Contacts of the helix formed by residues 386 - 404 (chain B) in PDB entry 5ULM
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 ALA 386 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL* 1.3 82.5 - - - +
387B SER* 1.3 67.1 + - - +
388B ASP* 3.3 7.4 - - + +
389B MET* 3.0 26.1 + - + +
390B TYR* 3.3 9.4 + - - -
426B GLU* 4.9 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL 3.8 1.4 + - - -
386B ALA* 1.3 70.8 - - - +
388B ASP* 1.3 54.0 + - - +
390B TYR* 3.0 13.8 + - - +
391B CYS* 2.8 49.1 + - - -
422B ALA* 4.4 8.0 - - - +
426B GLU* 4.2 37.1 + - - +
428B THR* 3.8 19.1 + - - +
430B GLN* 5.0 2.6 + - - -
431B SER* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B PHE* 3.5 29.4 - - + -
386B ALA* 3.3 6.5 + - + +
387B SER* 1.3 76.6 - - - +
389B MET* 1.3 59.4 + - + +
391B CYS* 3.8 6.9 - - - +
392B LEU* 2.9 23.4 + - - +
430B GLN* 4.2 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B HIS* 4.3 14.4 - - + +
350B HIS* 4.1 26.5 - - + +
353B PHE* 4.0 22.0 - - + -
375B MET* 3.8 25.9 - - + +
378B MET* 3.9 15.5 - - - +
379B VAL* 4.0 18.2 - - + -
385B VAL 4.6 7.0 - - - +
386B ALA* 3.0 24.1 + - + +
388B ASP* 1.3 75.2 - - + +
390B TYR* 1.3 68.7 + - + +
391B CYS 3.4 0.3 + - - -
392B LEU 3.4 7.3 + - - -
393B VAL* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B VAL* 3.3 26.3 - - + +
385B VAL* 3.2 34.3 + - - -
386B ALA 3.3 11.1 + - - -
387B SER* 3.0 7.2 + - - +
389B MET* 1.3 79.5 - - - +
391B CYS* 1.3 58.5 + - - +
393B VAL* 3.4 4.3 + - - +
394B GLY* 3.1 23.2 + - - -
418B TRP* 3.7 37.7 - + + +
421B LYS* 3.7 39.5 + - + -
422B ALA* 3.6 29.2 - - + -
425B SER* 4.1 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B SER* 2.8 33.4 + - - +
388B ASP* 3.9 5.4 - - - +
390B TYR* 1.3 76.0 - - - +
392B LEU* 1.3 58.6 + - - +
394B GLY 3.4 0.3 + - - -
395B ARG* 2.8 29.3 + - - +
419B PHE* 3.5 22.8 - - + -
422B ALA* 4.2 3.1 - - - -
430B GLN* 3.6 34.8 - - - +
431B SER* 3.8 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B PHE* 3.6 47.1 - - + +
356B ALA* 4.0 3.1 - - + -
357B PHE* 3.8 40.8 - - + +
360B ASN* 5.2 3.1 - - - +
375B MET* 3.8 18.8 - - + -
388B ASP 2.9 18.0 + - - +
389B MET 3.9 3.8 - - - +
390B TYR 3.4 0.4 - - - -
391B CYS* 1.3 73.9 - - - +
393B VAL* 1.3 66.2 + - - +
395B ARG* 3.1 15.2 + - + -
396B ILE* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.0 9.2 - - + -
375B MET* 3.6 35.7 - - + -
376B ILE* 4.1 7.0 - - + -
379B VAL* 4.5 2.0 - - + -
389B MET 3.4 13.1 + - - +
390B TYR 3.6 6.7 - - - +
392B LEU* 1.3 75.7 - - - +
394B GLY* 1.3 62.3 + - - +
396B ILE* 3.2 19.8 + - - +
397B TYR* 3.3 27.6 + - + -
418B TRP* 3.5 45.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B TYR 3.1 12.9 + - - -
391B CYS 3.7 4.0 - - - -
392B LEU 3.2 0.2 - - - -
393B VAL* 1.3 75.4 - - - +
395B ARG* 1.3 56.8 + - - +
397B TYR* 3.4 3.9 + - - +
398B LYS* 2.8 28.1 + - - +
415B GLY* 4.0 6.1 - - - -
418B TRP* 3.9 18.3 - - - +
419B PHE* 3.5 24.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PHE* 3.3 37.5 - - - -
360B ASN* 4.4 5.8 - - - +
361B ARG* 3.6 26.6 - - - +
391B CYS 2.8 20.9 + - - +
392B LEU* 3.1 15.7 + - + +
394B GLY* 1.3 71.3 - - - +
396B ILE* 1.3 59.4 + - - +
398B LYS* 3.8 23.3 - - + +
399B ASP* 2.8 37.4 + - - +
