Contacts of the strand formed by residues 273 - 278 (chain B) in PDB entry 6DDE
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 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASN* 3.9 20.6 + - + +
231B ALA* 4.5 0.9 - - + -
244B GLY* 3.4 20.2 - - - +
245B SER* 3.3 30.2 + - - +
246B ASP* 4.0 7.6 - - - +
248B ALA* 5.4 1.2 - - - +
249B THR 6.0 0.2 - - - +
250B CYS* 3.6 20.0 - - - -
272B GLY* 1.3 73.4 - - - -
274B THR* 1.3 72.3 + - - +
275B SER 3.4 7.6 - - - +
276B VAL* 3.7 17.7 - - + -
287B ALA 3.8 0.4 - - - -
288B GLY 3.4 34.3 - - - +
289B TYR* 3.6 19.0 - - + +
290B ASP* 3.5 4.5 - - - +
314B ARG* 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASN* 3.4 24.9 - - + +
273B ILE* 1.3 77.9 + - - +
275B SER* 1.3 62.4 + - - +
288B GLY 2.9 8.8 + - - -
290B ASP* 2.3 32.4 + - - -
314B ARG* 3.4 12.8 + - - +
315B VAL 3.3 14.0 + - - +
316B SER* 3.3 32.1 - - - +
332B TRP* 5.9 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 3.7 4.7 - - - -
273B ILE* 3.4 1.5 - - - +
274B THR* 1.3 83.1 - - - +
276B VAL* 1.3 67.6 + - - +
286B LEU 3.5 1.6 - - - +
288B GLY* 2.6 36.9 + - - -
315B VAL* 5.7 1.8 - - - -
316B SER 3.7 11.4 - - - -
317B CYS* 3.7 6.4 - - - -
318B LEU* 3.1 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 3.4 20.7 - - + +
232B ILE 4.5 3.3 - - - +
233B CYS* 3.3 32.7 - - - +
242B ALA* 3.8 16.4 - - + +
244B GLY* 4.0 7.0 - - - +
250B CYS* 3.8 19.3 - - + -
273B ILE* 3.7 20.4 - - + -
275B SER* 1.3 83.0 + - - +
277B SER* 1.3 65.3 + - - +
285B LEU* 3.7 22.9 - - + -
286B LEU 3.4 4.3 - - - -
287B ALA* 4.2 3.6 - - - -
318B LEU 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B CYS* 3.6 9.6 - - - -
276B VAL* 1.3 79.6 - - - +
278B PHE* 1.3 61.9 + - - +
285B LEU* 3.7 0.6 - - - -
286B LEU* 2.8 34.1 + - - +
318B LEU* 3.1 34.8 + - - +
319B GLY* 5.1 0.2 - - - -
320B VAL* 3.3 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B CYS* 3.6 19.6 - - - +
234B PHE 3.5 17.7 - - - +
235B PHE* 3.5 40.6 - + + -
236B PRO* 4.0 11.0 - - + -
242B ALA* 3.6 32.5 - - + -
252B LEU* 3.8 13.0 - - + -
277B SER* 1.3 75.0 - - - +
279B SER* 1.3 69.8 + - - +
282B GLY* 3.9 13.0 - - - -
284B LEU* 3.8 12.3 - - - -
285B LEU* 3.6 18.8 - - + -
286B LEU* 5.5 0.9 - - - -
299B ALA* 4.1 9.2 - - + -
320B VAL* 3.2 27.9 - - - +
----------------------------------------------------------
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