Contacts of the helix formed by residues 372 - 386 (chain X) in PDB entry 5G04
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 SER 372 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309X ASP* 4.4 14.2 + - - -
339X ALA* 3.9 11.7 - - - +
340X GLU* 4.8 8.7 - - - -
343X VAL* 4.9 2.1 - - - +
366X ILE* 5.5 1.4 - - - +
369X ASN* 3.6 22.3 + - - +
370X SER 3.4 5.2 - - - +
371X ASN* 1.3 80.3 - - - +
373X VAL* 1.3 65.4 + - - +
374X GLN 3.3 1.2 + - - -
375X ALA* 3.4 27.7 + - - +
376X LEU* 4.2 2.3 + - - +
402X LEU* 5.4 0.7 - - - +
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Residues in contact with VAL 373 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309X ASP* 5.1 1.7 + - - +
371X ASN 3.7 11.4 - - - +
372X SER* 1.3 68.4 - - - +
374X GLN* 1.3 90.9 + - - +
375X ALA 3.0 2.5 - - - -
376X LEU* 2.8 18.9 + - - +
377X LEU* 3.4 18.9 + - + +
399X ALA* 5.1 3.1 - - + +
402X LEU* 3.2 44.9 - - + +
403X ALA* 3.7 22.2 - - + +
406X ARG* 4.8 18.4 - - + +
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Residues in contact with GLN 374 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282X PHE* 3.7 31.2 - - - -
309X ASP* 3.1 41.8 + - - +
310X VAL* 4.1 19.0 - - - +
313X TYR* 5.5 8.2 - - + -
343X VAL* 4.6 4.9 - - + -
347X CYS* 6.1 1.6 - - - -
372X SER 3.3 0.4 - - - -
373X VAL* 1.3 92.3 - - - +
375X ALA* 1.3 55.7 + - - +
377X LEU* 3.5 26.5 - - + +
378X LEU* 2.9 32.9 + - + +
406X ARG* 4.5 7.4 + - - -
408X ASP* 3.9 11.9 + - - +
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Residues in contact with ALA 375 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343X VAL* 3.9 13.0 - - + +
362X GLY 4.2 5.9 - - - +
365X ALA* 3.8 37.0 - - + +
366X ILE* 4.0 8.2 - - + +
372X SER* 3.4 24.0 + - - +
374X GLN* 1.3 78.5 - - - +
376X LEU* 1.3 61.9 + - - +
378X LEU* 3.3 7.9 - - - +
379X LYS* 3.2 21.0 + - - +
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Residues in contact with LEU 376 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366X ILE* 4.3 31.1 - - + +
372X SER 4.2 1.5 + - - +
373X VAL 2.8 14.5 + - - +
375X ALA* 1.3 75.0 - - - +
377X LEU* 1.3 60.3 - - - +
379X LYS* 3.2 12.9 + - + +
380X GLY* 3.2 9.7 + - - -
395X HIS* 3.7 29.3 - - - +
398X GLU* 3.6 33.2 - - + +
399X ALA* 3.6 22.2 - - + +
402X LEU* 3.5 30.1 - - + -
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Residues in contact with LEU 377 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313X TYR* 6.0 5.6 - - + -
373X VAL* 3.4 25.8 + - + +
374X GLN* 3.5 39.5 - - + +
376X LEU* 1.3 76.0 - - - +
378X LEU* 1.3 66.6 + - - +
380X GLY* 3.3 2.6 + - - +
381X ALA* 3.1 24.9 + - + +
395X HIS 5.7 0.2 - - - -
396X PHE* 4.1 21.4 - - + +
399X ALA* 4.1 16.5 - - + +
403X ALA* 5.4 0.4 - - + -
408X ASP* 4.4 13.5 - - + +
409X CYS* 4.6 23.8 - - + +
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Residues in contact with LEU 378 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313X TYR* 6.2 0.7 - - + -
343X VAL* 3.5 36.8 - - + +
346X GLY* 3.8 12.6 - - - -
347X CYS* 3.5 40.6 - - - +
350X PHE* 2.9 50.1 - - + -
358X ALA* 5.1 2.4 - - - +
362X GLY* 4.2 20.4 - - - -
374X GLN* 2.9 21.7 + - + +
375X ALA 3.3 5.6 - - - +
377X LEU* 1.3 76.7 - - + +
379X LYS* 1.3 64.4 + - - +
381X ALA* 3.5 0.7 + - - -
382X ALA* 3.4 3.5 + - - +
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Residues in contact with LYS 379 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LYS* 6.2 0.4 - - - +
