Contacts of the helix formed by residues 388 - 410 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G ASP* 2.9 12.3 + - + +
386G GLY 3.2 0.2 - - - -
387G ASP* 1.3 78.2 - - + +
389G ILE* 1.3 65.0 + - - +
390G TYR* 3.3 6.8 + - - +
391G LEU* 3.0 42.6 + - + +
392G ARG* 2.9 24.7 + - - +
434G ASP 4.9 4.4 + - - -
436G MET* 3.5 27.0 - - - +
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Residues in contact with ILE 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ARG* 3.9 36.3 - - - +
189G GLY 4.1 5.7 - - - +
190G CYS* 4.2 17.9 - - + +
193G SER* 4.0 32.5 + - - +
194G ILE* 4.3 15.5 - - + -
252G PRO* 5.3 0.7 - - - +
387G ASP 3.8 2.5 + - - +
388G ASN* 1.3 72.2 + - - +
390G TYR* 1.3 64.0 + - - +
392G ARG* 3.4 31.6 + - - +
393G ALA* 3.4 13.2 + - - +
436G MET* 3.7 28.2 - - + -
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Residues in contact with TYR 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 4.1 14.3 - - + +
190G CYS* 4.0 18.8 - - - -
388G ASN* 3.2 2.7 + - - -
389G ILE* 1.3 81.6 - - - +
391G LEU* 1.3 63.4 - - + +
393G ALA* 3.2 6.1 + - - +
394G LYS* 2.9 47.0 + - + +
432G LEU* 3.9 4.0 - - - +
433G PRO 2.5 29.9 + - - -
434G ASP 4.1 5.4 - - - -
435G ASP 3.7 14.6 - - - -
436G MET* 3.6 39.0 - - + -
439G PHE* 3.2 58.5 - + + +
440G MET* 5.4 0.2 - - - -
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Residues in contact with LEU 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G ASP* 3.5 29.6 - - + +
388G ASN* 3.0 36.1 + - + +
390G TYR* 1.3 80.4 - - + +
392G ARG* 1.3 60.4 + - - +
394G LYS* 3.4 31.8 + - - +
395G ASN* 2.9 43.9 + - - +
434G ASP* 4.1 31.6 - - - +
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Residues in contact with ARG 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ARG* 3.9 3.6 - - - +
6G TYR 4.6 0.6 + - - +
193G SER* 4.8 0.8 + - - -
252G PRO* 3.0 39.4 + - + +
255G LEU* 4.0 12.6 - - - +
256G VAL* 3.6 8.1 - - - +
259G GLU* 2.6 45.4 + - - -
382G ILE* 3.4 35.3 - - + +
385G ASP* 3.7 9.0 + - - +
386G GLY* 2.8 39.9 + - - -
388G ASN 2.9 18.6 + - - +
389G ILE* 3.4 26.0 - - - +
391G LEU* 1.3 76.0 - - - +
393G ALA* 1.3 59.7 - - - +
395G ASN* 3.4 7.5 + - - +
396G ALA* 2.9 27.6 + - - +
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Residues in contact with ALA 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 3.7 17.5 - - + -
189G GLY* 4.0 17.5 - - - +
249G ILE* 4.1 9.0 - - + +
252G PRO* 3.8 22.4 - - + -
389G ILE 3.4 15.5 - - - +
390G TYR* 3.2 5.5 + - - +
392G ARG* 1.3 82.8 - - - +
394G LYS* 1.3 56.2 + - - +
396G ALA* 3.2 5.5 + - - +
397G ALA* 3.0 25.6 + - - +
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Residues in contact with LYS 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 3.8 26.0 - - + +
390G TYR* 2.9 47.2 + - + +
391G LEU* 3.7 21.2 - - - +
393G ALA* 1.3 72.1 - - - +
395G ASN* 1.3 69.1 + - - +
397G ALA* 3.1 5.8 + - - +
398G ILE* 3.0 42.8 + - + +
429G LEU* 3.9 21.0 + - + +
430G GLU* 6.3 0.2 - - - +
432G LEU* 4.3 6.6 + - + -
433G PRO 3.6 10.7 + - - -
434G ASP* 2.9 24.6 + - - -
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Residues in contact with ASN 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381G SER* 3.1 35.7 + - - +
384G LYS* 3.7 18.3 - - - +
