Contacts of the strand formed by residues 283 - 289 (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 LEU 283 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ASN* 3.8 11.0 - - + +
252D HIS 4.5 3.8 - - - +
253D ALA* 3.5 30.7 - - + +
268D LEU* 3.8 16.1 - - + +
271D ALA* 3.0 24.3 + - + -
272D ALA* 3.5 12.0 - - - +
281D MET 3.3 1.9 + - - +
282D ALA* 1.3 71.6 - - - +
284D SER* 1.3 55.2 + - - +
285D VAL 3.2 27.8 - - - +
388D LEU* 3.4 18.8 - - + +
412D THR* 5.9 0.7 - - - -
413D CYS* 4.1 4.9 - - + -
439D PRO* 3.3 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ALA 5.2 0.5 + - - -
250D LYS* 3.5 35.5 + - - +
251D ASN 3.1 14.8 + - - -
272D ALA* 5.4 0.4 - - - +
282D ALA* 3.4 10.6 + - - -
283D LEU* 1.3 74.1 - - - +
285D VAL* 1.3 62.9 + - - +
383D ILE* 6.3 0.9 - - - -
384D PHE 6.3 0.7 - - - -
387D VAL 3.9 15.1 - - - +
388D LEU* 3.6 6.5 - - - -
389D GLN* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D LYS* 3.5 35.0 - - + -
251D ASN 3.2 2.8 + - - -
252D HIS* 3.2 31.6 - - + +
253D ALA 2.9 23.7 + - - -
283D LEU* 3.2 7.9 - - - +
284D SER* 1.3 81.1 - - - +
286D ALA* 1.3 62.6 + - - +
287D VAL* 3.9 7.2 - - + -
379D TYR* 4.0 14.6 - - + -
388D LEU* 4.4 0.9 - - - -
389D GLN* 3.3 12.6 - - + +
391D VAL* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ALA* 3.5 7.2 - - + +
255D VAL* 5.0 2.9 - - + -
268D LEU* 4.2 21.3 - - + -
285D VAL* 1.3 73.9 - - - +
287D VAL* 1.3 61.6 + - - +
288D ALA 3.8 0.4 - - - -
297D LEU* 3.9 23.6 - - + -
388D LEU* 4.3 12.3 - - + +
389D GLN 2.9 12.0 + - - +
390D VAL* 3.3 8.5 - - + +
391D VAL 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D HIS* 3.8 33.4 - - + -
253D ALA 2.7 14.4 + - - +
254D ILE* 3.3 6.3 - - + +
255D VAL* 2.9 26.4 + - - -
285D VAL* 4.0 7.4 - - + -
286D ALA* 1.3 72.1 - - - +
288D ALA* 1.3 60.1 + - - +
289D VAL 3.9 0.5 + - - -
391D VAL* 3.4 7.6 - - + +
393D VAL* 3.6 24.7 - - + -
399D ALA* 3.4 37.5 - - + +
402D LEU* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D VAL* 3.9 7.9 - - + +
286D ALA 3.6 0.8 + - - -
287D VAL* 1.3 71.9 - - - +
289D VAL* 1.3 62.3 + - - +
290D GLY 3.5 2.8 - - - +
293D ALA* 4.2 7.0 - - + -
294D GLY* 3.7 33.4 - - - +
297D LEU* 4.3 17.7 - - + -
390D VAL* 4.7 2.9 - - + -
391D VAL 2.9 12.0 + - - +
392D ARG* 3.5 4.9 - - + -
393D VAL* 3.1 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ILE* 4.0 10.1 - - + -
255D VAL 3.2 22.2 + - - +
256D MET* 3.5 31.0 - - + -
257D PRO* 3.9 21.0 - - + +
287D VAL 3.9 0.4 + - - -
288D ALA* 1.3 69.4 - - - +
290D GLY* 1.3 61.7 - - - +
292D ALA* 4.9 0.7 - - - +
293D ALA* 3.9 12.8 + - - +
393D VAL* 3.3 14.4 - - + +
394D ALA 3.4 21.3 - - - +
395D THR* 3.6 20.0 - - - +
396D MET* 3.7 4.5 - - - +
----------------------------------------------------------
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