Contacts of the helix formed by residues 424 - 431 (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 GLU 424 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33T LEU* 3.9 25.6 - - + +
45T TYR* 3.0 40.5 + - + +
278T PHE* 3.9 22.8 - - + -
281T LEU* 5.9 0.9 - - + +
421T GLU 4.3 5.5 - - - +
423T GLU* 1.3 70.3 - - - +
425T ARG* 1.3 64.2 + - - +
427T LEU* 3.3 28.3 + - - +
428T TRP* 3.4 21.8 + - - +
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Residues in contact with ARG 425 (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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29T ALA* 6.2 0.2 - - - +
30T LEU* 3.5 56.7 - - + +
31T LYS 4.5 1.2 - - - +
32T GLY* 4.7 7.3 - - - +
33T LEU* 5.0 15.7 - - + -
45T TYR* 6.1 2.2 - - + -
423T GLU* 3.3 3.5 - - - +
424T GLU* 1.3 76.9 - - - +
426T LEU* 1.3 61.7 + - + +
428T TRP* 3.9 6.2 + - - +
429T LEU* 3.6 25.8 + - - +
721T GLU* 3.2 19.2 + - - -
722T THR 3.4 3.8 + - - -
723T LEU* 2.8 31.1 + - - +
724T PHE* 3.2 29.8 + - - +
725T GLY* 3.4 9.6 - - - +
727T ARG* 4.6 11.2 - - - +
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Residues in contact with LEU 426 (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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379T LEU* 3.4 49.2 - - + +
380T LEU* 3.8 26.0 - - + -
420T LEU* 4.1 15.5 - - + -
423T GLU* 3.5 22.3 + - + +
424T GLU 3.3 0.4 - - - -
425T ARG* 1.3 75.2 - - + +
427T LEU* 1.3 61.7 + - - +
428T TRP 3.2 2.0 - - - -
429T LEU* 3.3 9.0 + - + -
430T TYR* 3.0 28.2 + - - +
725T GLY 3.2 26.5 - - - +
726T ARG* 5.0 1.3 - - - -
727T ARG* 4.0 21.8 - - - +
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Residues in contact with LEU 427 (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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417T TRP* 3.8 22.4 - - + -
420T LEU* 3.5 34.1 - - + +
421T GLU* 3.6 34.8 - - - +
423T GLU 3.3 10.7 + - - +
424T GLU* 3.3 32.3 + - - +
425T ARG 3.5 0.2 - - - -
426T LEU* 1.3 75.3 - - - +
428T TRP* 1.3 59.5 + - - +
430T TYR* 3.7 6.0 - - + +
431T ARG* 3.1 44.7 + - - +
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Residues in contact with TRP 428 (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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424T GLU 3.4 14.2 + - - +
425T ARG* 4.0 7.6 - - - +
426T LEU 3.2 0.2 - - - -
427T LEU* 1.3 76.6 - - - +
429T LEU* 1.3 64.2 + - + +
431T ARG* 5.1 1.6 - - - -
432T GLU* 3.1 57.7 + - + +
433T VAL* 3.8 6.9 + - + -
724T PHE* 3.8 35.0 - + + +
763T LEU* 4.4 29.4 - - + -
811T TYR* 5.2 9.4 - + - -
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Residues in contact with LEU 429 (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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379T LEU* 4.1 24.2 - - + -
425T ARG 3.6 13.9 + - - +
426T LEU* 3.3 10.8 + - + +
427T LEU 3.3 0.4 - - - -
428T TRP* 1.3 84.0 - - + +
430T TYR* 1.3 55.7 + - - +
433T VAL* 3.4 23.3 - - + +
434T GLU* 2.9 32.6 + - - +
724T PHE* 3.9 27.1 - - + +
725T GLY 3.6 33.0 - - - +
726T ARG* 3.8 26.0 - - + +
759T ASP* 4.4 6.1 - - - +
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Residues in contact with TYR 430 (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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371T ASP* 3.4 28.0 + - - +
372T ASP 3.0 32.5 + - - -
375T LEU* 3.9 26.0 - - + -
376T LEU* 3.7 27.5 - - + +
379T LEU* 4.0 12.3 - - + -
413T PHE* 4.7 0.2 - - - -
417T TRP* 3.8 21.8 - + - -
420T LEU* 4.3 8.1 - - + -
426T LEU 3.0 15.9 + - - +
427T LEU* 3.5 5.8 + - + +
428T TRP 3.2 0.2 - - - -
429T LEU* 1.3 80.3 - - - +
431T ARG* 1.3 60.1 - - + +
432T GLU 3.7 0.2 - - - -
434T GLU* 4.2 12.1 - - + -
435T ARG* 3.2 54.1 + - + +
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Residues in contact with ARG 431 (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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417T TRP* 5.0 10.5 - - - -
421T GLU* 5.5 1.4 + - - -
427T LEU* 3.1 34.2 + - - +
428T TRP* 4.7 0.9 - - - +
430T TYR* 1.3 80.7 - - + +
432T GLU* 1.3 73.1 + - + +
435T ARG* 3.4 26.5 + - - +
436T PRO* 3.4 18.4 - - - +
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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