Contacts of the helix formed by residues 388 - 403 (chain X) in PDB entry 5A31
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 ARG 388 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356X SER* 5.6 0.4 - - - +
383X LEU* 2.9 24.9 + - + +
386X MET* 3.7 36.0 - - + +
387X GLY* 1.3 75.8 - - - +
389X VAL* 1.3 57.6 + - - +
390X GLN 3.5 1.6 - - - -
391X GLU* 3.0 46.3 + - + +
392X ALA* 2.9 28.3 + - - +
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Residues in contact with VAL 389 (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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384X ARG* 5.5 10.8 - - + +
387X GLY 3.0 13.2 + - - +
388X ARG* 1.3 69.4 - - - +
390X GLN* 1.3 66.3 + - + +
392X ALA* 3.2 7.3 + - + +
393X ILE* 2.8 52.7 + - + +
419X ALA* 5.9 6.3 - - + -
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Residues in contact with GLN 390 (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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388X ARG 3.5 0.2 - - - -
389X VAL* 1.3 83.8 - - + +
391X GLU* 1.3 62.3 + - - +
393X ILE* 3.4 14.5 + - + +
394X ILE* 3.4 26.9 + - + +
397X ARG* 5.2 2.3 + - - +
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Residues in contact with GLU 391 (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* 3.4 31.9 - - + +
383X LEU* 3.9 5.1 - - + +
388X ARG* 3.0 55.5 + - + +
389X VAL 3.3 0.4 - - - -
390X GLN* 1.3 77.1 - - - +
392X ALA* 1.3 61.1 + - - +
394X ILE* 2.9 35.2 - - + +
395X HIS* 3.1 10.2 - - - +
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Residues in contact with ALA 392 (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 3.5 21.8 - - - +
383X LEU* 3.5 16.7 - - + +
384X ARG* 3.8 9.9 - - + +
388X ARG 2.9 17.5 + - - +
389X VAL* 3.5 9.6 - - + +
391X GLU* 1.3 76.0 - - - +
393X ILE* 1.3 63.3 + - + +
395X HIS* 3.2 15.6 + - - +
396X PHE* 3.1 26.2 + - + -
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Residues in contact with ILE 393 (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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389X VAL* 2.8 47.6 + - + +
390X GLN* 3.6 11.7 - - + +
391X GLU 3.3 0.2 - - - -
392X ALA* 1.3 76.7 - - + +
394X ILE* 1.3 63.5 + - - +
396X PHE* 3.2 18.4 + - + +
397X ARG* 3.3 39.7 + - + +
416X CYS* 4.0 33.7 - - + +
419X ALA* 5.6 6.7 - - + -
420X SER* 6.3 1.8 - - - +
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Residues in contact with ILE 394 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390X GLN* 3.4 14.9 + - + +
391X GLU* 2.9 31.4 - - + +
393X ILE* 1.3 77.2 - - - +
395X HIS* 1.3 75.4 + - + +
397X ARG* 3.3 35.3 + - - +
398X GLU* 3.1 28.3 + - + +
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Residues in contact with HIS 395 (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 10.0 - - + +
366X ILE* 5.7 2.7 - - + -
376X LEU* 3.3 41.0 - - + +
379X LYS* 3.6 27.9 - - + +
380X GLY* 4.2 8.3 - - - -
383X LEU* 3.3 28.1 - - + +
391X GLU* 3.1 26.1 + - - +
392X ALA 3.2 7.7 + - - +
394X ILE* 1.3 86.3 - - + +
396X PHE* 1.3 59.3 + - + +
398X GLU* 3.2 17.7 + - - +
399X ALA* 2.8 29.5 + - - +
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Residues in contact with PHE 396 (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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377X LEU* 3.7 35.2 - - + -
380X GLY* 3.7 12.3 - - - -
381X ALA* 3.5 30.5 - - + -
384X ARG* 5.3 10.5 - - + -
392X ALA* 3.1 35.2 + - + -
393X ILE* 3.2 9.5 + - - +
395X HIS* 1.3 77.4 - - - +
397X ARG* 1.3 57.0 + - + +
399X ALA* 3.2 5.5 + - + +
