Contacts of the helix formed by residues 380 - 394 (chain G) in PDB entry 4P0S
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 380 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378G SER 4.4 1.8 - - - +
379G LEU* 1.3 99.3 - - + +
381G GLU* 1.4 60.0 + - - +
382G SER* 4.8 5.8 - - - +
383G THR* 3.1 46.7 - - + +
384G LEU* 3.6 6.6 + - - +
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Residues in contact with GLU 381 (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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375G HIS* 4.9 21.5 + - + +
379G LEU 4.0 0.6 + - - -
380G PRO* 1.4 67.1 - - - +
382G SER* 1.3 66.8 + - - +
383G THR 3.0 2.2 + - - -
384G LEU* 3.7 5.0 + - - +
385G LEU* 3.5 28.4 + - + +
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Residues in contact with SER 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G PRO* 4.8 5.6 - - - +
381G GLU* 1.3 79.6 - - - +
383G THR* 1.3 68.4 + - - +
385G LEU* 3.9 8.4 - - - +
386G GLN* 3.1 26.3 + - - +
441H LYS* 5.9 2.4 + - - -
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Residues in contact with THR 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G ILE* 6.0 2.0 - - + -
379G LEU* 4.2 15.7 - - + -
380G PRO* 3.1 28.8 - - + +
381G GLU 3.0 0.6 - - - -
382G SER* 1.3 80.8 + - - +
384G LEU* 1.3 81.2 + - + +
386G GLN* 3.0 10.4 + - - +
387G ALA* 3.0 18.1 + - + +
1M G 5.3 23.0 + - + +
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Residues in contact with LEU 384 (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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337G LEU* 4.8 11.4 - - + +
340G LEU* 4.3 20.2 - - + -
341G CYS* 3.5 25.4 - - - -
344G ILE* 4.1 10.1 - - + -
377G LEU* 4.6 13.2 - - + -
379G LEU* 3.6 43.7 - - + +
380G PRO 3.6 6.0 + - - +
381G GLU* 3.7 5.8 + - - +
382G SER 3.7 0.2 - - - -
383G THR* 1.3 79.8 - - + +
385G LEU* 1.3 55.3 + - - +
387G ALA* 2.7 26.5 + - - +
388G VAL* 2.8 24.2 + - + +
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Residues in contact with LEU 385 (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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381G GLU* 3.5 24.4 + - + +
382G SER* 3.9 7.4 - - - +
383G THR 3.3 0.2 - - - -
384G LEU* 1.3 77.2 - - - +
386G GLN* 1.3 59.4 + - - +
388G VAL* 3.4 6.2 + - + +
389G THR* 2.6 38.3 + - - +
401G ARG* 4.1 28.3 - - - +
434H ASP* 4.7 25.1 - - + +
435H PHE* 5.1 7.9 - - + -
438H ALA* 4.7 9.0 - - + -
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Residues in contact with GLN 386 (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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382G SER 3.1 14.7 + - - +
383G THR* 3.0 15.0 + - - +
384G LEU 3.0 0.4 - - - -
385G LEU* 1.3 79.0 - - - +
387G ALA* 1.3 54.8 + - - +
389G THR* 3.2 4.4 + - - -
390G ASN* 2.9 53.9 + - - +
438H ALA* 3.5 24.7 + - - +
441H LYS* 3.2 50.8 + - - +
445H GLU* 4.5 1.2 + - - -
1M G 3.7 24.5 - - - +
2M A 3.9 4.7 - - - +
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Residues in contact with ALA 387 (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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340G LEU* 5.2 3.8 - - + -
344G ILE* 4.5 19.3 - - + -
349G PHE* 5.3 9.4 - - + -
383G THR* 3.0 9.9 + - + +
384G LEU* 2.7 20.3 + - - +
386G GLN* 1.3 73.9 - - - +
388G VAL* 1.3 60.3 + - + +
389G THR 3.1 0.2 + - - -
390G ASN* 3.1 7.4 + - - +
391G THR* 2.5 34.7 + - - +
1M G 5.3 8.5 - - - +
