Contacts of the strand formed by residues 278 - 284 (chain D) in PDB entry 5E9W
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 PHE 278 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D THR* 3.7 15.0 - - + +
201D VAL 3.7 4.9 - - - -
202D LEU* 3.5 49.8 - - + -
224D VAL* 3.9 7.2 - - + -
271D PHE* 3.2 46.0 - + - -
276D MET* 3.7 26.5 - - + -
277D CYS* 1.3 73.2 - - - +
279D ASP* 1.3 64.2 + - - +
280D ILE 3.9 11.4 - - - +
281D CYS* 5.5 0.4 - - + -
303D ASN 5.2 2.9 - - - -
304D ALA 5.6 2.5 - - - -
307D ARG* 3.0 26.3 + - + +
308D LEU* 3.3 13.9 - - + +
309D SER* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 4.0 5.1 - - + +
195D LYS* 3.0 44.1 + - - +
198D ASP 3.3 12.9 - - - +
199D ILE* 3.3 15.7 - - + -
200D THR* 2.7 35.9 + - - +
278D PHE* 1.3 76.4 - - - +
280D ILE* 1.3 64.8 + - - +
308D LEU* 4.0 2.5 - - - -
309D SER* 4.2 8.7 + - - -
312D GLY* 3.2 7.3 - - - -
313D TYR 3.0 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE 5.3 0.9 - - - +
187D PHE* 3.7 34.3 - - + +
188D LEU* 4.0 24.2 - - + +
191D VAL* 3.7 13.9 - - + -
199D ILE* 5.1 0.9 - - + -
200D THR 3.4 2.6 + - - -
201D VAL* 3.3 20.5 - - + +
202D LEU 2.9 24.1 + - - -
215D TRP* 4.3 7.4 - - + -
278D PHE* 3.9 2.7 - - - +
279D ASP* 1.3 86.7 - - + +
281D CYS* 1.3 73.6 + - - +
282D SER 4.1 2.2 - - - +
308D LEU* 4.0 3.8 - - - -
313D TYR* 3.3 16.6 - - + +
315D ILE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LEU* 3.3 28.3 - - + +
204D LEU* 4.1 14.1 - - - -
278D PHE* 5.6 0.9 - - + -
280D ILE* 1.3 76.1 - - - +
282D SER* 1.3 61.4 + - - +
283D CYS* 4.9 0.2 - - - -
304D ALA* 3.4 49.6 - - + +
308D LEU* 3.7 4.8 - - + +
313D TYR 2.8 11.9 + - - +
314D PHE* 3.5 8.5 - - + -
315D ILE* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 4.2 5.0 - - - +
202D LEU 2.9 11.0 + - - -
203D ASP* 3.4 10.7 + - - +
204D LEU 3.0 24.9 + - - -
211D ASP* 4.8 1.0 + - - -
215D TRP* 3.5 35.8 - - - -
280D ILE* 4.0 1.7 - - - -
281D CYS* 1.3 72.1 - - - +
283D CYS* 1.3 59.9 + - - +
284D GLN* 3.0 30.2 + - - +
315D ILE* 3.6 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 3.8 24.5 - - + +
281D CYS* 4.9 1.6 - - - -
282D SER* 1.3 73.2 + - - +
284D GLN* 1.3 62.1 + - - +
285D PHE 3.7 0.9 + - - -
286D VAL* 3.5 29.8 + - - -
287D CYS* 3.5 25.8 - - - -
300D MET* 4.5 3.8 - - - -
304D ALA* 6.0 0.2 - - - -
314D PHE* 3.9 18.8 - - + -
315D ILE 2.8 13.8 + - - +
316D GLY* 3.0 19.6 - - - -
317D THR 3.3 5.5 + - - +
470D PHE* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LYS* 3.6 29.6 - - + +
183D LEU* 3.9 15.3 - - - +
184D ILE* 4.7 4.9 - - + +
203D ASP* 5.3 1.9 + - - +
204D LEU 4.4 0.6 + - - -
211D ASP* 3.7 9.0 - - - +
282D SER* 3.0 28.2 + - - +
283D CYS* 1.3 71.5 - - - +
285D PHE* 1.3 72.7 + - + +
286D VAL* 3.2 6.9 - - - +
315D ILE* 3.9 9.7 + - - +
316D GLY* 3.8 15.6 - - - -
317D THR* 2.8 37.0 + - - +
501D SAH 2.9 45.7 + - - +
----------------------------------------------------------
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