400X ILE* 2.9 36.3 + - + +
412X GLY* 4.8 20.6 - - - -
413X LEU* 5.1 1.3 - - - +
416X CYS* 4.2 22.4 - - - -
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Residues in contact with ARG 397 (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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765H ASP* 5.1 17.6 + - - +
767H ASP 5.5 9.3 + - - -
390X GLN* 5.2 2.0 + - - +
393X ILE* 3.3 41.0 + - + +
394X ILE* 3.3 31.2 + - - +
396X PHE* 1.3 76.7 - - + +
398X GLU* 1.3 58.8 + - - +
400X ILE* 2.8 30.4 - - + +
401X ARG* 3.6 6.9 + - - +
413X LEU* 5.1 12.1 - - + -
416X CYS* 6.1 2.9 - - + -
417X TYR* 5.3 6.5 - - + +
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Residues in contact with GLU 398 (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* 4.5 9.6 - - - +
376X LEU* 3.0 34.3 - - + +
394X ILE* 3.1 18.6 + - - +
395X HIS* 3.2 30.5 + - - +
397X ARG* 1.3 73.7 - - - +
399X ALA* 1.3 61.6 + - - +
401X ARG* 2.9 33.8 - - - +
402X LEU* 3.4 13.5 + - + +
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Residues in contact with ALA 399 (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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373X VAL* 4.1 11.1 - - + +
376X LEU* 3.6 21.9 - - + +
377X LEU* 4.5 17.9 - - + +
395X HIS 2.8 21.9 + - - +
396X PHE* 3.2 10.7 + - + +
398X GLU* 1.3 70.4 - - - +
400X ILE* 1.3 65.4 + - + +
402X LEU* 3.2 7.4 + - - +
403X ALA* 3.1 21.1 + - - +
409X CYS* 4.6 6.3 - - + +
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Residues in contact with ILE 400 (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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762H TRP* 5.6 4.7 - - - +
765H ASP* 4.1 19.7 - - - +
396X PHE* 2.9 23.1 + - + +
397X ARG* 2.8 28.5 - - - +
399X ALA* 1.3 71.5 - - - +
401X ARG* 1.3 64.7 + - + +
403X ALA 3.0 23.6 - - - +
409X CYS* 3.2 35.7 - - + +
410X TYR* 6.3 1.8 - - + -
413X LEU* 3.2 54.7 - - + +
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Residues in contact with ARG 401 (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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734H PRO* 5.3 4.0 + - - +
735H LYS* 3.2 53.6 - - - +
762H TRP* 5.9 4.2 - - - +
766H LEU* 4.6 15.0 - - - +
397X ARG 3.8 4.0 - - - +
398X GLU* 2.9 39.7 - - - +
400X ILE* 1.3 85.9 - - + +
402X LEU* 1.3 70.2 + - + +
403X ALA* 3.5 2.6 + - - -
404X PRO* 4.9 3.5 - - - +
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Residues in contact with LEU 402 (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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181X LYS* 5.6 11.2 - - + +
366X ILE* 4.9 10.8 - - + -
370X SER* 4.0 23.6 - - - +
371X ASN 5.5 1.2 - - - +
372X SER 5.7 0.7 - - - +
373X VAL* 3.4 27.6 - - + +
376X LEU* 3.8 29.2 - - + -
398X GLU* 3.4 8.5 - - + +
399X ALA 3.2 4.3 + - - +
401X ARG* 1.3 87.5 - - + +
403X ALA* 1.3 57.4 + - - +
404X PRO* 3.5 10.0 - - - +
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Residues in contact with ALA 403 (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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373X VAL* 3.6 28.5 - - + -
399X ALA 3.1 9.3 + - - +
400X ILE 3.0 17.4 - - - +
401X ARG 4.5 1.1 - - - -
402X LEU* 1.3 76.2 - - - +
404X PRO* 1.4 62.2 - - + +
405X CYS 4.2 0.2 + - - -
406X ARG* 4.4 11.2 - - + -
409X CYS* 3.3 32.9 - - + -
410X TYR* 5.2 2.9 + - - -
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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
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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