Contacts of the strand formed by residues 271 - 278 (chain B) in PDB entry 4Y2H
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 271 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.5 28.9 - - + -
191B LEU* 3.7 29.6 - - + -
254B ALA* 4.0 12.1 - - + -
256B LEU* 4.5 18.2 - - + -
263B LEU* 6.2 0.2 - - + -
266B GLU* 4.5 4.3 - - + +
267B LEU* 3.9 26.5 - - + +
270B GLY* 1.3 76.8 - - - -
272B GLY* 1.3 60.3 + - - +
342B THR* 3.5 2.6 - - - -
343B LEU* 2.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PHE* 3.3 26.8 - - - +
254B ALA* 4.4 4.0 - - - +
270B GLY 4.2 0.6 + - - -
271B VAL* 1.3 79.1 - - - +
273B GLY* 1.3 58.5 + - - -
341B ILE 3.1 13.0 - - - -
342B THR* 4.3 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PHE* 3.6 15.1 + - - -
272B GLY* 1.3 74.1 - - - -
274B ARG* 1.3 68.6 + - - -
275B PHE 4.2 0.2 + - - -
340B GLU* 3.6 5.2 - - - +
341B ILE* 3.0 36.5 + - - +
342B THR* 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG 4.7 4.7 - - - +
253B PHE* 4.5 7.0 - - - +
273B GLY* 1.3 79.1 - - - -
275B PHE* 1.3 64.6 + - - +
339B GLY 3.3 12.4 + - - +
340B GLU* 3.1 50.6 + - + +
358B ARG* 5.7 2.0 - - - +
366B GLU* 5.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 3.8 41.1 - - + -
195B PRO* 6.1 0.4 - - + -
251B GLN* 4.1 16.2 - - + -
252B ARG 5.4 0.2 - - - +
253B PHE* 5.0 3.4 - - + -
274B ARG* 1.3 79.7 - - - +
276B ARG* 1.3 66.2 - - - +
277B CYS* 5.1 5.4 - - - -
288B PHE* 3.8 34.8 - + - -
337B VAL* 4.2 5.8 - - + -
338B SER* 3.2 23.3 - - - -
339B GLY* 3.0 56.7 + - - +
340B GLU* 3.6 12.8 - - - -
341B ILE* 4.3 9.6 - - + -
357B LEU* 4.3 4.5 - - + -
358B ARG 4.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B GLN* 3.3 19.3 + - - +
275B PHE* 1.3 76.3 - - - +
277B CYS* 1.3 70.2 + - - +
336B ASP* 2.8 40.4 + - - +
337B VAL 3.3 10.5 - - - +
338B SER* 3.9 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE 6.0 0.2 - - - -
195B PRO* 3.7 21.1 - - - -
248B ALA* 3.7 20.9 - - + -
249B ARG* 4.0 6.7 - - + +
251B GLN* 3.5 25.4 - - + +
275B PHE* 5.1 5.2 - - - -
276B ARG* 1.3 82.3 - - - +
278B SER* 1.3 60.6 + - - +
336B ASP* 3.8 7.6 - - - +
337B VAL* 2.9 47.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA* 3.3 15.0 - - - +
249B ARG 4.6 1.8 + - - +
277B CYS* 1.3 77.8 + - - +
279B CYS* 1.3 63.8 + - - +
280B TYR* 3.7 5.5 + - - -
334B ASP* 3.4 35.3 + - - +
335B THR 3.4 3.5 + - - -
336B ASP* 4.8 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