358X ALA 5.2 2.9 - - - -
359X LEU* 3.2 54.0 + - + +
360X TYR* 4.8 1.4 - - - +
362X GLY 4.8 4.9 - - - -
363X ALA* 3.1 37.4 - - - +
366X ILE* 4.1 11.0 - - + -
375X ALA 3.2 9.3 + - - +
376X LEU* 3.2 10.3 + - - +
378X LEU* 1.3 79.4 - - - +
380X GLY* 1.3 62.0 + - - +
382X ALA* 3.4 8.3 + - - +
383X LEU* 3.2 25.0 + - + +
395X HIS* 3.9 28.0 - - + +
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Residues in contact with GLY 380 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376X LEU 3.2 10.4 + - - -
377X LEU* 3.3 5.1 + - - -
378X LEU 3.3 0.6 - - - -
379X LYS* 1.3 78.7 - - - +
381X ALA* 1.3 55.2 + - - +
383X LEU* 3.2 11.5 + - - +
384X ARG* 3.0 22.3 + - - +
392X ALA* 3.9 2.1 - - - +
395X HIS* 4.3 13.8 - - - +
396X PHE* 3.5 29.0 - - - -
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Residues in contact with ALA 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X PHE* 3.7 29.2 - - + -
377X LEU* 3.1 14.1 + - + +
378X LEU* 4.9 0.2 - - - -
379X LYS 3.4 0.4 - - - -
380X GLY* 1.3 72.5 - - - +
382X ALA* 1.3 63.8 + - - +
384X ARG* 3.3 8.7 + - - +
385X ASN* 3.2 30.6 + - - +
396X PHE* 3.5 10.8 - - + -
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Residues in contact with ALA 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X PHE* 3.3 26.7 - - + -
355X TYR* 3.5 24.2 - - + +
358X ALA* 3.8 22.0 - - + -
359X LEU* 4.2 8.7 - - + +
378X LEU 3.9 1.8 - - - +
379X LYS 3.4 10.9 + - - +
380X GLY 3.3 0.2 - - - -
381X ALA* 1.3 75.6 - - - +
383X LEU* 1.3 61.9 - - - +
386X MET* 3.2 25.2 + - - +
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Residues in contact with LEU 383 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359X LEU* 3.7 28.3 - - + -
379X LYS* 3.2 20.0 + - + +
380X GLY* 3.2 8.0 + - - +
382X ALA* 1.3 76.9 - - - +
384X ARG* 1.3 63.2 + - - +
385X ASN 3.6 0.2 + - - -
386X MET* 3.6 19.7 + - - +
388X ARG* 4.1 32.4 + - + +
391X GLU* 4.0 25.8 - - + +
392X ALA* 3.6 19.7 - - + +
395X HIS* 3.6 39.7 - - + +
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Residues in contact with ARG 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380X GLY 3.0 12.8 + - - +
381X ALA* 3.3 14.1 + - - +
383X LEU* 1.3 79.1 - - - +
385X ASN* 1.3 64.2 + - - +
386X MET 4.6 2.1 - - - -
387X GLY* 5.3 4.3 - - - -
389X VAL* 5.7 12.6 - - + +
392X ALA* 3.9 11.4 - - + +
396X PHE* 4.8 6.9 - - + -
412X GLY* 4.2 7.7 + - - -
415X GLU* 2.8 62.5 + - - +
416X CYS* 4.1 24.1 - - - +
418X LEU* 6.2 0.4 - - - +
419X ALA* 5.5 7.5 - - - +
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Residues in contact with ASN 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X PHE* 4.9 8.5 - - - +
355X TYR* 2.8 50.7 + - + -
381X ALA* 3.2 15.0 + - - +
384X ARG* 1.3 80.1 - - - +
386X MET* 1.3 63.5 + - - +
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Residues in contact with MET 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355X TYR* 3.5 27.2 - - + -
356X SER* 5.4 8.7 - - - +
359X LEU* 6.1 3.8 - - + -
382X ALA 3.2 17.8 + - - +
383X LEU* 3.9 15.3 - - - +
384X ARG 3.5 1.5 - - - -
385X ASN* 1.3 81.9 - - - +
387X GLY* 3.0 48.1 + - - +
388X ARG* 3.8 30.1 - - + -
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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
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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