - - +
405B CYS* 3.2 40.6 - - - -
406B GLY* 3.5 21.5 - - - +
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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
----------------------------------------------------------
292B THR* 4.2 15.0 - - + +
296B VAL* 4.1 17.0 - - + -
360B LEU* 5.5 0.2 - - - -
365B ILE* 3.8 19.1 - - + -
366B ILE 3.1 7.0 - - - +
367B TYR* 3.6 30.9 + - - -
368B ARG* 3.3 6.4 + - - -
388B TYR* 3.3 37.9 + - - +
389B GLY 3.3 4.1 - - - +
390B MET* 1.3 83.7 - - - +
392B LYS* 1.3 60.0 + - - +
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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