Contacts of the helix formed by residues 394 - 413 (chain C) in PDB entry 3J8B
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 394 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C ASP 2.7 11.3 - - - +
393C PRO* 1.3 73.7 - - + +
395C VAL* 1.3 62.8 + - - +
396C GLN 3.3 2.7 - - - -
397C ILE* 3.3 21.7 + - + +
398C LEU* 3.6 4.2 + - - +
459C ARG* 6.0 2.9 - - + +
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C THR* 5.8 4.7 - - - -
357C CYS* 5.7 8.1 - - - +
360C LEU* 6.3 0.7 - - + -
388C ILE* 4.3 11.4 - - - +
391C ALA 2.7 22.9 - - - +
392C ASP* 2.9 20.1 + - + +
393C PRO 3.4 1.6 - - - -
394C PRO* 1.3 77.2 - - - +
396C GLN* 1.3 57.4 + - - +
398C LEU* 2.6 33.5 + - + +
399C TYR* 2.7 14.8 + - + +
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Residues in contact with GLN 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ILE 4.6 4.7 + - - -
389C GLN* 5.1 8.5 - - - +
391C ALA 3.9 4.6 + - - +
393C PRO 4.7 7.8 + - - +
394C PRO 3.3 0.4 - - - -
395C VAL* 1.3 76.6 - - - +
397C ILE* 1.3 61.9 + - - +
399C TYR* 3.4 8.2 + - - +
400C ASN* 3.1 24.8 + - - +
435C LEU 4.6 5.9 - - - +
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PRO* 3.3 12.6 + - + +
395C VAL 3.0 0.6 - - - -
396C GLN* 1.3 77.8 - - - +
398C LEU* 1.3 51.2 + - - +
400C ASN* 5.0 1.3 - - - -
401C ARG* 2.3 49.8 + - + +
435C LEU 5.1 4.0 - - - -
436C LEU* 4.7 17.2 - - - +
437C GLY* 5.6 2.0 - - - -
461C VAL* 4.8 16.2 - - + -
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C CYS* 6.0 0.9 - - - -
360C LEU* 3.3 32.8 - - + +
361C CYS 5.4 0.2 - - - +
394C PRO 3.6 2.6 + - - +
395C VAL* 2.6 25.3 + - - +
397C ILE* 1.3 74.6 - - - +
399C TYR* 1.3 54.1 + - - +
401C ARG* 4.1 4.7 - - - -
402C THR* 2.8 37.3 + - - +
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 5.1 0.9 - - - +
388C ILE* 3.9 35.2 - - + +
389C GLN* 5.4 1.3 - - - -
395C VAL* 2.7 13.9 + - + +
396C GLN* 3.7 10.1 - - - +
398C LEU* 1.3 74.7 - - - +
400C ASN* 1.3 59.4 + - + +
402C THR* 4.9 0.5 - - - -
403C MET* 3.5 19.8 + - - +
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Residues in contact with ASN 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C GLN 3.1 14.9 + - - +
397C ILE* 4.2 0.9 - - - +
399C TYR* 1.3 74.9 - - + +
401C ARG* 1.3 60.9 + - - +
402C THR 3.4 0.4 - - - -
403C MET* 3.5 5.8 + - - +
404C VAL* 2.9 29.5 + - - +
426C ILE* 5.5 10.8 - - + -
435C LEU* 3.9 21.5 - - + +
436C LEU* 5.1 5.6 - - + -
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Residues in contact with ARG 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C TYR* 6.1 1.8 - - + -
397C ILE* 2.3 49.2 + - + +
398C LEU* 4.1 3.4 - - - -
400C ASN* 1.3 68.9 - - - +
402C THR* 1.3 57.0 + - - +
404C VAL* 3.4 7.8 + - - +
405C GLN* 2.9 27.1 + - - +
436C LEU* 6.0 4.6 - - + +
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Residues in contact with THR 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 4.5 10.1 - - - -
363C ILE* 4.5 10.3 - - - -
364C TYR* 4.4 24.9 - - - +
367C ALA* 5.4 0.9 - - - +
398C LEU* 2.8 25.2 + - - -
399C TYR 4.9 0.7 - - - -
401C ARG* 1.3 71.7 - - - +
403C MET* 1.3 59.3 + - - +
405C GLN* 3.6 7.7 - - - +
406C LEU* 3.0 30.8 + - - +
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Residues in contact with MET 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TYR 3.5 19.3 + - - +
400C ASN* 3.5 7.4 + - - +
401C ARG 3.3 0.2 - - - -
402C THR* 1.3 76.3 - - - +
404C VAL* 1.3 66.3 + - - +
406C LEU* 3.4 3.8 + - - +
407C GLY* 2.9 21.1 + - - -
422C ALA* 5.0 13.6 - - + +
423C LEU* 6.1 1.2 - - - -
426C ILE* 5.7 9.0 - - + -
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Residues in contact with VAL 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ASN 2.9 14.2 + - - +
