Contacts of the helix formed by residues 388 - 408 (chain C) in PDB entry 4BPU
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 LEU 388 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 4.5 10.5 - - + +
20C LEU* 3.9 28.9 - - + +
22C PRO* 4.9 5.2 - - + -
321C PHE* 4.5 7.6 - - + -
330C ILE* 4.0 32.8 - - + -
332C VAL* 4.4 11.7 - - + -
348C PRO* 4.8 5.2 - - + -
353C ILE* 4.4 23.8 - - + +
386C THR* 3.1 14.3 - - - +
387C SER* 1.3 79.7 - - - +
389C ALA* 1.3 62.1 - - - +
390C PRO* 3.5 0.7 - - - -
391C TYR* 3.3 18.2 + - + +
392C VAL* 3.3 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C THR* 3.5 20.4 + - - +
388C LEU* 1.3 75.2 - - - +
390C PRO* 1.3 69.3 - - + +
392C VAL* 3.0 11.4 + - - +
393C LYS* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C THR 4.4 1.6 - - - +
387C SER* 3.5 20.6 - - - +
388C LEU 3.6 0.2 - - - -
389C ALA* 1.3 96.5 - - + +
391C TYR* 1.3 73.5 + - + +
393C LYS* 3.4 12.9 - - + +
394C VAL* 3.3 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PHE* 4.8 2.7 - - + -
332C VAL* 4.0 26.9 - - + -
333C PRO* 3.8 40.4 - - + +
342C PHE* 5.1 9.9 - + - -
346C THR* 3.9 13.3 + - - -
347C VAL* 4.2 4.1 - - - +
348C PRO* 3.3 38.9 - - + +
387C SER 3.5 17.7 - - - -
388C LEU* 3.5 12.1 - - + +
389C ALA 3.0 0.8 - - - -
390C PRO* 1.3 82.9 - - + +
392C VAL* 1.3 61.2 + - - +
393C LYS 3.1 1.3 - - - -
394C VAL* 3.2 11.4 + - + +
395C PHE* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PRO* 4.5 13.9 - - + -
25C GLN* 3.3 37.9 - - + +
321C PHE* 4.0 18.6 - - + -
388C LEU* 3.3 27.1 - - + +
389C ALA* 3.0 9.5 + - - +
391C TYR* 1.3 73.8 - - - +
393C LYS* 1.3 55.7 + - - +
395C PHE* 3.2 8.9 + - + +
396C GLU* 2.7 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ALA 2.8 12.2 + - - +
390C PRO* 3.4 16.6 - - + +
391C TYR 3.1 0.2 - - - -
392C VAL* 1.3 75.2 - - - +
394C VAL* 1.3 60.2 + - + +
396C GLU* 3.0 19.8 + - + +
397C HIS* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 5.4 3.8 - - + -
333C PRO* 4.3 13.9 - - + +
334C ILE 4.2 9.4 - - - +
335C ASP* 4.1 42.4 - - + +
390C PRO 3.3 15.7 + - - +
391C TYR* 3.2 12.7 + - + +
393C LYS* 1.3 75.5 - - + +
395C PHE* 1.3 58.1 + - - +
397C HIS* 3.2 9.1 + - + +
398C PHE* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PRO* 5.1 2.0 - - + -
25C GLN* 3.5 40.2 - - + -
26C TYR* 4.1 5.6 - + - -
29C TRP* 3.9 34.1 - + + -
156C LEU* 3.7 25.8 - - + -
320C PRO* 5.5 1.3 - - + -
321C PHE* 3.3 36.8 - + + -
333C PRO* 4.1 5.6 - - + +
391C TYR 2.9 13.0 + - - +
392C VAL* 3.4 12.1 - - + +
394C VAL* 1.3 78.6 - - - +
396C GLU* 1.3 56.6 + - - +
398C PHE* 3.2 32.6 - + - +
399C LEU* 2.8 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN* 3.0 37.8 + - + +
28C ARG* 4.2 14.2 + - - +
392C VAL* 2.7 23.4 + - - +
393C LYS* 3.0 26.0 + - + +
395C PHE* 1.3 72.2 - - - +
397C HIS* 1.3 59.8 + - - +
399C LEU* 3.1 9.7 + - - +
400C GLU* 2.8 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLN* 6.5 1.6 - - + -
393C LYS* 2.8 13.1 + - + +
394C VAL* 3.7 11.0 + - - +
396C GLU* 1.3 72.9 - - - +
398C PHE* 1.3 66.3 + - - +
