Contacts of the helix formed by residues 390 - 402 (chain D) in PDB entry 3BJT
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 TYR 390 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ARG* 4.8 2.4 + - - -
21D ALA* 4.6 6.1 - - - -
23D ALA 3.2 26.8 + - - -
24D ASP 3.3 18.2 + - - -
25D THR 3.7 11.1 - - - -
26D PHE* 3.7 27.8 - + + -
29D HIS* 3.6 33.7 - + + +
388D ALA 3.5 1.2 + - - -
389D ILE* 1.3 74.7 - - - +
391D HIS* 1.3 61.4 + - - +
392D LEU* 3.0 37.1 + - + +
393D GLN* 3.2 45.0 - - + +
394D LEU* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 391 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 4.8 2.2 - - - +
44D ASN* 6.0 2.9 - - - -
386D GLU* 3.9 17.0 + - - +
387D ALA 5.4 0.2 - - - -
389D ILE* 3.3 30.2 + - + +
390D TYR* 1.3 71.7 - - - +
392D LEU* 1.3 68.3 + - - +
394D LEU* 3.9 12.3 - - + +
395D PHE* 3.1 24.4 + - - +
421D PHE* 3.8 14.6 - + + -
445D ARG* 3.5 26.1 + - + -
446D PRO 4.2 2.5 - - - -
447D ARG* 3.3 68.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C GLU* 5.6 2.2 - - - +
400C ARG* 3.4 46.4 - - + +
21D ALA 4.5 12.2 + - - +
22D MET* 4.3 12.6 - - - +
23D ALA 3.1 29.8 - - - +
24D ASP* 5.1 0.9 - - - -
390D TYR* 3.0 20.1 - - + +
391D HIS* 1.3 83.8 - - - +
393D GLN* 1.3 66.1 + - - +
395D PHE* 4.2 0.7 - - - +
396D GLU* 3.5 21.0 + - + +
447D ARG* 5.2 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.1 23.7 + - - +
393B GLN* 3.1 26.7 + - - +
400C ARG* 5.5 4.0 - - - +
26D PHE* 4.3 6.5 - - - +
390D TYR* 3.2 37.7 + - + +
392D LEU* 1.3 80.7 - - - +
394D LEU* 1.3 64.1 + - - +
396D GLU* 4.0 7.1 - - - +
397D GLU* 3.0 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 5.5 9.0 - - + -
30B MET* 6.5 1.1 - - + -
318D ASN* 5.9 4.3 - - + +
389D ILE* 4.0 25.6 - - + -
390D TYR 3.3 15.6 + - - +
391D HIS* 4.0 9.2 - - + +
392D LEU 3.2 1.0 - - - -
393D GLN* 1.3 78.8 - - - +
395D PHE* 1.3 65.0 + - - +
397D GLU* 3.0 14.2 + - + +
398D LEU* 3.0 35.8 + - + +
445D ARG* 4.0 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ARG* 4.3 8.1 - - - -
418C GLU* 4.9 0.2 - - - -
391D HIS* 3.1 17.3 + - - +
392D LEU 4.2 0.7 - - - +
394D LEU* 1.3 77.5 - - - +
396D GLU* 1.3 63.2 + - - +
398D LEU* 3.0 5.7 + - - +
399D ARG* 2.8 58.5 + - + +
414D VAL* 4.5 8.3 - - + -
417D VAL* 3.5 24.5 - - + -
418D GLU* 3.1 39.5 - - + -
421D PHE* 3.6 31.0 - + + -
444D TYR* 3.7 36.1 - + + +
445D ARG 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LEU* 5.1 1.9 - - - +
396C GLU* 3.8 39.6 - - + +
399C ARG* 4.9 1.8 - - - +
400C ARG* 5.9 3.8 - - - +
392D LEU* 3.5 17.3 + - + +
393D GLN* 4.0 7.4 - - - +
394D LEU 3.4 0.4 - - - -
395D PHE* 1.3 79.8 - - + +
397D GLU* 1.3 64.5 + - - +
399D ARG* 3.4 19.1 + - - +
400D ARG* 3.0 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.5 23.3 - - + +
26B PHE* 2.8 34.9 + - - +
27B LEU* 3.1 30.7 + - + +
30B MET* 5.4 0.2 - - - +
393D GLN* 3.0 42.5 + - + +
394D LEU* 3.0 11.3 + - + +
396D GLU* 1.3 81.8 + - - +
398D LEU* 1.3 61.5 + - + +
399D ARG 3.2 0.2 - - - -
400D ARG* 3.5 3.2 + - - +
401D LEU* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 398 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.4 29.8 - - + -
318D ASN* 4.4 24.0 - - + +
319D ARG* 4.7 4.7 - - + -
394D LEU* 3.0 23.8 + - + +
395D PHE* 3.0 6.3 + - - +
397D GLU* 1.3 74.0 - - - +
399D ARG* 1.3 60.7 + - - +
401D LEU* 4.6 3.6 - - + +
402D ALA* 3.0 30.3 + - - +
443D ARG 3.2 24.2 - - - +
444D TYR* 3.8 23.0 - - + +
445D ARG* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LEU* 6.2 1.8 - - - +
395C PHE* 4.1 8.3 - - - -
396C GLU* 3.5 23.6 + - - +
399C ARG* 2.7 38.1 - - - +
418C GLU* 2.6 41.5 + - - +
395D PHE* 2.8 62.1 + - + +
396D GLU* 3.4 18.7 + - - +
398D LEU* 1.3 77.1 - - - +
400D ARG* 1.3 64.8 + - - +
402D ALA* 3.2 18.9 + - - +
414D VAL* 4.8 5.6 - - + -
444D TYR* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 3.6 17.5 + - - -
25B THR* 5.2 6.8 - - + +
24C ASP* 2.8 48.0 + - - +
390C TYR* 4.2 2.0 + - - -
392C LEU* 3.4 45.8 + - + +
396D GLU* 3.0 42.3 + - - +
397D GLU* 3.8 5.8 - - - +
399D ARG* 1.3 79.7 - - + +
401D LEU* 1.3 67.5 + - + +
402D ALA 3.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 5.0 2.5 - - - +
25B THR* 3.5 39.3 - - + +
27B LEU* 4.1 19.7 - - + -
28B GLU* 4.3 13.7 - - + +
319D ARG* 3.9 30.8 - - + -
397D GLU 3.0 21.0 + - - +
398D LEU* 4.0 4.7 - - + +
400D ARG* 1.3 75.6 - - + +
402D ALA* 1.3 61.1 + - - +
403D PRO* 3.5 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C LYS* 4.6 4.2 - - + +
398D LEU 3.0 21.7 + - - +
399D ARG* 3.2 13.8 + - - +
400D ARG 4.0 4.2 - - - +
401D LEU* 1.3 77.2 - - - +
403D PRO* 1.3 73.2 - - + +
404D ILE* 3.8 1.9 + - - +
443D ARG* 4.7 11.0 - - - +
444D TYR* 3.4 28.5 - - + +
----------------------------------------------------------
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