Contacts of the helix formed by residues 392 - 410 (chain M) in PDB entry 5GJQ
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 ASN 392 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H ARG* 3.9 19.6 - - - +
228M PRO* 4.6 2.9 - - + -
229M PRO* 4.6 8.9 - - - +
230M GLY* 3.5 33.8 - - - +
231M THR* 3.8 3.8 - - - +
356M MET* 3.6 29.7 - - + +
357M PRO* 4.6 2.2 - - - -
391M PHE* 1.3 82.9 - - - +
393M GLY* 1.3 65.8 + - - +
394M ALA 3.8 1.9 + - - -
395M GLN* 3.0 40.1 + - - +
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Residues in contact with GLY 393 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230M GLY 2.9 18.6 + - - -
231M THR* 3.7 5.9 - - - +
357M PRO* 4.7 5.7 - - - +
365M ILE* 4.5 12.2 - - - +
391M PHE 4.1 1.1 - - - -
392M ASN* 1.3 68.1 - - - +
394M ALA* 1.3 62.9 + - - -
395M GLN 2.9 2.1 + - - -
396M CYS* 2.9 26.0 + - - +
397M LYS 3.7 1.2 + - - -
501M ADP 3.4 24.9 - - - -
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Residues in contact with ALA 394 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H ARG* 4.3 9.4 - - - -
334H PRO* 3.3 28.4 - - + +
230M GLY 3.5 7.1 + - - +
392M ASN* 3.2 2.8 + - - +
393M GLY* 1.3 74.2 - - - +
395M GLN* 1.3 52.1 + - - +
397M LYS* 2.9 22.6 + - - +
398M ALA* 2.5 36.2 + - - +
501M ADP 3.7 26.0 + - + +
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Residues in contact with GLN 395 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H ARG* 5.2 3.0 - - - +
334H PRO* 3.4 28.7 - - + +
356M MET* 5.7 0.2 - - - +
390M ASP 4.4 1.9 - - - +
391M PHE* 3.7 29.1 - - + -
392M ASN* 3.0 41.0 + - - +
393M GLY 2.9 1.0 + - - -
394M ALA* 1.3 78.4 - - - +
396M CYS* 1.3 52.2 + - - +
398M ALA* 3.9 1.3 - - - -
399M VAL* 2.7 34.1 + - - +
427M VAL* 2.9 28.6 + - + +
428M GLN 5.5 3.0 + - - -
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Residues in contact with CYS 396 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357M PRO* 6.0 0.2 - - - -
362M ARG* 4.0 33.2 - - - -
365M ILE* 4.2 15.9 - - + -
366M MET* 4.1 33.2 - - + +
388M THR* 4.9 2.9 - - - -
391M PHE* 4.3 14.3 - - - +
393M GLY* 3.3 14.6 - - - +
395M GLN* 1.3 73.6 - - - +
397M LYS* 1.3 55.1 + - - +
399M VAL* 2.9 10.5 + - - +
400M CYS* 2.4 38.0 + - - +
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Residues in contact with LYS 397 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H GLU* 4.6 14.4 - - - +
307H ASP* 5.1 0.8 + - - -
333H ARG* 5.3 0.8 - - - +
335H GLY* 3.3 34.1 - - - +
338H ASP* 6.4 0.4 - - - -
365M ILE* 5.2 0.6 - - + +
366M MET* 5.9 0.2 - - - +
369M HIS* 3.1 34.0 - - + +
393M GLY 3.7 0.9 + - - +
394M ALA* 2.9 27.4 + - - +
396M CYS* 1.3 79.8 - - - +
398M ALA* 1.3 50.6 + - - +
400M CYS* 2.8 6.9 + - - +
401M VAL* 2.3 53.3 + - + +
501M ADP 2.9 39.1 + - + +
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Residues in contact with ALA 398 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H PRO* 3.4 27.6 - - + -
338H ASP* 5.4 6.3 - - + -
394M ALA 2.5 15.1 + - - +
395M GLN 3.3 2.7 - - - +
397M LYS* 1.3 73.6 - - - +
399M VAL* 1.3 53.3 + - - +
401M VAL* 3.0 11.3 + - - +
402M GLU* 2.5 41.0 + - + +
427M VAL* 3.2 24.6 - - + +
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Residues in contact with VAL 399 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366M MET* 4.7 10.5 - - + -
391M PHE* 4.2 12.1 - - + -
395M GLN 2.7 13.3 + - - +
396M CYS* 3.2 9.9 - - - +
398M ALA* 1.3 69.5 - - - +
400M CYS* 1.3 58.3 + - - +
403M ALA* 2.7 37.8 + - + +
420M TYR* 3.6 18.4 - - + +
423M GLY* 3.5 4.0 - - - +
424M ILE* 3.2 39.3 - - + +
427M VAL* 2.4 51.3 - - + +
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Residues in contact with CYS 400 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366M MET* 4.7 8.7 - - + +
369M HIS* 3.3 42.6 - - + -
370M SER* 4.0 5.6 - - - -
373M MET* 4.1 19.6 - - - +
396M CYS 2.4 18.0 + - - +
397M LYS* 2.8 17.4 + - - +
399M VAL* 1.3 76.5 - - - +
401M VAL* 1.3 64.5 + - - +
403M ALA* 3.5 5.7 + - - +
404M GLY* 3.2 13.5 + - - -
420M TYR* 4.9 10.8 - - + -
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Residues in contact with VAL 401 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H ILE* 4.9 4.3 - - - +
207H GLU* 3.4 52.7 - - + +
208H PRO 4.5 8.3 - - - +
