Contacts of the strand formed by residues 272 - 276 (chain B) in PDB entry 2AG1
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 272 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.2 48.2 - - + +
201B LEU* 3.7 26.9 - - + +
204B ALA* 3.9 13.7 - - + -
206B ARG 3.8 1.3 + - - +
207B PRO* 3.6 8.0 - - + +
208B VAL* 3.1 26.2 + - - +
270B PRO* 3.4 2.2 - - - +
271B ASP* 1.3 82.6 - - - +
273B VAL* 1.3 79.0 + - - +
274B LEU* 4.2 3.8 - - + +
296B ALA* 4.2 0.7 - - - -
297B GLN* 3.1 27.4 - - + +
299B ILE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.3 12.1 - - + +
210B VAL* 4.0 20.9 - - + -
260B LEU* 6.3 0.7 - - + -
270B PRO* 4.7 4.0 - - + -
272B LEU* 1.3 80.6 - - - +
274B LEU* 1.3 60.5 - - - +
275B MSE 3.5 25.1 - - + -
291B LEU 5.7 0.2 - - - +
292B ILE* 3.7 31.4 - - + -
293B PRO* 4.4 7.4 - - + -
296B ALA* 4.0 17.9 - - + -
297B GLN 2.8 8.1 + - - -
298B VAL* 3.4 8.9 - - + +
299B ILE 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 5.6 3.8 - - + -
201B LEU* 5.0 10.1 - - + -
208B VAL 2.8 13.9 + - - +
209B ILE* 3.2 24.9 - - + +
210B VAL 2.7 30.2 + - - -
227B PHE* 4.1 23.8 - - + -
272B LEU* 4.2 9.3 - - + +
273B VAL* 1.3 69.8 - - - +
275B MSE 1.3 56.9 + - - +
276B LEU* 3.8 24.9 - - + -
299B ILE* 3.5 38.4 - - + +
301B VAL* 4.6 5.2 - - + -
329B LEU* 4.3 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B VAL* 3.5 10.8 - - + +
273B VAL* 3.5 19.7 - - + -
274B LEU* 1.3 70.3 - - - +
276B LEU* 1.3 60.6 + - - +
277B GLY 3.7 0.9 - - - -
278B ALA* 3.0 40.8 - - + +
279B ARG 3.9 15.3 - - - +
280B PHE* 3.5 44.4 - - + +
284B THR* 4.2 13.5 - - + -
292B ILE* 4.3 12.1 - - + -
298B VAL* 3.7 14.4 - - + -
299B ILE 2.9 13.5 + - - +
300B GLN* 3.7 9.8 - - + +
301B VAL* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 3.8 14.8 - - + -
210B VAL 2.9 9.9 + - - -
211B LEU* 3.6 27.2 - - + -
212B GLY 3.1 21.1 + - - +
215B ALA* 4.4 0.7 + - - +
224B LEU* 5.5 3.1 - - + -
227B PHE* 5.4 3.6 - - + -
274B LEU* 3.8 33.9 - - + -
275B MSE 1.3 75.4 - - - +
277B GLY* 1.3 55.4 + - - +
278B ALA 3.2 2.7 - - - -
301B VAL* 3.9 20.0 - - + -
322B VAL* 3.7 24.7 - - + +
325B THR* 4.3 16.2 - - + -
326B ILE* 3.9 20.9 - - + -
329B LEU* 4.5 6.3 - - + -
----------------------------------------------------------
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