400C GLU* 3.2 19.6 + - + +
401C ASN* 3.0 52.5 + - - -
404C LYS* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TRP* 3.8 21.5 - + - -
154C HIS* 4.2 26.5 + - + -
155C ARG 4.3 10.8 - - - +
156C LEU* 3.8 33.0 - - + -
170C CYS* 3.8 21.5 - - - -
394C VAL* 2.9 14.7 + - + +
395C PHE* 3.2 36.6 - + - +
397C HIS* 1.3 79.6 + - - +
399C LEU* 1.3 66.3 + - + +
401C ASN* 3.7 4.8 + - - +
402C LEU* 3.4 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN* 3.4 43.7 - - + +
28C ARG* 3.8 31.4 - - + +
29C TRP* 3.5 37.0 - - + +
395C PHE* 2.8 21.4 + - + +
396C GLU* 3.1 8.3 + - - +
398C PHE* 1.3 89.2 - - + +
400C GLU* 1.3 59.9 + - - +
402C LEU* 3.0 11.9 + - + +
403C ASP* 2.9 32.9 + - - +
406C ARG* 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG* 4.6 11.5 + - - +
396C GLU* 2.8 28.8 + - - +
397C HIS* 3.2 22.5 + - + +
399C LEU* 1.3 73.1 - - - +
401C ASN* 1.3 63.6 + - - +
403C ASP* 3.0 12.1 + - - +
404C LYS* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LYS 5.8 1.8 - - - +
154C HIS* 3.2 20.5 - - + +
397C HIS* 3.0 49.7 + - - +
398C PHE* 4.3 4.6 - - - +
400C GLU* 1.3 76.8 - - - +
402C LEU* 1.3 56.9 + - - +
404C LYS* 3.4 24.8 + - - +
405C SER* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TRP* 4.2 6.3 - - + +
32C TYR* 4.0 19.5 - - + -
154C HIS* 3.3 37.9 + - + +
170C CYS* 4.4 12.6 - - + +
175C ARG* 5.7 0.9 - - - +
398C PHE* 3.4 43.0 + - + +
399C LEU* 3.1 20.2 - - + +
401C ASN* 1.3 81.6 - - - +
403C ASP* 1.3 57.7 + - - +
405C SER* 3.7 2.3 + - - -
406C ARG* 3.4 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG* 3.7 20.6 + - - -
33C GLY* 5.4 0.7 - - - -
399C LEU* 2.9 17.9 + - - +
400C GLU* 3.0 10.8 + - + +
402C LEU* 1.3 75.0 - - - +
404C LYS* 1.3 65.8 + - + +
406C ARG* 2.3 51.8 + - - +
407C LYS* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C HIS* 6.3 0.8 - - - -
400C GLU* 2.9 30.1 + - - +
401C ASN* 3.4 24.7 + - - +
403C ASP* 1.3 75.8 - - + +
405C SER* 1.3 63.9 + - - +
407C LYS* 3.3 8.0 + - + +
408C GLY* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LYS* 5.4 6.1 - - - +
154C HIS* 3.1 39.4 + - - -
401C ASN 2.9 7.0 + - - -
402C LEU* 4.0 2.7 - - - -
403C ASP 3.2 0.2 - - - -
404C LYS* 1.3 77.2 - - - +
406C ARG* 1.3 63.7 + - - +
407C LYS 3.5 0.5 + - - -
408C GLY 3.9 14.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG 4.9 5.3 + - - -
32C TYR* 3.6 56.4 + - - +
33C GLY* 3.9 14.8 - - - +
35C VAL* 3.9 23.8 - - + -
172C GLU* 5.6 6.1 - - + +
175C ARG* 5.1 3.5 - - - +
399C LEU 4.8 0.2 + - - -
402C LEU* 3.4 26.5 + - + +
403C ASP* 2.3 46.0 + - - +
405C SER* 1.3 78.7 - - - +
407C LYS* 1.3 67.5 + - + +
408C GLY 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASP* 2.9 31.6 + - - +
404C LYS* 4.0 6.3 - - + +
406C ARG* 1.3 80.9 - - + +
408C GLY* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LYS 3.1 12.0 + - - -
405C SER* 3.9 13.7 - - - -
406C ARG 4.6 1.0 - - - +
407C LYS* 1.3 86.2 - - - +
----------------------------------------------------------
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