Contacts of the helix formed by residues 388 - 410 (chain C) in PDB entry 2I2X
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 388 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C ASP* 2.9 13.8 + - + +
387C ASP* 1.3 80.7 - - + +
389C ILE* 1.3 62.5 + - - +
390C TYR* 3.0 11.3 + - - +
391C LEU* 2.9 41.5 + - + +
392C ARG* 2.9 26.4 + - - +
434C ASP 5.0 3.6 + - - -
436C MET* 3.7 21.7 - - - +
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Residues in contact with ILE 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG* 3.7 38.4 - - - +
189C GLY 3.7 7.9 - - - +
190C CYS* 4.2 9.4 - - + +
193C SER* 4.0 28.3 + - - +
194C ILE* 3.9 28.5 - - + +
252C PRO* 5.3 0.7 - - - +
387C ASP 3.7 2.5 + - - +
388C ASN* 1.3 72.1 + - - +
390C TYR* 1.3 62.0 + - - +
392C ARG* 3.8 21.2 + - - +
393C ALA* 3.5 19.9 + - - +
436C MET* 3.7 28.6 - - + -
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Residues in contact with TYR 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.6 22.7 - - + -
190C CYS* 4.1 16.8 - - - -
388C ASN* 3.1 1.8 + - - +
389C ILE* 1.3 79.0 - - - +
391C LEU* 1.3 67.0 + - + +
393C ALA* 3.3 4.5 + - - +
394C LYS* 2.8 47.1 + - - +
432C LEU* 3.6 10.4 - - - +
433C PRO 2.6 29.6 + - - -
434C ASP 3.6 13.9 - - - -
435C ASP 3.9 7.9 - - - -
436C MET* 3.5 42.0 - - + -
439C PHE* 3.2 43.2 - + + +
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Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ASP* 3.6 31.4 - - + +
388C ASN* 2.9 31.6 + - + +
390C TYR* 1.3 85.6 - - + +
392C ARG* 1.3 53.8 + - - +
394C LYS* 3.6 29.4 - - - +
395C ASN* 2.7 56.7 + - - +
434C ASP* 3.9 32.1 - - + +
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Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.1 4.0 - - - +
6C TYR 4.6 0.8 + - - +
193C SER* 4.9 0.8 + - - -
252C PRO* 3.1 37.7 + - + +
255C LEU* 3.9 12.6 - - - +
256C VAL* 3.4 11.7 - - - +
259C GLU* 2.5 45.6 + - - -
382C ILE* 3.2 40.6 - - + +
385C ASP 3.5 6.3 + - - +
386C GLY* 2.9 32.0 + - - -
388C ASN 2.9 18.2 + - - +
389C ILE* 3.8 21.7 + - - +
391C LEU* 1.3 75.1 - - - +
393C ALA* 1.3 65.2 + - - +
395C ASN* 3.3 9.6 + - - +
396C ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.7 17.7 - - + -
189C GLY* 4.0 14.6 - - - -
249C ILE* 4.2 7.7 - - + +
252C PRO* 3.7 23.6 - - + -
389C ILE 3.5 16.8 - - - +
390C TYR* 3.3 5.1 + - - +
391C LEU 3.2 0.4 - - - -
392C ARG* 1.3 79.4 - - - +
394C LYS* 1.3 64.0 + - - +
396C ALA* 3.3 4.4 + - - +
397C ALA* 3.0 22.2 + - - +
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Residues in contact with LYS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.9 16.5 - - + +
390C TYR* 2.8 47.1 + - + +
391C LEU* 3.2 21.9 + - + +
393C ALA* 1.3 76.8 - - - +
395C ASN* 1.3 65.0 + - - +
397C ALA* 3.3 4.7 + - - +
398C ILE* 3.1 42.9 + - + +
429C LEU* 4.0 19.1 + - + +
430C GLU* 6.0 0.6 + - - +
432C LEU* 4.0 15.9 + - + -
433C PRO 3.4 11.4 + - - -
434C ASP* 3.1 21.6 + - - -
