Contacts of the strand formed by residues 387 - 393 (chain D) in PDB entry 4ZZ7
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 VAL 387 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ALA* 4.5 6.6 + - - +
273D PHE* 4.0 4.4 - - - -
284D SER* 3.9 20.3 - - - +
332D VAL* 4.4 4.7 - - + -
336D ILE* 4.2 18.4 - - + -
367D THR* 3.5 23.8 - - + +
369D ILE* 3.6 25.6 - - + -
383D ILE* 4.1 39.5 - - + -
385D GLY 2.8 13.7 + - - +
386D PRO* 1.3 84.1 - - + +
388D LEU* 1.3 67.0 + - - +
389D GLN* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 4.8 17.0 - - + -
272D ALA* 3.8 12.8 - - + -
273D PHE* 3.9 15.9 - - + -
283D LEU* 3.4 27.6 - - + +
284D SER 3.6 10.1 - - - +
285D VAL 4.3 1.8 - - - +
286D ALA* 4.3 14.8 - - + +
297D LEU* 6.0 1.8 - - + -
301D MET* 4.1 33.2 - - + -
367D THR 3.2 6.4 + - - +
368D LEU* 3.5 14.0 - - + +
369D ILE* 3.0 24.8 + - - +
387D VAL* 1.3 75.7 - - - +
389D GLN* 1.3 70.0 + - - +
390D VAL* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 389 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D LYS* 3.3 23.7 + - - -
284D SER 3.0 12.1 + - - +
285D VAL* 3.3 9.7 - - + +
286D ALA* 2.9 25.6 + - - +
339D ALA* 5.2 1.0 - - - +
369D ILE* 3.4 21.7 - - + +
372D VAL* 3.9 28.5 - - + +
378D SER* 3.2 46.2 + - - +
379D TYR* 3.6 9.4 - - - +
383D ILE* 3.7 9.3 - - - +
387D VAL* 4.4 4.7 - - + -
388D LEU* 1.3 78.6 - - - +
390D VAL* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 3.3 13.9 - - + +
288D ALA* 4.7 5.4 - - + -
294D GLY 5.1 2.0 - - - +
297D LEU* 3.9 25.6 - - + -
298D VAL* 4.2 15.5 - - + -
301D MET* 6.5 0.2 - - + -
368D LEU* 3.4 30.7 - - + -
369D ILE 2.8 8.8 + - - +
370D ASP* 3.9 14.8 - - - +
371D HIS 3.4 6.1 + - - -
372D VAL* 3.1 25.3 + - - +
388D LEU* 5.0 3.8 - - + -
389D GLN* 1.3 76.8 - - - +
391D VAL* 1.3 71.7 + - - +
392D ARG* 4.9 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D VAL* 3.8 19.1 - - + -
286D ALA 3.0 7.3 + - - +
287D VAL* 3.4 6.1 - - + -
288D ALA* 2.9 26.3 + - - -
372D VAL* 3.3 41.5 - - + +
373D THR* 5.3 3.8 - - - -
374D PRO* 5.5 3.6 - - + -
379D TYR* 4.4 11.0 - - + -
390D VAL* 1.3 75.9 - - - +
392D ARG* 1.3 74.9 + - - +
393D VAL* 4.2 7.2 - - + -
402D LEU* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ALA 3.5 6.1 - - - +
290D GLY 5.2 0.2 - - - +
291D ASP* 3.4 41.8 + - + +
294D GLY* 3.4 31.0 + - - -
295D ASP* 3.0 27.6 + - - -
298D VAL* 3.7 4.2 - - - +
370D ASP* 2.6 43.1 + - - +
371D HIS* 3.5 31.9 + - - +
372D VAL 4.8 1.0 + - - -
390D VAL* 4.9 3.3 - - + +
391D VAL* 1.3 81.3 - - - +
393D VAL* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 3.6 30.7 - - + -
288D ALA 3.1 8.3 + - - +
289D VAL* 4.1 5.8 - - - -
290D GLY* 2.8 27.5 + - - -
391D VAL* 4.2 10.3 - - + -
392D ARG* 1.3 80.8 - - - +
394D ALA* 1.3 60.8 + - - +
395D THR 3.5 18.8 - - - +
398D ASP* 4.0 19.5 - - + +
399D ALA* 4.0 10.1 - - + +
402D LEU* 4.7 5.4 - - + -
----------------------------------------------------------
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