419B PHE* 3.5 5.1 - - + -
509B TRP* 4.5 3.6 + - - -
512B LYS* 3.9 12.1 - - - +
513B SER* 3.6 27.5 + - - +
516B GLU* 3.1 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ALA 5.0 0.4 - - - +
360B ASN* 3.6 35.7 - - + +
368B ARG* 4.1 18.2 - - + +
371B ALA* 3.9 25.8 - - + +
372B LEU* 3.7 33.9 - - + -
375B MET* 4.5 5.4 - - + -
392B LEU* 2.9 34.5 + - + +
393B VAL* 3.2 15.0 + - - +
395B ARG* 1.3 76.0 - - - +
397B TYR* 1.3 59.2 + - - +
399B ASP* 3.8 1.7 - - - +
400B MET* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.8 22.5 - - + +
376B ILE* 3.7 18.5 - - - +
393B VAL* 3.3 37.9 + - + -
394B GLY 3.7 1.3 - - - +
396B ILE* 1.3 73.8 - - - +
398B LYS* 1.3 58.3 + - - +
400B MET* 3.1 20.8 + - + +
401B PHE* 2.9 28.9 + - - +
411B SER* 3.3 28.7 - - - +
414B HIS* 3.8 42.1 - + + +
415B GLY* 3.5 10.8 - - - +
418B TRP* 3.8 16.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLY 2.8 22.3 + - - +
395B ARG* 3.6 17.8 - - + +
397B TYR* 1.3 70.2 - - - +
399B ASP* 1.3 64.0 + - - +
401B PHE* 3.2 9.9 + - - +
402B LEU* 2.9 27.9 + - + +
412B ARG* 6.0 0.2 - - - +
415B GLY* 4.6 1.8 - - - -
419B PHE* 4.4 8.5 - - + -
434B ASN* 3.5 22.7 + - - +
437B VAL* 6.2 1.3 - - + -
438B LEU* 4.6 18.6 - - + -
513B SER* 3.3 22.4 + - - +
516B GLU* 2.8 43.0 + - - -
517B THR* 3.5 10.5 + - - +
520B ILE* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ASN* 2.8 18.6 + - - +
361B ARG* 2.7 28.1 + - - -
368B ARG* 3.7 20.9 - - - +
395B ARG* 2.8 30.0 + - - +
396B ILE 3.8 2.9 - - - +
398B LYS* 1.3 75.8 - - - +
400B MET* 1.3 57.2 + - - +
402B LEU* 4.4 6.4 - - - +
403B ASP* 2.8 41.1 + - - +
516B GLU* 2.9 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ARG* 4.0 27.1 - - + +
372B LEU* 4.3 11.0 - - + -
396B ILE* 2.9 30.0 + - - +
397B TYR* 3.4 24.0 - - + +
399B ASP* 1.3 74.7 - - - +
401B PHE* 1.3 57.8 + - - +
403B ASP* 3.9 1.2 - - - +
404B SER* 3.1 30.5 + - - -
408B ASP* 4.1 9.3 - - - +
411B SER* 3.4 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TYR 2.9 12.2 + - - +
398B LYS* 3.3 9.9 - - - +
400B MET* 1.3 73.6 - - - +
402B LEU* 1.3 64.5 + - - +
404B SER* 2.7 20.9 + - - -
406B PHE* 3.2 60.9 + + - -
408B ASP 3.2 32.1 - - - +
409B THR* 4.6 4.0 - - + -
411B SER* 4.2 1.0 - - - -
412B ARG* 3.6 30.5 - - + +
438B LEU* 4.0 16.2 - - + -
441B ALA* 3.8 32.3 - - + -
520B ILE* 4.1 10.8 - - + -
524B PHE* 3.9 8.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 2.9 19.1 + - - +
399B ASP* 4.0 5.8 - - - +
401B PHE* 1.3 72.3 - - - +
403B ASP* 1.3 66.9 + - - +
405B ASN* 3.0 21.1 + - - -
406B PHE* 3.6 35.4 + - + -
516B GLU* 3.9 44.0 - - + +
519B LEU* 4.9 18.4 - - + -
520B ILE* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ARG* 5.0 3.8 + - - -
363B ASN* 4.1 8.3 + - - +
368B ARG* 2.8 38.8 + - - +
399B ASP* 2.8 24.1 + - - +
400B MET* 3.9 2.2 - - - +
402B LEU* 1.3 84.6 - - - +
404B SER* 1.3 55.3 + - - +
405B ASN* 3.2 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B MET 3.1 13.4 + - - -
401B PHE 2.7 19.8 + - - -
402B LEU 3.2 0.2 - - - -
403B ASP* 1.3 74.1 - - - +
405B ASN* 1.3 64.6 + - - +
407B THR* 2.7 32.8 + - - +
408B ASP* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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