Contacts of the helix formed by residues 353 - 363 (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 ALA 353 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307T VAL* 6.1 1.8 - - - -
309T PHE* 5.6 0.2 - - - -
348T ALA* 3.3 35.3 - - - +
350T GLY 3.5 18.6 - - - +
351T LEU 3.4 1.4 - - - -
352T LEU* 1.3 76.2 - - - +
354T LYS* 1.3 58.8 + - - +
356T LEU* 4.0 3.3 + - - +
357T SER* 3.1 25.6 + - - -
369T PRO* 3.7 13.1 - - + +
370T GLY 4.6 2.0 - - - +
371T ASP 4.3 5.6 - - - +
372T ASP* 3.1 11.2 + - + +
438T SER* 6.3 0.2 - - - -
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Residues in contact with LYS 354 (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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352T LEU* 3.2 1.1 - - - -
353T ALA* 1.3 76.2 - - - +
355T ASP* 1.3 87.7 + - - +
356T LEU 3.2 0.2 - - - -
357T SER* 3.2 11.3 + - - -
358T VAL* 3.2 20.6 + - + +
369T PRO* 4.3 9.3 - - - +
372T ASP* 4.6 3.4 + - - +
438T SER* 3.6 34.0 - - - +
441T LEU* 4.2 21.7 + - + +
442T ALA* 4.3 11.1 - - + +
445T GLU* 3.0 27.1 + - - +
563T ARG* 4.9 3.4 - - - +
564T PHE 3.3 28.2 + - - +
565T ASN* 5.1 3.2 - - - +
566T GLN* 5.6 2.0 - - - +
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Residues in contact with ASP 355 (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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309T PHE* 4.1 16.7 - - + -
311T LEU* 5.4 1.6 - - + +
314T LYS 4.8 1.2 - - - +
316T PRO* 3.4 46.4 - - + +
352T LEU* 3.4 35.4 + - + +
354T LYS* 1.3 103.5 + - - +
356T LEU* 1.3 58.1 + - - +
358T VAL* 3.9 7.7 + - - -
359T LEU* 4.0 4.0 + - - +
563T ARG* 4.5 13.9 + - - -
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Residues in contact with LEU 356 (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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307T VAL* 3.9 28.3 - - + -
309T PHE* 3.8 46.6 - - + -
311T LEU* 6.2 0.2 - - + -
321T LEU* 4.4 9.4 - - + -
324T LEU* 4.2 17.9 - - + -
342T LEU* 4.4 16.2 - - + +
345T LEU* 5.4 3.4 - - + -
348T ALA* 4.3 11.4 - - + -
352T LEU 3.5 5.9 + - - +
353T ALA* 4.3 6.3 - - - +
354T LYS 3.2 0.6 - - - -
355T ASP* 1.3 75.2 - - - +
357T SER* 1.3 63.6 + - - +
358T VAL 3.2 2.0 - - - -
359T LEU* 3.2 19.6 + - + +
360T ALA* 3.4 10.9 + - - +
367T LEU* 4.5 12.3 - - + +
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Residues in contact with SER 357 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348T ALA* 3.8 10.2 - - - +
353T ALA 3.1 15.5 + - - -
354T LYS 3.2 10.1 + - - -
356T LEU* 1.3 79.6 - - - +
358T VAL* 1.3 59.9 + - - +
360T ALA* 3.4 3.6 + - - +
361T LEU* 3.2 30.9 + - - +
367T LEU* 3.2 33.5 + - - +
369T PRO* 3.3 17.5 - - - +
442T ALA* 4.3 9.4 - - - -
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Residues in contact with VAL 358 (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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316T PRO* 4.2 4.3 - - + -
317T MET* 3.4 37.1 - - + +
354T LYS* 3.2 21.1 - - + +
355T ASP* 4.0 8.5 - - - +
356T LEU 3.2 0.2 - - - -
357T SER* 1.3 76.8 - - - +
359T LEU* 1.3 61.4 + - - +
361T LEU* 3.6 9.1 + - - +
362T ARG* 3.7 5.7 + - - +
442T ALA* 3.8 26.0 - - - +
445T GLU* 3.5 33.4 - - - +
446T ALA* 3.9 19.6 - - - +
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Residues in contact with LEU 359 (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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311T LEU* 4.8 8.3 - - + -
316T PRO* 3.4 17.2 - - + +
317T MET* 5.6 0.4 - - - -
319T ALA 3.5 10.5 - - - +
321T LEU* 4.1 33.9 - - + +
339T TYR* 4.5 11.4 - - + +
342T LEU* 3.9 24.5 - - + -
355T ASP 4.0 6.3 + - - +
356T LEU* 3.2 16.9 + - + +
358T VAL* 1.3 78.9 - - - +
360T ALA* 1.3 60.5 + - - +
362T ARG* 3.2 40.4 + - - +
363T GLU* 3.7 17.3 + - - +
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Residues in contact with ALA 360 (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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342T LEU* 4.6 16.6 - - + -
356T LEU 3.4 7.8 + - - +
357T SER 3.7 8.1 - - - +
358T VAL 3.3 0.6 - - - -
359T LEU* 1.3 76.4 - - - +
361T LEU* 1.3 61.0 + - - +
362T ARG 3.1 5.2 + - - -
363T GLU* 3.2 4.5 + - - +
364T GLY 3.2 7.1 + - - -
365T LEU* 3.0 45.6 + - + +
367T LEU* 4.0 23.6 - - + -
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Residues in contact with LEU 361 (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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357T SER* 3.2 19.3 + - - +
358T VAL 3.6 1.3 + - - +
359T LEU 3.5 0.2 - - - -
360T ALA* 1.3 77.5 - - - +
362T ARG* 1.3 59.4 + - - +
364T GLY* 3.8 7.9 + - - -
365T LEU 3.4 18.8 - - - +
366T GLY* 4.2 12.1 - - - -
367T LEU 4.8 4.7 - - - +
442T ALA* 3.8 26.9 - - + +
443T HIS* 3.9 39.0 - - + +
446T ALA* 3.9 20.3 - - + +
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Residues in contact with ARG 362 (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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317T MET* 2.9 52.4 + - + +
318T TRP* 4.1 2.2 + - - -
319T ALA 2.9 26.5 + - - -
339T TYR* 4.2 13.5 + - - -
358T VAL 3.7 10.7 + - - +
359T LEU* 3.2 29.1 - - - +
360T ALA 3.1 0.8 - - - -
361T LEU* 1.3 78.0 - - - +
363T GLU* 1.3 85.7 + - - +
364T GLY 3.3 1.0 + - - -
446T ALA* 5.4 0.9 - - - +
554T HIS* 4.5 4.7 + - + -
556T ARG* 3.3 48.3 + - + +
557T THR* 5.5 5.6 - - + -
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Residues in contact with GLU 363 (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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339T TYR* 3.6 36.2 - - + +
342T LEU* 5.1 1.8 - - + -
343T ARG* 3.5 30.6 + - - +
359T LEU 3.7 14.6 - - - +
360T ALA* 3.2 8.2 + - - +
362T ARG* 1.3 89.4 + - - +
364T GLY* 1.3 59.7 + - - +
556T ARG* 2.9 30.1 + - - -
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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