Contacts of the helix formed by residues 393 - 411 (chain g) in PDB entry 5M32
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 393 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357g PRO* 3.5 15.1 - - - +
365g ILE* 4.0 9.1 - - - +
391g PHE 3.3 3.0 - - - -
392g ASN* 1.3 76.2 - - - +
394g ALA* 1.3 55.9 + - - +
396g CYS* 2.5 37.7 - - - -
397g LYS 3.6 5.7 + - - -
502g ADP 3.4 25.6 + - - -
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Residues in contact with ALA 394 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333c ARG* 4.0 18.4 - - + +
334c PRO* 4.0 20.7 - - - +
230g GLY 3.8 11.0 - - - +
392g ASN* 3.0 16.3 + - - +
393g GLY* 1.3 76.7 - - - +
395g GLN* 1.3 63.5 + - - +
397g LYS* 3.3 23.8 - - + +
398g ALA 3.4 3.6 + - - -
502g ADP 3.7 23.5 - - + +
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Residues in contact with GLN 395 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333c ARG* 4.2 9.3 - - - +
334c PRO* 3.4 39.2 - - + +
391g PHE* 3.2 33.7 - - + +
392g ASN* 2.8 58.2 + - - +
394g ALA* 1.3 76.0 - - - +
396g CYS* 1.3 54.9 + - - +
398g ALA* 3.0 5.0 + - - +
399g VAL* 2.6 37.3 + - - +
427g VAL* 4.5 9.9 - - + +
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Residues in contact with CYS 396 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362g ARG* 4.6 16.8 - - + +
365g ILE* 4.5 13.2 - - + -
366g MET* 4.0 26.8 - - + +
391g PHE* 4.8 8.2 - - + +
393g GLY* 2.5 60.1 - - - -
395g GLN* 1.3 75.2 - - - +
397g LYS* 1.3 66.1 + - - +
399g VAL* 3.5 13.2 + - - +
400g CYS* 3.3 24.3 + - - -
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Residues in contact with LYS 397 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207c GLU* 5.8 4.7 - - - +
307c ASP* 5.0 4.4 + - - -
334c PRO 5.1 6.7 + - - +
335c GLY* 5.0 13.0 - - - -
365g ILE* 4.8 0.4 - - - +
369g HIS* 2.5 46.8 + - + +
393g GLY 3.6 4.6 + - - +
394g ALA* 3.3 16.7 + - - +
395g GLN 3.1 0.2 - - - -
396g CYS* 1.3 81.2 - - - +
398g ALA* 1.3 76.9 + - + +
400g CYS* 3.1 15.2 + - - +
401g VAL* 3.3 13.0 + - + +
502g ADP 1.8 43.9 + - + +
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Residues in contact with ALA 398 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334c PRO* 3.8 28.7 - - + -
338c ASP* 4.9 9.2 - - + +
394g ALA 3.4 1.4 + - - -
395g GLN 3.0 9.1 + - - +
397g LYS* 1.3 80.1 - - + +
399g VAL* 1.3 59.0 + - - +
400g CYS 2.8 2.0 - - - -
401g VAL* 2.2 46.8 + - + -
402g GLU* 3.0 16.5 + - + -
427g VAL* 5.2 4.9 - - + -
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Residues in contact with VAL 399 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366g MET* 4.0 16.2 - - + -
384g LEU* 6.2 0.2 - - + -
391g PHE* 5.3 6.5 - - + -
395g GLN* 2.6 24.8 + - + +
396g CYS* 3.5 15.5 - - - +
398g ALA* 1.3 72.9 - - - +
400g CYS* 1.3 50.2 + - - +
402g GLU* 4.4 10.2 - - - +
403g ALA* 2.7 39.8 + - - +
420g TYR* 4.2 20.2 - - + +
423g GLY* 5.3 0.2 - - - -
424g ILE* 3.3 39.3 - - + +
427g VAL* 3.7 18.1 - - + +
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Residues in contact with CYS 400 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366g MET* 3.5 38.6 - - - -
369g HIS* 4.4 7.4 - - + -
370g SER* 3.8 26.9 - - - +
373g MET* 3.5 14.0 - - + +
396g CYS 3.5 12.6 - - - -
397g LYS 3.1 10.2 + - - +
398g ALA 2.5 5.5 + - - -
399g VAL* 1.3 76.5 - - - +
401g VAL* 1.3 57.5 + - - +
403g ALA* 3.4 1.9 + - - +
404g GLY 3.0 23.0 + - - -
420g TYR* 3.8 18.9 - - - -
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Residues in contact with VAL 401 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206c ILE* 4.1 9.1 - - + +
207c GLU* 3.2 49.1 - - + +
208c PRO 6.0 0.2 - - - -
209c PRO* 5.1 8.1 - - + -
338c ASP* 4.8 10.3 - - - +
373g MET* 3.7 16.2 - - + -
397g LYS* 3.3 13.0 + - + +
398g ALA* 2.2 40.6 + - + +
400g CYS* 1.3 71.5 - - + +
402g GLU* 1.3 62.0 + - + +
404g GLY* 3.4 3.5 + - - -
405g MET* 3.0 20.8 + - - +
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Residues in contact with GLU 402 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209c PRO* 4.9 9.2 - - + -
338c ASP* 5.9 3.4 - - + +
339c ARG* 3.6 24.3 + - + +
398g ALA* 3.0 20.5 + - + +
399g VAL* 4.4 4.2 - - - -