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Residues in contact with ASN 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C SER* 3.0 33.6 + - - +
384C LYS* 3.7 16.8 - - - +
385C ASP* 2.8 34.6 + - - +
391C LEU* 2.7 40.3 + - - +
392C ARG* 3.4 3.1 - - - +
394C LYS* 1.3 77.8 + - - +
396C ALA* 1.3 52.1 + - - +
398C ILE* 3.3 6.6 + - - +
399C GLU* 2.8 36.9 + - - +
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Residues in contact with ALA 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ALA* 3.6 27.4 - - - +
252C PRO* 4.5 0.7 - - + -
378C VAL* 4.0 10.2 - - + +
381C SER* 3.4 10.9 + - - -
382C ILE* 3.7 17.7 - - + -
392C ARG 3.0 13.2 + - - +
393C ALA* 3.4 11.4 - - - +
395C ASN* 1.3 76.3 - - - +
397C ALA* 1.3 57.1 + - - +
399C GLU* 3.4 1.0 + - - +
400C CYS* 2.9 30.8 + - - +
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 5.3 0.2 - - + -
245C ILE* 4.2 6.2 - - + +
248C ALA* 4.3 6.7 - - - -
249C ILE* 3.8 19.9 - - + +
393C ALA 3.0 10.4 + - - +
394C LYS* 3.3 9.4 + - - +
396C ALA* 1.3 79.3 - - - +
398C ILE* 1.3 61.3 + - - +
400C CYS* 3.3 9.1 - - - +
401C CYS* 3.2 25.3 + - - -
429C LEU* 3.8 31.0 - - + +
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Residues in contact with ILE 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LYS* 3.1 33.9 + - + +
395C ASN* 4.0 3.8 - - - +
397C ALA* 1.3 73.5 - - - +
399C GLU* 1.3 66.8 + - - +
401C CYS* 3.0 8.0 + - - +
402C ASN* 2.8 34.4 + - - +
426C LYS* 4.5 10.1 - - + +
429C LEU* 3.7 40.6 - - + +
430C GLU* 3.9 30.1 - - + +
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Residues in contact with GLU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG* 2.6 47.5 + - - +
378C VAL* 4.4 3.6 - - - -
381C SER* 3.6 27.9 - - - +
384C LYS* 4.9 7.3 + - - -
395C ASN 2.8 22.1 + - - +
396C ALA 3.7 2.9 - - - +
398C ILE* 1.3 72.0 - - - +
400C CYS* 1.3 51.6 + - - +
402C ASN* 3.0 15.6 + - - +
403C ILE* 2.8 50.5 + - + +
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Residues in contact with CYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C VAL* 3.8 47.1 - - - -
245C ILE* 4.1 10.8 - - + -
248C ALA* 3.5 14.1 - - + -
369C MET* 4.0 10.8 - - + -
378C VAL* 4.7 1.9 - - + +
396C ALA 2.9 14.3 + - - +
397C ALA* 3.3 12.1 - - - +
399C GLU* 1.3 75.5 - - - +
401C CYS* 1.3 56.6 + - - +
403C ILE* 3.3 11.9 + - - +
404C ILE* 3.0 31.1 + - - +
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Residues in contact with CYS 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE* 3.8 26.7 - - - -
397C ALA 3.2 15.9 + - - -
398C ILE* 3.0 10.8 + - - +
400C CYS* 1.3 78.8 - - - +
402C ASN* 1.3 63.0 + - - +
404C ILE* 3.5 1.9 + - - +
405C GLU* 3.1 29.2 + - - +
422C LEU* 4.1 16.3 - - + +
426C LYS* 3.9 43.7 - - + -
429C LEU* 4.0 6.7 - - - -
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Residues in contact with ASN 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG* 3.9 15.0 - - - +
398C ILE* 2.8 27.6 + - - +
399C GLU* 3.0 18.6 + - - +
401C CYS* 1.3 74.3 - - - +
403C ILE* 1.3 66.1 - - - +
405C GLU* 3.2 10.6 + - - +
406C GLU* 3.0 32.0 + - + +
