Contacts of the helix formed by residues 388 - 410 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K ASP* 3.0 11.2 + - + +
387K ASP* 1.3 79.5 - - + +
389K ILE* 1.3 56.8 + - - +
390K TYR* 3.1 12.1 + - - +
391K LEU* 3.1 39.8 + - + +
392K ARG* 2.9 31.6 + - - +
434K ASP 4.8 3.6 + - - -
436K MET* 3.6 22.8 - - - +
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Residues in contact with ILE 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ARG* 3.8 39.5 - - - +
189K GLY 3.8 10.0 - - - +
190K CYS* 4.1 8.1 - - - +
193K SER* 3.8 26.4 + - - +
194K ILE* 3.8 30.7 - - + +
252K PRO* 5.4 0.5 - - - +
387K ASP 3.9 1.2 + - - +
388K ASN* 1.3 73.1 + - - +
390K TYR* 1.3 65.4 + - - +
392K ARG* 3.7 21.4 + - - +
393K ALA* 3.6 18.2 + - - +
436K MET* 3.9 25.6 - - + -
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Residues in contact with TYR 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU* 3.3 24.0 - - + -
190K CYS* 4.0 16.6 - - - -
388K ASN* 3.1 2.1 + - - +
389K ILE* 1.3 80.1 - - - +
391K LEU* 1.3 74.8 + - + +
393K ALA* 3.0 6.0 + - - +
394K LYS* 2.9 42.5 + - - +
432K LEU* 3.5 12.3 - - - +
433K PRO 2.9 29.0 + - - -
434K ASP 3.5 15.9 - - - -
435K ASP 4.2 0.9 - - - -
436K MET* 3.6 39.3 - - + -
439K PHE* 3.2 49.3 - + + +
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Residues in contact with LEU 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385K ASP* 3.9 31.2 - - + +
388K ASN* 3.1 27.7 + - + +
390K TYR* 1.3 81.8 - - - +
392K ARG* 1.3 56.7 + - - +
394K LYS* 3.2 18.3 + - + +
395K ASN* 2.8 46.0 + - - +
434K ASP* 3.8 47.6 - - + +
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Residues in contact with ARG 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ARG* 4.0 3.8 - - - +
6K TYR 4.8 0.2 + - - -
193K SER* 5.5 1.0 + - - -
252K PRO* 2.9 40.1 + - + +
255K LEU* 3.8 12.3 - - - +
256K VAL* 3.5 12.5 - - - +
259K GLU* 2.6 45.0 + - - -
382K ILE* 3.5 31.7 - - + +
385K ASP 3.5 8.5 + - - +
386K GLY* 2.9 32.1 + - - -
388K ASN 2.9 22.4 + - - +
389K ILE* 3.7 24.4 + - - +
391K LEU* 1.3 76.6 - - - +
393K ALA* 1.3 58.7 + - - +
395K ASN* 3.3 11.0 - - - +
396K ALA* 3.1 26.2 + - - +
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Residues in contact with ALA 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU* 3.6 20.9 - - + +
189K GLY* 3.8 20.4 - - - -
249K ILE* 4.1 7.3 - - + +
252K PRO* 3.9 19.5 - - + -
389K ILE 3.6 11.2 - - - +
390K TYR* 3.0 9.4 + - - +
392K ARG* 1.3 80.0 - - - +
394K LYS* 1.3 62.7 + - - +
396K ALA* 3.4 2.8 + - - +
397K ALA* 3.1 23.9 + - - +
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Residues in contact with LYS 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU* 3.8 17.0 - - + +
390K TYR* 2.9 45.5 + - + +
391K LEU* 3.8 16.9 - - - +
393K ALA* 1.3 75.7 - - - +
395K ASN* 1.3 65.0 + - - +
397K ALA* 3.4 4.6 + - - +
398K ILE* 3.1 42.8 + - + +
429K LEU* 3.8 21.9 + - + +
430K GLU* 5.7 0.4 + - - +
432K LEU* 3.8 17.3 + - + -
433K PRO 3.4 12.1 - - - -
434K ASP* 3.0 25.3 + - - -
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Residues in contact with ASN 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381K SER* 2.8 34.5 + - - +