401g VAL* 1.3 78.5 - - + +
403g ALA* 1.3 62.5 + - - +
404g GLY 3.3 0.7 - - - -
405g MET* 3.4 8.6 - - + +
406g ILE* 3.0 30.8 + - - +
423g GLY* 2.6 31.1 - - - +
426g GLU* 3.2 31.5 - - - +
427g VAL* 4.2 12.1 - - + +
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Residues in contact with ALA 403 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399g VAL 2.7 25.3 + - - +
400g CYS 3.4 5.2 - - - +
402g GLU* 1.3 79.7 - - - +
404g GLY* 1.3 58.8 + - - +
406g ILE* 3.5 6.9 - - - +
407g ALA* 3.0 28.3 + - - +
415g LEU* 5.0 1.6 - - + -
419g ASP* 3.6 25.0 - - + +
420g TYR* 3.9 24.7 - - + -
423g GLY* 4.6 4.5 - - - -
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Residues in contact with GLY 404 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204c LEU* 4.8 2.5 - - - +
206c ILE* 3.7 24.1 - - - +
373g MET* 4.4 0.2 - - - -
400g CYS 3.0 14.7 + - - -
401g VAL 3.8 0.9 - - - -
403g ALA* 1.3 75.1 - - - +
405g MET* 1.3 57.9 + - - +
407g ALA* 3.2 9.0 + - - +
408g LEU* 3.0 30.1 + - - +
415g LEU* 4.0 14.6 - - - +
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Residues in contact with MET 405 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189c GLU* 3.2 34.8 - - - +
201c PHE* 3.6 36.6 - - + -
206c ILE* 3.8 20.8 - - + +
208c PRO* 3.9 3.4 - - + -
209c PRO* 3.7 27.8 - - + -
339c ARG* 3.9 6.7 - - - +
401g VAL 3.0 6.9 + - - +
402g GLU* 3.5 21.3 - - + +
403g ALA 3.2 0.8 - - - -
404g GLY* 1.3 76.8 - - - +
406g ILE* 1.3 58.1 + - + +
408g LEU* 3.2 15.4 + - - +
409g ARG* 2.9 24.8 + - + +
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Residues in contact with ILE 406 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186c LYS* 6.1 1.6 - - - +
339c ARG* 4.5 14.6 - - - +
402g GLU* 3.0 31.4 + - - +
403g ALA* 3.5 6.3 - - - +
405g MET* 1.3 74.7 - - + +
407g ALA* 1.3 62.1 + - - +
408g LEU 3.2 0.2 - - - -
409g ARG* 3.4 37.6 + - + +
410g ARG* 3.0 27.2 + - - +
419g ASP* 3.4 40.3 - - - +
422g GLU* 4.1 22.7 - - + +
423g GLY* 4.5 6.5 - - - -
426g GLU* 5.5 5.2 - - + -
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Residues in contact with ALA 407 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204c LEU* 5.4 4.3 - - + -
403g ALA 3.0 19.6 + - - +
404g GLY* 3.3 8.5 - - - +
405g MET 3.2 0.2 - - - -
406g ILE* 1.3 79.3 - - - +
408g LEU* 1.3 57.9 + - - +
410g ARG* 3.9 9.5 + - - +
411g GLY 3.7 2.1 + - - -
412g ALA* 3.2 25.1 + - - +
414g GLU 5.2 0.7 - - - +
415g LEU* 3.7 21.3 - - + +
419g ASP* 3.5 28.0 - - - +
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Residues in contact with LEU 408 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200c ARG* 3.0 57.4 + - + +
201c PHE* 3.6 42.2 - - + -
204c LEU* 5.1 11.2 - - + +
206c ILE* 3.7 23.8 - - + -
404g GLY 3.0 10.1 + - - +
405g MET* 3.2 20.2 + - - +
407g ALA* 1.3 75.3 - - - +
409g ARG* 1.3 62.9 + - + +
410g ARG 3.2 1.6 - - - -
411g GLY* 3.1 10.3 + - - +
412g ALA 4.1 6.5 - - - +
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Residues in contact with ARG 409 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182c GLU* 4.5 14.5 + - - -
185c GLU* 4.6 22.3 + - + +
186c LYS* 5.2 7.1 - - - +
189c GLU* 6.3 2.5 - - + -
405g MET* 2.9 14.9 + - + +
406g ILE* 3.1 41.0 + - + +
408g LEU* 1.3 78.6 - - + +
410g ARG* 1.3 65.3 + - - +
411g GLY 3.6 0.2 + - - -
422g GLU* 3.8 17.6 + - - +
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Residues in contact with ARG 410 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406g ILE 3.0 9.7 + - - +
407g ALA* 3.9 10.2 + - - +
408g LEU 3.2 0.2 - - - -
409g ARG* 1.3 81.2 - - - +
411g GLY* 1.3 57.2 + - - +
412g ALA* 3.5 21.2 - - - +
414g GLU 3.4 21.0 + - - -
416g THR* 4.1 13.8 + - - +
418g GLU* 5.0 5.7 + - - +
419g ASP* 2.5 43.4 + - - -
422g GLU* 5.9 0.2 + - - -
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Residues in contact with GLY 411 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200c ARG* 3.9 14.7 + - - -
408g LEU 3.1 18.3 + - - -
409g ARG 4.6 0.2 - - - -
410g ARG* 1.3 78.3 - - - +
412g ALA* 1.3 64.4 + - - +
413g THR* 3.8 6.6 + - - +
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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