Contacts of the helix formed by residues 274 - 281 (chain B) in PDB entry 6A5T
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 274 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 5.0 8.5 - - + -
261B ILE* 3.0 41.6 + - + +
262B LYS 3.3 6.3 - - - -
263B ALA* 3.0 41.5 - - + +
273B PRO* 1.3 70.8 - - - +
275B VAL* 1.3 61.8 + - + +
276B ILE 2.9 4.5 - - - -
277B VAL* 2.4 40.8 + - + +
278B PHE* 3.0 40.0 + - + -
309B CYS* 5.3 4.1 - - - +
371B LEU* 6.3 1.6 - - + -
375B VAL* 4.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PRO* 5.3 0.2 - - - +
274B ILE* 1.3 75.7 - - + +
276B ILE* 1.3 62.2 + - - +
278B PHE* 4.2 11.7 - - + -
279B ARG* 2.9 45.4 + - - +
286B ASP* 4.2 0.2 - - - +
289B ILE* 3.7 30.1 - - + -
306B LEU* 6.4 0.9 - - + -
309B CYS* 3.8 41.0 - - + +
310B ILE* 3.9 22.4 - - + -
313B GLY* 4.9 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ILE* 3.6 13.9 - - + -
273B PRO* 3.1 37.5 - - + +
275B VAL* 1.3 77.3 - - - +
277B VAL* 1.3 60.0 + - + +
279B ARG* 3.7 4.5 - - - +
280B ALA* 2.9 28.1 + - - +
313B GLY* 4.8 18.5 - - - +
315B VAL* 6.4 0.7 - - + -
316B ILE* 5.0 16.6 - - + -
322B ALA* 4.3 13.1 - - + +
325B PHE* 3.5 40.2 - - + -
326B ILE* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ALA* 4.5 14.6 - - + -
265B LEU* 5.1 7.2 - - + -
272B ILE* 3.5 38.4 - - + -
273B PRO 3.9 2.0 - - - +
274B ILE* 2.4 45.8 + - + +
276B ILE* 1.3 68.6 - - + +
278B PHE* 1.3 68.2 + - + +
280B ALA* 3.2 9.4 + - + +
281B LEU* 2.9 29.8 + - + +
326B ILE* 5.0 4.9 - - + -
349B LEU* 5.3 7.4 - - + -
371B LEU* 4.8 15.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
274B ILE* 3.0 42.2 + - + -
275B VAL* 3.9 12.8 - - + +
277B VAL* 1.3 75.2 - - + +
279B ARG* 1.3 68.7 + - - +
281B LEU* 3.0 15.0 + - + +
282B GLY 3.3 3.5 + - - -
283B VAL* 3.0 31.7 - - + +
289B ILE* 4.1 22.0 - - + -
292B HIS* 6.4 2.5 - - + -
293B ILE* 4.1 21.5 - - + -
368B THR* 4.4 13.0 - - + -
371B LEU* 3.4 48.0 - - + -
372B GLY* 4.5 2.0 - - - -
375B VAL* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 2.9 26.7 + - - +
276B ILE* 3.9 3.8 - - - +
278B PHE* 1.3 74.6 - - - +
280B ALA* 1.3 61.8 + - - +
282B GLY* 3.2 9.5 + - - -
283B VAL 3.0 21.3 + - - +
284B VAL* 3.4 36.9 + - + +
286B ASP* 2.4 41.5 + - - -
289B ILE* 4.0 5.6 - - + -
310B ILE* 4.0 4.8 + - - +
313B GLY 2.7 22.4 + - - -
314B PHE* 3.3 30.1 + - - +
316B ILE* 2.3 42.3 + - + +
317B GLN* 4.1 7.5 - - - +
318B ASP 5.1 5.8 - - - +
319B LYS* 4.7 4.6 - - - +
322B ALA* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE 2.9 18.4 + - - +
277B VAL* 3.3 11.9 - - - +
278B PHE 3.0 0.4 - - - -
279B ARG* 1.3 78.0 - - - +
281B LEU* 1.3 63.1 + - - +
282B GLY 3.1 1.4 + - - -
319B LYS* 4.4 22.4 - - - +
322B ALA* 4.0 16.3 - - + +
323B LEU* 4.5 13.1 - - + +
326B ILE* 3.8 24.0 - - + -
349B LEU* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 2.9 21.2 + - + +
278B PHE* 3.0 5.5 + - - +
280B ALA* 1.3 79.4 - - - +
282B GLY* 1.3 58.2 + - - +
319B LYS* 6.2 0.7 - - - -
323B LEU* 6.1 1.3 - - + -
349B LEU* 3.4 49.1 - - + +
353B LEU* 5.2 8.5 - - + -
354B LEU* 5.5 2.2 - - + -
364B GLU* 3.3 35.0 - - + +
367B LYS* 5.1 17.3 - - + -
368B THR* 4.2 18.1 - - + +
371B LEU* 4.4 21.8 - - + -
----------------------------------------------------------
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