426C LYS* 2.8 28.1 + - - +
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C TYR* 3.6 18.8 - - + -
369C MET* 4.6 5.2 - - + -
374C ASN* 3.5 53.8 - - + +
377C ARG* 3.7 35.4 - - + +
378C VAL* 3.6 20.4 - - + -
399C GLU* 2.8 27.6 + - + +
400C CYS* 3.5 8.3 - - - +
402C ASN* 1.3 72.0 - - - +
404C ILE* 1.3 67.5 + - + +
406C GLU* 3.4 3.9 + - - +
407C GLY 3.1 18.0 + - - -
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Residues in contact with ILE 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C THR* 4.4 2.0 - - + -
244C VAL* 4.3 9.6 - - + -
365C PRO* 3.5 36.3 - - + +
368C TYR* 3.9 19.3 - - + -
369C MET* 4.0 13.5 - - + -
400C CYS* 3.0 30.5 + - - +
401C CYS 4.0 3.4 - - - +
403C ILE* 1.3 75.2 - - + +
405C GLU* 1.3 52.7 + - - +
407C GLY* 3.3 2.6 + - - +
408C ALA* 2.8 32.4 + - - +
412C LEU* 4.0 10.1 - - + +
414C LEU* 3.9 19.1 - - + -
422C LEU* 3.9 26.0 - - + -
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Residues in contact with GLU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C CYS 3.1 17.9 + - - +
402C ASN* 3.5 12.6 - - - +
404C ILE* 1.3 73.6 - - - +
406C GLU* 1.3 59.4 - - + +
408C ALA* 3.2 8.1 + - - +
409C ALA* 2.9 27.9 + - - +
422C LEU* 3.6 22.9 - - + +
423C ALA* 4.8 9.7 - - - +
426C LYS* 3.3 40.5 - - - +
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Residues in contact with GLU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C TYR* 4.7 1.3 - - - +
377C ARG* 2.8 45.9 + - - -
402C ASN* 3.0 14.3 + - + +
403C ILE* 3.6 5.6 - - - +
405C GLU* 1.3 73.7 - - + +
407C GLY* 1.3 67.8 + - - +
409C ALA* 3.0 17.6 + - - +
410C GLY* 3.1 9.0 + - - -
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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
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362C TYR* 6.0 0.2 - - - -
368C TYR* 3.3 35.9 + - - -
403C ILE 3.1 11.5 + - - -
404C ILE 3.6 3.6 - - - -
406C GLU* 1.3 75.3 - - - +
408C ALA* 1.3 52.0 + - - +
410C GLY* 2.8 22.8 + - - -
411C LYS 3.4 0.7 + - - -
412C LEU* 3.1 23.7 + - - -
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Residues in contact with ALA 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C ILE 2.8 19.3 + - - +
405C GLU* 3.6 8.5 - - - +
406C GLU 3.2 0.2 - - - -
407C GLY* 1.3 72.4 - - - +
409C ALA* 1.3 60.2 + - - +
410C GLY 3.5 7.1 + - - +
412C LEU* 3.4 19.1 - - - +
414C LEU* 3.9 26.7 - - + +
419C THR* 5.6 4.3 - - + +
422C LEU* 6.0 0.7 - - + -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLU 2.9 13.0 + - - +
406C GLU* 3.0 13.4 + - - +
408C ALA* 1.3 76.1 - - - +
410C GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLU 3.1 6.5 + - - -
407C GLY* 2.8 11.2 + - - -
408C ALA 3.6 7.6 - - - +
409C ALA* 1.3 81.8 - - - +
411C LYS* 1.3 65.8 + - - -
412C LEU 4.3 0.9 - - - +
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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
------------------------------------------------------------
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