Contacts of the helix formed by residues 366 - 378 (chain D) in PDB entry 2BKU
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 ILE 366 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D ILE* 5.0 4.7 - - + -
326D VAL* 3.8 25.8 - - + -
355D LEU* 4.3 7.6 - - + -
358D PHE* 3.8 32.8 - - + +
359D ALA* 3.9 30.3 - - + +
362D CYS* 4.3 4.1 + - + +
363D GLY 3.0 22.7 + - - +
365D HIS* 1.3 77.7 - - - +
367D LEU* 1.3 65.5 + - - +
368D GLU 3.6 0.2 - - - -
369D PRO* 3.4 9.9 - - + +
370D VAL* 3.3 26.7 - - + +
396D ILE* 4.0 14.8 - - + -
400D PRO* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D ASN* 2.9 34.3 + - + +
366D ILE* 1.3 74.5 - - - +
368D GLU* 1.3 66.8 + - - +
370D VAL* 3.4 1.4 + - - +
371D LEU* 2.9 40.1 + - + +
396D ILE* 4.0 20.6 - - + +
397D MET* 6.0 1.6 - - + -
400D PRO* 3.9 22.0 - - + -
404D GLN* 3.5 42.0 - - + +
405D ARG* 5.5 2.7 - - + +
408D TYR* 3.9 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LYS* 5.6 7.0 + - - -
364D ASN 4.6 0.6 + - - -
365D HIS 4.3 2.6 + - - +
367D LEU* 1.3 77.7 - - - +
369D PRO* 1.3 72.0 - - + +
371D LEU* 3.9 4.9 - - - +
372D GLU* 3.0 56.0 + - + +
408D TYR* 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D ILE* 3.7 28.5 - - + +
323D LYS* 5.8 7.6 - - + -
326D VAL* 4.2 18.2 - - + -
327D PRO* 5.3 6.7 - - + -
330D LEU* 3.8 6.6 - - + +
365D HIS 3.6 9.6 - - - +
366D ILE* 3.4 14.1 - - - +
368D GLU* 1.3 98.0 - - + +
370D VAL* 1.3 59.9 + - - +
372D GLU* 3.9 12.1 - - - +
373D PHE* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D VAL* 4.4 5.4 - - + -
330D LEU* 4.4 12.6 - - + -
355D LEU* 4.3 15.3 - - + -
366D ILE* 3.3 28.8 + - + +
367D LEU 3.4 2.1 + - - +
368D GLU 3.2 0.8 - - - -
369D PRO* 1.3 73.8 - - - +
371D LEU* 1.3 62.5 + - + +
373D PHE* 3.3 3.3 + - - +
374D VAL* 2.8 45.0 + - + +
392D ALA* 3.9 23.6 - - + +
396D ILE* 3.8 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D LEU* 2.9 32.1 + - + +
368D GLU* 4.0 3.8 - - - +
370D VAL* 1.3 73.0 - - - +
372D GLU* 1.3 61.1 + - + +
374D VAL* 3.8 6.1 - - + +
375D GLU* 2.9 33.0 + - - +
393D PHE* 3.6 36.8 - - + -
396D ILE* 4.5 8.7 - - + -
408D TYR* 3.3 55.4 - - + +
412D ALA* 5.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D GLU* 3.0 52.3 + - + +
369D PRO* 3.9 9.0 - - - +
371D LEU* 1.3 75.3 - - + +
373D PHE* 1.3 64.8 + - - +
375D GLU* 4.1 9.7 - - - +
376D GLN* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D PRO* 5.5 1.1 - - + -
330D LEU* 3.4 52.3 - - + -
331D ASN* 4.4 3.4 - - - -
333D LEU* 4.8 0.4 - - + -
334D THR* 4.6 6.1 - - + -
369D PRO 3.3 13.9 + - - +
370D VAL 3.5 6.5 - - - +
372D GLU* 1.3 80.0 - - - +
374D VAL* 1.3 65.7 + - - +
376D GLN* 3.2 3.0 + - - -
377D ASN* 2.7 59.2 + - - +
388D ALA* 3.7 39.3 - - + -
389D ALA* 4.0 3.4 - - - -
392D ALA* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D VAL* 2.8 32.9 + - + +
371D LEU* 3.8 9.0 - - + +
373D PHE* 1.3 72.9 - - - +
375D GLU* 1.3 57.8 + - - +
377D ASN 3.1 0.7 + - - -
378D ILE* 2.8 55.9 + - + +
389D ALA* 3.2 33.2 - - - +
392D ALA* 3.9 13.2 - - + -
393D PHE* 4.0 28.0 - - + +
412D ALA* 5.8 5.2 - - + -
416D ILE* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D LEU 2.9 19.1 + - - +
372D GLU* 4.1 9.0 - - - +
374D VAL* 1.3 79.2 - - + +
376D GLN* 1.3 58.7 + - - +
378D ILE* 3.5 20.1 - - + +
379D THR* 5.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D GLU* 3.2 19.7 + - - +
373D PHE* 3.2 4.2 + - - +
374D VAL 3.1 0.8 - - - -
375D GLU* 1.3 78.7 - - - +
377D ASN* 1.3 66.7 + - - +
378D ILE 3.7 0.2 - - - -
379D THR* 5.2 1.8 - - - -
380D ALA* 4.5 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D PHE* 2.7 60.6 + - + +
376D GLN* 1.3 85.5 - - - +
378D ILE* 1.3 66.2 + - - +
379D THR 3.2 4.1 + - - -
380D ALA* 3.4 16.2 + - - +
385D ASN* 2.8 43.4 - - - +
386D ARG* 3.4 17.0 + - - -
389D ALA* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D VAL* 2.8 30.1 + - + +
375D GLU* 3.5 19.7 - - + +
377D ASN* 1.3 77.6 - - - +
379D THR* 1.3 76.2 + - + +
380D ALA 3.7 0.2 - - - -
386D ARG* 3.4 18.2 - - - +
389D ALA* 3.8 17.3 - - + -
390D VAL* 4.1 11.4 - - + +
415D SER* 4.4 22.2 - - - +
416D ILE* 4.8 10.5 - - + -
419D LEU* 3.5 38.2 - - + +
----------------------------------------------------------
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