209H PRO* 4.6 3.4 - - + -
338H ASP* 5.3 7.4 - - + +
373M MET* 5.9 1.1 - - - -
397M LYS* 2.3 45.3 + - + +
398M ALA* 3.2 11.0 - - - +
400M CYS* 1.3 69.5 - - + +
402M GLU* 1.3 69.6 + - + +
404M GLY* 2.9 13.5 + - - -
405M MET* 3.2 23.3 + - + +
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Residues in contact with GLU 402 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H PRO* 5.5 0.4 - - + -
338H ASP* 4.7 7.3 - - + +
339H ARG* 4.5 17.6 + - + +
340H LYS 5.3 0.2 + - - -
398M ALA* 2.5 20.6 + - + +
399M VAL 3.8 1.3 - - - +
401M VAL* 1.3 72.8 - - + +
403M ALA* 1.3 54.2 + - - +
405M MET* 2.9 25.5 + - + +
406M ILE* 2.7 48.1 + - + +
423M GLY* 3.1 1.5 - - - +
426M GLU* 2.2 36.0 - - - +
427M VAL* 2.3 54.3 + - + +
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Residues in contact with ALA 403 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399M VAL 2.7 21.8 + - - +
400M CYS 3.7 4.0 - - - +
402M GLU* 1.3 73.5 - - - +
404M GLY* 1.3 51.5 + - - +
406M ILE* 3.1 8.4 - - - +
407M ALA* 2.5 36.9 + - - +
415M LEU* 4.2 8.3 - - + -
419M ASP* 3.4 33.5 - - - +
420M TYR* 3.8 22.2 - - + +
423M GLY* 4.0 1.5 - - - -
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Residues in contact with GLY 404 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H LEU* 4.8 2.0 - - - +
206H ILE* 4.2 14.3 - - - +
373M MET* 4.7 6.7 - - - -
400M CYS 3.2 10.1 + - - -
401M VAL 2.9 10.8 + - - -
403M ALA* 1.3 72.6 - - - +
405M MET* 1.3 64.7 + - - -
407M ALA* 2.8 5.5 + - - +
408M LEU* 2.8 23.6 + - - +
415M LEU* 4.0 17.9 - - - +
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Residues in contact with MET 405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H GLU* 3.5 24.9 - - + +
201H PHE* 4.6 2.2 - - + -
206H ILE* 4.1 19.0 - - + +
207H GLU 4.3 4.9 - - - +
208H PRO* 4.3 3.6 - - - -
209H PRO* 3.1 37.9 - - + -
339H ARG* 2.9 41.5 - - - +
401M VAL* 3.2 10.6 + - + +
402M GLU* 2.9 32.0 + - + -
404M GLY* 1.3 69.4 - - - +
406M ILE* 1.3 64.0 + - - +
408M LEU* 3.1 17.8 + - - +
409M ARG* 3.2 19.2 + - - +
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Residues in contact with ILE 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339H ARG* 5.2 9.4 - - - +
402M GLU* 2.7 33.5 + - + +
403M ALA* 3.1 9.2 - - - +
405M MET* 1.3 72.0 - - - +
407M ALA* 1.3 67.4 + - - +
409M ARG* 3.0 40.2 + - - +
410M ARG* 4.3 4.9 + - - +
419M ASP* 4.1 16.8 - - + +
422M GLU* 3.6 33.7 - - + +
423M GLY* 3.6 26.2 - - - +
426M GLU* 5.3 4.7 - - + -
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Residues in contact with ALA 407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H LEU* 6.4 0.4 - - - -
403M ALA 2.5 17.5 + - - +
404M GLY 2.8 6.6 + - - +
406M ILE* 1.3 73.4 - - - +
408M LEU* 1.3 57.4 + - - -
409M ARG 3.4 0.2 + - - -
410M ARG* 3.8 12.7 + - - +
411M GLY 3.8 1.4 + - - -
412M ALA* 3.7 23.2 + - + +
414M GLU 5.3 0.4 - - - -
415M LEU* 2.9 40.6 - - + +
419M ASP* 3.5 25.1 - - - +
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Residues in contact with LEU 408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H ARG* 3.5 42.4 - - + +
201H PHE* 4.5 27.1 - - + +
204H LEU* 5.1 17.2 - - + +
206H ILE* 5.2 4.3 - - + -
404M GLY 2.8 13.8 + - - +
405M MET* 3.1 11.6 + - - +
406M ILE 3.1 0.2 + - - -
407M ALA* 1.3 70.3 - - - +
409M ARG* 1.3 70.4 + - - +
411M GLY* 2.7 25.3 + - - +
412M ALA 5.1 2.2 - - - +
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Residues in contact with ARG 409 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H GLU* 5.3 15.7 + - - +
189H GLU* 4.8 12.3 + - - +
339H ARG* 4.3 18.4 - - - +
405M MET* 3.2 25.7 + - - +
406M ILE* 3.0 30.9 + - - +
408M LEU* 1.3 74.4 - - - +
410M ARG* 1.3 58.8 + - + +
411M GLY* 2.5 14.8 + - - -
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Residues in contact with ARG 410 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406M ILE* 4.8 3.5 - - - +
407M ALA* 3.8 11.5 + - - +
409M ARG* 1.3 82.5 - - + +
411M GLY* 1.3 49.9 + - - +
412M ALA* 2.4 46.1 + - - +
414M GLU 5.8 0.2 + - - -
416M THR* 3.9 8.0 + - - -
418M GLU* 4.8 12.3 + - - +
419M ASP* 2.0 46.6 + - - +
422M GLU* 5.2 4.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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