Contacts of the helix formed by residues 389 - 394 (chain T) in PDB entry 1BGX
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 GLY 389 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H THR* 6.2 1.3 - - - -
384T ASN* 3.5 13.1 - - - +
386T THR* 3.2 19.1 + - - -
388T GLU* 1.3 69.6 - - - +
390T VAL* 1.3 59.9 + - - +
392T ARG* 2.2 28.6 + - - +
393T ARG* 3.2 28.8 + - - +
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Residues in contact with VAL 390 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351T LEU* 5.6 1.3 - - + -
373T PRO 4.2 9.9 - - - +
374T MET* 4.6 8.7 - - + -
377T ALA* 3.9 21.1 - - + -
384T ASN* 4.1 15.9 - - + +
386T THR 3.2 19.0 + - - +
387T PRO* 4.8 3.6 - - + +
388T GLU 3.3 0.4 - - - -
389T GLY* 1.3 75.5 - - - +
391T ALA* 1.3 62.1 + - - +
394T TYR* 3.2 32.9 + - + +
412T LEU* 3.5 24.1 - - + +
416T LEU* 3.9 28.5 - - + -
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Residues in contact with ALA 391 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387T PRO 4.0 12.7 + - - +
388T GLU 3.2 8.4 + - - +
390T VAL* 1.3 79.1 - - - +
392T ARG* 1.3 60.1 + - - +
395T GLY 3.0 15.6 + - - -
396T GLY* 2.9 23.3 + - - -
397T GLU* 3.9 24.7 - - - +
398T TRP 4.5 0.2 - - - +
408T LEU* 4.0 21.8 - - + -
412T LEU* 4.0 10.5 - - + +
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Residues in contact with ARG 392 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H THR* 6.2 1.0 - - - +
57H ASP* 5.4 2.6 + - - -
63H LYS 5.4 3.1 - - - -
66H ILE 4.1 10.8 + - - -
67H SER* 3.4 34.4 + - - +
68H ILE 4.9 12.4 + - - +
69H THR* 6.2 2.7 - - - +
386T THR* 4.3 2.6 + - - -
388T GLU* 2.4 35.9 + - - +
389T GLY* 2.2 46.3 + - - +
391T ALA* 1.3 73.7 - - - +
393T ARG* 1.3 59.1 + - - +
395T GLY* 4.3 3.4 + - - -
396T GLY 3.5 15.0 + - - +
397T GLU* 4.7 13.7 - - + -
398T TRP 5.3 2.7 - - - +
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Residues in contact with ARG 393 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381T ASP* 3.5 18.1 + - - +
383T SER* 2.9 28.1 + - - -
384T ASN* 2.9 31.6 + - - +
389T GLY 3.2 16.8 + - - +
391T ALA 3.3 0.6 - - - -
392T ARG* 1.3 79.0 - - - +
394T TYR* 1.3 80.3 + - + +
395T GLY 3.4 1.0 + - - -
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Residues in contact with TYR 394 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290T SER* 4.8 2.3 + - - -
377T ALA* 4.7 11.1 - - + +
380T LEU* 4.8 18.4 - - + +
381T ASP* 4.9 4.0 - - - +
384T ASN* 4.0 28.8 + - - -
390T VAL* 3.2 29.8 + - + +
391T ALA 3.9 0.2 - - - -
393T ARG* 1.3 95.3 + - + +
395T GLY* 1.3 57.8 + - - +
412T LEU* 4.4 6.3 - - + -
415T ASN* 4.6 19.4 + - + +
416T LEU* 4.0 34.8 - - + -
419T ARG* 6.0 6.7 - - + -
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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