385G ASP* 2.8 32.2 + - - +
391G LEU* 2.9 35.6 + - - +
392G ARG 3.5 2.5 - - - +
394G LYS* 1.3 77.2 + - - +
396G ALA* 1.3 59.8 + - - +
398G ILE* 4.2 6.2 - - - +
399G GLU* 2.8 34.7 + - - +
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Residues in contact with ALA 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G ALA* 3.4 30.3 - - - +
252G PRO* 4.4 1.8 - - + -
378G VAL* 4.2 8.1 - - + +
381G SER* 3.9 10.3 + - - -
382G ILE* 4.1 15.5 - - + -
392G ARG 2.9 14.6 + - - +
393G ALA* 3.3 13.0 - - - +
395G ASN* 1.3 74.7 - - - +
397G ALA* 1.3 58.4 + - - +
399G GLU* 3.8 1.2 - - - +
400G CYS* 2.9 31.2 + - - +
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Residues in contact with ALA 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 5.2 0.2 - - + -
245G ILE* 4.3 5.3 - - + +
248G ALA* 4.6 2.2 - - - +
249G ILE* 3.9 22.2 - - + +
393G ALA 3.0 11.9 + - - +
394G LYS* 3.1 10.7 + - - +
396G ALA* 1.3 77.2 - - - +
398G ILE* 1.3 56.8 + - - +
400G CYS* 3.3 8.2 - - - +
401G CYS* 3.1 29.8 + - - -
429G LEU* 3.7 33.6 - - + +
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Residues in contact with ILE 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G LYS* 3.0 40.3 + - + +
395G ASN* 4.2 4.9 - - - +
397G ALA* 1.3 71.9 - - - +
399G GLU* 1.3 68.6 + - - +
401G CYS* 2.9 21.2 + - + +
402G ASN* 2.9 29.4 + - - +
426G LYS* 5.4 4.0 - - + +
429G LEU* 4.0 32.5 - - + +
430G GLU* 4.1 28.3 - - + +
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Residues in contact with GLU 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377G ARG* 2.6 50.8 + - - +
378G VAL* 4.3 4.0 - - - -
381G SER* 3.2 30.1 - - - +
384G LYS* 4.4 8.5 + - - -
395G ASN 2.8 22.5 + - - +
396G ALA 3.8 2.9 - - - +
398G ILE* 1.3 74.3 - - - +
400G CYS* 1.3 58.0 + - - +
402G ASN* 3.2 11.5 + - - +
403G ILE* 2.9 44.1 + - + +
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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
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244G VAL* 3.9 36.8 - - - -
245G ILE* 4.1 13.9 - - - -
248G ALA* 3.5 21.5 - - + -
369G MET* 4.0 10.5 - - + -
378G VAL* 4.7 1.5 - - + +
396G ALA 2.9 19.7 + - - +
397G ALA* 3.3 6.5 - - - +
399G GLU* 1.3 76.4 - - - +
401G CYS* 1.3 56.6 + - - +
403G ILE* 3.6 11.0 - - - +
404G ILE* 3.0 30.1 + - - +
422G LEU* 6.3 0.2 - - - -
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Residues in contact with CYS 401 (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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245G ILE* 4.0 26.5 - - - -
397G ALA 3.1 18.8 + - - -
398G ILE* 2.9 10.8 + - - +
400G CYS* 1.3 76.1 - - - +
402G ASN* 1.3 56.9 + - - +
404G ILE* 3.3 3.5 + - - +
405G GLU* 2.8 34.4 + - - +
422G LEU* 4.0 18.2 - - + +
426G LYS* 4.1 43.1 - - + -
429G LEU* 4.3 7.0 - - - -
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Residues in contact with ASN 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377G ARG* 4.1 13.9 - - - +
398G ILE* 2.9 35.5 + - - +
399G GLU* 3.6 13.4 + - - +
401G CYS* 1.3 74.9 - - - +
403G ILE* 1.3 63.7 + - - +
405G GLU* 3.1 13.3 + - - +
406G GLU* 2.8 35.5 + - + +
426G LYS* 3.5 24.6 + - - +