384K LYS* 3.7 15.8 - - - +
385K ASP* 2.8 36.1 + - - +
391K LEU* 2.8 34.7 + - - +
392K ARG* 3.3 6.0 - - - +
394K LYS* 1.3 74.0 + - - +
396K ALA* 1.3 58.9 + - - +
398K ILE* 3.3 5.9 + - - +
399K GLU* 2.8 31.2 + - - +
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Residues in contact with ALA 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248K ALA* 3.5 28.0 - - - +
252K PRO* 4.4 3.4 - - + -
378K VAL* 3.7 11.8 - - + +
381K SER* 3.5 10.5 + - - -
382K ILE* 3.7 24.5 - - + -
392K ARG 3.1 7.1 + - - +
393K ALA 3.4 4.5 + - - +
394K LYS 3.4 0.2 - - - -
395K ASN* 1.3 78.1 - - - +
397K ALA* 1.3 58.0 + - - +
399K GLU* 3.8 1.0 - - - +
400K CYS* 2.9 30.8 + - - +
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Residues in contact with ALA 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU* 5.2 0.4 - - + -
245K ILE* 4.3 5.9 - - + +
248K ALA* 4.6 2.4 - - - +
249K ILE* 3.8 24.6 - - + +
393K ALA 3.1 17.7 + - - +
394K LYS* 3.6 7.0 - - - +
396K ALA* 1.3 77.6 - - - +
398K ILE* 1.3 56.2 + - - +
400K CYS* 3.3 8.7 - - - +
401K CYS* 3.1 29.3 + - - -
429K LEU* 3.7 29.3 - - + +
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Residues in contact with ILE 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394K LYS* 3.1 46.3 + - + +
395K ASN* 4.1 4.5 - - - +
397K ALA* 1.3 70.8 - - - +
399K GLU* 1.3 68.9 + - - +
400K CYS 3.1 1.6 - - - -
401K CYS* 3.0 7.7 + - - +
402K ASN* 2.9 31.0 + - - +
426K LYS* 3.8 23.3 - - + +
429K LEU* 3.8 30.7 - - + +
430K GLU* 4.0 20.4 - - - +
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Residues in contact with GLU 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377K ARG* 2.6 52.7 + - + +
378K VAL* 4.2 3.6 - - - -
381K SER* 3.6 27.6 - - - +
384K LYS* 4.3 9.9 + - - -
395K ASN 2.8 19.5 + - - +
396K ALA* 3.8 3.1 - - - +
398K ILE* 1.3 75.7 - - - +
400K CYS* 1.3 64.1 + - - +
402K ASN* 3.0 16.3 + - - +
403K ILE* 2.9 37.6 + - + +
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Residues in contact with CYS 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K VAL* 3.6 46.4 - - - -
245K ILE* 4.0 7.9 - - + -
248K ALA* 3.6 12.6 - - + -
369K MET* 3.9 18.6 - - + -
378K VAL* 4.7 2.1 - - + +
396K ALA 2.9 15.3 + - - +
397K ALA* 3.3 10.8 - - - +
399K GLU* 1.3 75.6 - - - +
401K CYS* 1.3 63.9 + - - +
403K ILE* 3.2 10.3 + - - +
404K ILE* 2.9 29.4 + - - +
422K LEU* 6.2 0.2 - - - -
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Residues in contact with CYS 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245K ILE* 3.8 26.9 - - - -
397K ALA 3.1 14.7 + - - -
398K ILE* 3.0 9.9 + - - +
400K CYS* 1.3 79.6 - - - +
402K ASN* 1.3 62.3 + - - +
404K ILE* 3.4 2.4 + - - +
405K GLU* 3.1 27.6 + - - +
422K LEU* 3.9 20.9 - - + +
426K LYS* 3.9 42.2 - - + -
429K LEU* 4.1 7.0 - - - -
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Residues in contact with ASN 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377K ARG* 4.0 13.4 - - - +
398K ILE* 2.9 29.1 + - - +
399K GLU* 3.6 16.0 + - - +
401K CYS* 1.3 71.8 - - - +
403K ILE* 1.3 60.7 + - - +