401C ARG* 3.4 12.3 - - - +
403C MET* 1.3 77.4 - - - +
405C GLN* 1.3 56.0 + - - +
407C GLY* 3.2 3.0 + - - -
408C ILE* 2.9 28.9 + - - +
423C LEU* 6.6 0.2 - - - -
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Residues in contact with GLN 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C TYR* 5.0 9.2 - - + +
367C ALA* 4.4 17.4 - - + +
368C LEU* 5.6 1.6 - - + +
401C ARG 2.9 17.2 + - - +
402C THR* 3.2 9.8 + - - +
404C VAL* 1.3 77.5 - - - +
406C LEU* 1.3 59.3 + - - +
408C ILE* 3.2 8.3 + - - +
409C CYS* 2.9 28.8 + - - +
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ALA* 4.4 15.0 - - + +
372C TRP* 5.8 2.7 - - + +
375C ALA* 5.3 8.3 - - + -
376C ARG* 6.1 1.6 - - - +
402C THR 3.0 15.3 + - - +
403C MET* 4.2 3.4 - - - +
405C GLN* 1.3 73.9 - - - +
407C GLY* 1.3 60.7 + - - +
409C CYS* 4.2 3.8 - - - +
410C ALA* 2.9 33.3 + - - +
422C ALA* 5.4 2.0 - - + -
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Residues in contact with GLY 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C MET 2.9 15.3 + - - -
404C VAL* 3.5 5.2 - - - -
406C LEU* 1.3 79.2 - - - +
408C ILE* 1.3 58.8 + - - +
410C ALA* 4.2 2.2 - - - +
411C PHE* 3.4 22.0 + - - +
419C ALA* 4.1 11.7 - - - +
422C ALA* 4.2 20.5 - - - +
423C LEU* 5.7 5.8 - - - -
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Residues in contact with ILE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C VAL 2.9 12.7 + - - +
405C GLN* 3.5 11.2 - - - +
406C LEU 3.1 0.2 - - - -
407C GLY* 1.3 77.1 - - - +
409C CYS* 1.3 60.3 + - - +
411C PHE* 3.1 7.0 + - - +
412C ARG* 2.9 27.1 + - - +
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Residues in contact with CYS 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ALA* 3.6 25.4 - - + +
372C TRP* 4.8 15.3 - - + +
405C GLN 2.9 13.8 + - - +
406C LEU* 4.2 5.4 - - - +
408C ILE* 1.3 76.9 - - - +
410C ALA* 1.3 57.1 + - - +
412C ARG* 3.1 10.7 + - - +
413C GLN* 2.9 27.2 + - - +
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Residues in contact with ALA 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TRP* 4.9 11.3 - - + +
406C LEU 2.9 19.9 + - - +
407C GLY* 4.2 4.3 - - - +
409C CYS* 1.3 77.1 - - - +
411C PHE* 1.3 59.0 + - - +
413C GLN* 3.3 13.1 + - - +
414C GLY 3.4 0.2 + - - -
415C LEU* 3.0 31.2 + - + +
418C ASP* 4.6 20.4 - - + -
419C ALA* 4.9 4.3 - - - +
422C ALA* 6.2 0.9 - - + -
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Residues in contact with PHE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLY 3.4 16.8 + - - +
408C ILE* 3.1 8.1 + - - +
410C ALA* 1.3 77.6 - - - +
412C ARG* 1.3 60.8 + - - +
413C GLN 3.1 0.4 - - - -
414C GLY* 2.9 18.6 + - - +
415C LEU 4.3 8.0 + - - +
419C ALA* 4.2 11.2 - - + -
475C VAL* 5.3 13.5 - - + -
565C VAL* 5.8 2.4 - - - +
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Residues in contact with ARG 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ILE 2.9 13.3 + - - +
409C CYS* 3.1 14.5 + - - +
411C PHE* 1.3 75.3 - - - +
413C GLN* 1.3 57.8 + - - +
414C GLY* 3.0 5.0 + - - -
561C GLU* 6.1 5.1 - - + +
565C VAL* 5.2 13.0 - - - +
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Residues in contact with GLN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TRP* 5.7 6.1 - - + -
409C CYS 2.9 12.7 + - - +
410C ALA* 3.4 14.1 - - - +
411C PHE 3.1 0.2 - - - -
412C ARG* 1.3 74.9 - - - +
414C GLY* 1.3 61.8 + - - +
415C LEU* 3.5 5.1 + - + +
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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
------------------------------------------------------------
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