Contacts of the helix formed by residues 373 - 380 (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 PRO 373 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306T PHE* 5.6 2.0 - - + -
350T GLY* 3.8 18.2 - - - -
351T LEU* 3.9 20.0 - - + +
371T ASP 4.4 1.1 - - - +
372T ASP* 1.3 90.6 - - - +
374T MET* 1.3 62.1 + - - +
375T LEU 3.3 0.2 - - - -
376T LEU* 3.8 14.4 - - + -
377T ALA* 3.4 19.8 + - - +
390T VAL* 4.2 4.5 - - + +
409T SER* 3.9 22.2 - - - +
412T LEU* 4.0 31.6 - - + +
413T PHE* 4.6 5.8 - - + +
416T LEU* 3.6 9.6 - - + +
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Residues in contact with MET 374 (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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351T LEU* 3.9 19.0 - - + +
352T LEU* 5.0 13.9 - - + +
372T ASP* 3.1 17.0 + - - +
373T PRO* 1.3 80.6 - - - +
375T LEU* 1.3 62.4 + - + +
377T ALA* 4.0 0.9 + - - +
378T TYR* 3.5 20.8 + - - +
384T ASN 4.3 4.4 - - - +
385T THR* 3.5 17.0 - - - +
386T THR 3.5 32.1 - - - +
387T PRO* 4.1 18.4 - - + -
390T VAL* 4.6 6.3 - - + -
565T ASN* 4.8 7.2 - - - +
567T THR* 3.5 35.2 - - + +
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Residues in contact with LEU 375 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370T GLY 5.7 0.9 - - - +
372T ASP* 3.4 24.4 + - + +
373T PRO 3.3 0.4 - - - -
374T MET* 1.3 77.5 - - + +
376T LEU* 1.3 62.8 + - - +
377T ALA 3.4 0.2 - - - -
378T TYR* 3.8 7.0 - - - +
379T LEU* 3.5 29.5 + - - +
430T TYR* 3.9 20.4 - - + -
434T GLU* 3.5 26.9 - - + +
435T ARG* 4.5 5.4 - - + +
438T SER* 3.9 12.8 - - - +
566T GLN* 3.2 41.1 - - + +
567T THR* 3.9 18.2 - - + -
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Residues in contact with LEU 376 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372T ASP 3.6 10.0 + - - +
373T PRO* 3.5 20.8 + - + +
374T MET 3.4 0.2 - - - -
375T LEU* 1.3 77.9 - - - +
377T ALA* 1.3 62.3 + - - +
378T TYR 3.6 0.2 + - - -
379T LEU* 3.6 6.1 + - - -
380T LEU* 3.5 21.7 + - - +
412T LEU 4.2 3.8 - - - +
413T PHE* 3.8 28.9 - - + -
416T LEU* 3.9 27.1 - - + +
417T TRP* 4.0 12.6 - - + +
420T LEU* 3.7 39.9 - - + +
430T TYR* 3.7 25.1 - - + +
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Residues in contact with ALA 377 (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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373T PRO 3.4 4.8 + - - +
374T MET 4.4 0.7 - - - +
376T LEU* 1.3 77.7 - - - +
378T TYR* 1.3 54.7 + - - +
379T LEU 3.3 0.2 - - - -
380T LEU* 4.0 7.1 - - - +
381T ASP* 2.7 39.9 + - - +
384T ASN* 3.9 16.3 + - + +
390T VAL* 3.9 27.4 - - + -
394T TYR* 4.7 6.5 - - + +
416T LEU* 3.7 19.7 - - + +
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Residues in contact with TYR 378 (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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374T MET 3.5 18.0 + - - +
375T LEU* 3.8 6.5 - - - +
376T LEU 3.3 0.6 - - - -
377T ALA* 1.3 79.1 - - - +
379T LEU* 1.3 61.5 + - + +
380T LEU 3.7 0.2 + - - -
381T ASP 3.8 13.9 - - - -
382T PRO* 3.8 22.3 - - + +
384T ASN 4.2 5.1 + - - +
385T THR* 4.0 20.4 - - + -
434T GLU* 3.8 17.9 - - - -
566T GLN 3.9 13.6 + - - -
567T THR* 3.4 29.0 + - + -
569T THR* 3.1 28.1 + - - -
570T ALA* 4.8 1.8 + - - -
571T THR 4.7 0.9 - - - -
572T GLY* 3.5 23.9 + - - -
726T ARG* 3.3 33.6 + - - +
727T ARG* 5.4 0.7 + - - +
762T LYS* 4.4 3.4 - - - -
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Residues in contact with LEU 379 (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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375T LEU 3.5 17.8 + - - +
376T LEU 3.6 4.7 + - - +
377T ALA 3.3 0.6 - - - -
378T TYR* 1.3 77.4 - - + +
380T LEU* 1.3 59.9 + - - +
420T LEU* 4.5 7.2 - - + -
426T LEU* 3.4 58.6 - - + +
429T LEU* 4.1 24.9 - - + +
430T TYR* 4.0 23.3 - - + +
434T GLU* 4.6 9.2 - - + -
726T ARG* 3.6 30.7 - - + +
727T ARG* 3.5 21.3 + - - +
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Residues in contact with LEU 380 (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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376T LEU 3.5 18.6 + - - +
377T ALA* 3.4 8.9 + - - +
378T TYR 3.4 0.4 - - - -
379T LEU* 1.3 80.7 - - - +
381T ASP* 1.3 60.5 - - + +
382T PRO* 4.5 1.1 - - - -
394T TYR* 4.8 13.0 - - + +
416T LEU* 4.2 21.3 - - + +
419T ARG* 3.9 40.6 - - + +
420T LEU* 4.2 7.4 - - + -
423T GLU* 4.6 3.8 - - + -
426T LEU* 3.8 20.9 - - + -
727T ARG* 4.2 5.4 - - - +
729T TYR* 3.3 24.9 - - - -
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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