405K GLU* 3.5 13.1 + - - +
406K GLU* 3.0 39.6 + - - +
426K LYS* 3.1 28.3 + - - +
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Residues in contact with ILE 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368K TYR* 3.4 17.5 - - + -
369K MET* 4.5 9.0 - - + -
374K ASN* 3.6 44.2 - - + +
377K ARG* 3.6 39.9 - - + +
378K VAL* 3.6 30.5 - - + -
399K GLU* 2.9 21.9 + - + +
400K CYS* 3.6 5.8 - - - +
402K ASN* 1.3 76.2 - - - +
404K ILE* 1.3 62.7 + - + +
406K GLU* 3.5 4.6 + - - +
407K GLY 3.1 18.0 + - - -
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Residues in contact with ILE 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K THR* 4.4 4.3 - - + -
244K VAL* 4.0 17.9 - - + -
365K PRO* 3.7 37.7 - - + +
368K TYR* 4.1 20.0 - - + -
369K MET* 4.2 13.2 - - + -
400K CYS* 2.9 22.2 + - - +
401K CYS 4.0 3.6 - - - +
403K ILE* 1.3 74.9 - - - +
405K GLU* 1.3 58.5 + - - +
407K GLY* 3.4 1.2 + - - -
408K ALA* 2.9 27.7 + - - +
412K LEU* 4.0 8.4 - - + +
414K LEU* 3.8 25.8 - - + -
422K LEU* 3.9 16.2 - - + -
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Residues in contact with GLU 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K CYS* 3.1 20.2 + - - +
402K ASN* 3.5 18.4 - - - +
403K ILE 3.4 0.2 - - - -
404K ILE* 1.3 73.2 - - - +
406K GLU* 1.3 65.8 + - + +
408K ALA* 3.1 9.5 + - - +
409K ALA* 3.0 22.4 + - - +
422K LEU* 4.2 15.6 - - + +
423K ALA* 6.2 0.3 - - - -
426K LYS* 3.4 33.1 - - - +
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Residues in contact with GLU 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K TYR* 4.7 2.2 - - - +
377K ARG* 2.6 46.4 + - - -
402K ASN* 3.0 20.1 + - - +
403K ILE* 3.8 4.7 - - - +
405K GLU* 1.3 79.4 - - + +
407K GLY* 1.3 61.7 - - - +
409K ALA* 3.2 16.9 + - - +
410K GLY* 3.3 9.5 + - - -
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Residues in contact with GLY 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362K TYR* 5.5 0.4 - - - -
368K TYR* 3.4 32.4 + - - -
403K ILE 3.1 11.5 + - - -
404K ILE 3.7 3.4 - - - -
405K GLU 3.3 0.2 - - - -
406K GLU* 1.3 76.5 - - - +
408K ALA* 1.3 56.6 + - - +
410K GLY* 3.0 14.7 + - - -
411K LYS 3.4 0.9 + - - -
412K LEU* 3.0 30.8 + - - -
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Residues in contact with ALA 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404K ILE 2.9 16.6 + - - +
405K GLU* 3.4 11.9 - - - +
407K GLY* 1.3 72.0 - - - +
409K ALA* 1.3 61.0 + - - +
410K GLY 3.3 7.8 + - - +
412K LEU* 3.3 19.4 - - - +
414K LEU* 4.0 24.2 - - + +
419K THR* 5.8 2.5 - - + +
422K LEU* 6.0 0.2 - - + -
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Residues in contact with ALA 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405K GLU 3.0 11.6 + - - +
406K GLU* 3.2 12.5 + - - +
408K ALA* 1.3 75.6 - - - +
410K GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406K GLU 3.3 6.7 + - - -
407K GLY* 3.0 10.9 + - - -
408K ALA 3.5 7.6 - - - +
409K ALA* 1.3 82.1 - - - +
411K LYS* 1.3 64.1 + - - -
412K LEU 4.5 0.3 - - - +
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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