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Residues in contact with VAL 388 (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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340G LEU* 5.3 11.2 - - + -
368G VAL* 5.1 13.7 - - + -
384G LEU* 2.8 23.5 + - + +
385G LEU* 4.0 6.7 - - - +
387G ALA* 1.3 75.3 - - + +
389G THR* 1.3 66.1 + - - +
391G THR* 3.0 9.6 + - - -
392G GLN* 2.9 21.8 + - - +
399G VAL* 3.5 35.3 - - + +
401G ARG* 4.0 28.7 - - + +
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Residues in contact with THR 389 (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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385G LEU* 2.6 29.5 + - - +
386G GLN* 3.4 4.3 - - - -
387G ALA 3.0 0.2 - - - -
388G VAL* 1.3 80.2 - - - +
390G ASN* 1.3 63.9 + - - +
392G GLN* 3.0 18.2 + - + +
393G VAL* 3.2 10.6 + - + +
401G ARG* 4.3 7.6 + - - -
435H PHE* 4.3 11.5 - - + -
438H ALA* 3.5 43.0 - - + +
439H PHE* 3.7 16.4 - - + +
442H ALA* 3.8 6.7 - - + +
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Residues in contact with ASN 390 (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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386G GLN* 2.9 34.7 + - - +
387G ALA* 3.1 3.8 + - - +
389G THR* 1.3 74.8 - - - +
391G THR* 1.3 57.6 + - - +
394G ILE* 2.8 57.5 + - + +
395G ASP* 5.2 0.7 - - - -
442H ALA* 2.9 33.3 + - - +
445H GLU* 3.9 10.3 + - - +
449H LYS* 4.9 0.2 - - - -
1M G 3.3 40.8 - - - +
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Residues in contact with THR 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G PHE* 3.3 26.8 - - + -
353G LYS* 4.1 23.4 + - + +
366G TYR* 4.9 5.8 - - + -
387G ALA 2.5 18.2 + - - -
388G VAL* 3.2 12.0 - - - -
390G ASN* 1.3 79.8 - - - +
392G GLN* 1.3 59.4 + - - +
395G ASP* 3.5 15.2 + - - +
396G GLY 3.4 15.6 + - - -
397G PHE* 3.6 24.3 + - + +
399G VAL* 4.9 7.2 - - + -
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Residues in contact with GLN 392 (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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388G VAL* 2.9 11.4 + - - +
389G THR* 3.0 9.2 + - - +
391G THR* 1.3 78.1 - - - +
393G VAL* 1.3 66.8 + - + +
396G GLY* 3.2 22.2 - - - -
397G PHE 3.7 11.8 - - - +
399G VAL* 3.6 25.7 - - + +
401G ARG* 4.2 11.4 + - - -
360H SER* 4.3 4.5 + - - +
422H GLN* 3.8 40.8 + - + +
424H GLN* 4.1 6.1 - - - +
435H PHE* 3.2 38.9 - - - -
439H PHE* 4.1 8.2 - - + -
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Residues in contact with VAL 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389G THR 3.2 13.5 + - - +
392G GLN* 1.3 78.1 - - + +
394G ILE* 1.3 68.3 + - + +
396G GLY* 3.9 4.5 + - - -
311H THR* 4.6 17.9 - - + +
439H PHE* 3.3 45.1 - - + -
442H ALA* 4.3 13.7 - - + -
443H VAL* 4.4 23.8 - - + -
446H ALA* 4.5 9.5 - - + +
450H LYS* 4.5 4.5 + - - -
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Residues in contact with ILE 394 (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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390G ASN* 2.8 47.0 + - + +
393G VAL* 1.3 72.3 - - + +
395G ASP* 1.3 71.5 + - - +
396G GLY* 3.0 5.4 + - - -
442H ALA 3.8 18.4 - - - +
445H GLU* 3.8 15.5 - - + +
446H ALA* 3.5 29.6 - - + +
449H LYS* 4.1 26.9 - - + -
450H LYS* 2.7 45.3 + - + +
1M G 4.7 0.2 - - - +
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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
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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