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Residues in contact with ILE 403 (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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368G TYR* 3.6 28.0 - - + -
369G MET* 4.4 9.4 - - + -
374G ASN* 3.5 42.6 - - + +
377G ARG* 3.7 34.5 - - + +
378G VAL* 3.7 18.6 - - + -
399G GLU* 2.9 29.6 + - + +
400G CYS* 3.6 7.4 - - - +
402G ASN* 1.3 76.1 - - - +
404G ILE* 1.3 65.2 + - + +
406G GLU* 3.2 4.7 + - - +
407G GLY 2.9 18.4 + - - -
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Residues in contact with ILE 404 (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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241G THR* 4.4 10.5 - - + -
244G VAL* 4.3 16.8 - - + -
365G PRO* 3.7 32.3 - - + +
368G TYR* 4.0 20.6 - - + -
369G MET* 4.2 11.7 - - + -
400G CYS* 3.0 24.2 + - - +
401G CYS 3.7 3.8 - - - +
403G ILE* 1.3 73.7 - - + +
405G GLU* 1.3 53.1 + - - +
407G GLY* 3.0 3.7 + - - +
408G ALA* 2.7 32.6 + - - +
412G LEU* 4.2 6.3 - - + +
414G LEU* 4.0 18.2 - - + -
422G LEU* 3.6 25.6 - - + -
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Residues in contact with GLU 405 (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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401G CYS 2.8 21.2 + - - +
402G ASN* 3.3 18.8 - - - +
404G ILE* 1.3 71.2 - - - +
406G GLU* 1.3 59.8 + - + +
408G ALA* 3.2 9.1 + - - +
409G ALA* 2.9 26.0 + - - +
422G LEU* 4.1 18.8 - - + +
423G ALA* 5.3 6.4 - - - +
426G LYS* 3.2 39.9 + - + +
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Residues in contact with GLU 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368G TYR* 4.7 2.0 - - - +
377G ARG* 2.9 43.9 + - - -
402G ASN* 2.8 22.9 + - + +
403G ILE* 3.6 4.3 - - - +
405G GLU* 1.3 75.0 - - + +
407G GLY* 1.3 60.9 + - - +
409G ALA* 3.2 9.7 + - - +
410G GLY* 2.9 23.9 + - - -
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Residues in contact with GLY 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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362G TYR* 5.9 0.2 - - - -
368G TYR* 3.4 33.9 + - - -
403G ILE 2.9 10.3 + - - -
404G ILE 3.4 3.6 - - - -
406G GLU* 1.3 76.4 - - - +
408G ALA* 1.3 55.4 + - - +
410G GLY* 2.9 17.2 + - - -
411G LYS 3.4 0.4 + - - -
412G LEU* 3.1 30.4 + - - -
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Residues in contact with ALA 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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404G ILE 2.7 15.0 + - - +
405G GLU* 3.4 13.0 - - - +
406G GLU 3.2 0.2 - - - -
407G GLY* 1.3 69.9 - - - +
409G ALA* 1.3 66.5 - - - +
410G GLY 3.5 2.6 + - - +
412G LEU* 3.7 19.9 - - - +
414G LEU* 3.6 27.4 - - + -
419G THR* 5.5 3.8 - - + +
422G LEU* 5.8 1.3 - - + -
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Residues in contact with ALA 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405G GLU 2.9 12.7 + - - +
406G GLU* 3.2 12.5 + - - +
408G ALA* 1.3 77.3 - - - +
410G GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406G GLU 2.9 10.1 + - - -
407G GLY* 2.9 12.7 + - - -
408G ALA 4.0 3.9 - - - +
409G ALA* 1.3 83.4 - - - +
411G LYS* 1.3 64.0 + - - +
412G LEU 4.6 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
------------------------------------------------------------
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