Contacts of the helix formed by residues 274 - 280 (chain J) in PDB entry 3STJ
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 SER 274 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241J LEU* 5.3 1.3 - - - -
242J LEU 3.7 9.0 - - - -
243J GLY* 3.6 21.8 + - - -
271J LEU* 2.6 26.1 + - - -
272J PRO 3.3 2.2 + - - -
273J GLY* 1.3 81.8 - - - +
275J GLY* 1.3 64.1 + - - +
276J SER 3.6 1.7 + - - -
277J ALA 3.2 13.3 + - - -
278J LYS* 3.1 23.7 + - - +
332J ASP* 3.4 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242J LEU 3.9 0.4 + - - -
274J SER* 1.3 71.4 - - - +
276J SER* 1.4 55.4 + - - +
278J LYS* 3.5 12.5 + - - +
279J ALA* 2.9 30.8 + - - +
329J VAL* 3.5 9.9 - - - +
330J THR* 3.4 27.2 + - - -
332J ASP* 2.9 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 276 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242J LEU* 2.8 36.2 + - - +
243J GLY 4.3 0.2 - - - -
244J ILE* 3.4 31.8 - - - +
270J VAL* 3.8 6.3 - - - -
274J SER* 3.2 2.6 - - - -
275J GLY* 1.4 73.8 - - - +
277J ALA* 1.3 61.1 + - - +
279J ALA* 3.6 0.6 + - - -
280J GLY 3.2 3.8 + - - -
281J VAL* 2.9 43.3 + - - +
316J LEU* 5.0 0.5 - - - +
329J VAL* 3.6 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270J VAL* 3.6 11.6 - - + +
271J LEU 3.5 21.8 - - - +
272J PRO* 4.4 3.4 - - + -
273J GLY* 4.0 11.9 - - - +
274J SER* 3.2 11.0 + - - +
276J SER* 1.3 75.1 - - - +
278J LYS* 1.4 56.4 + - + +
280J GLY* 2.9 26.2 + - - -
281J VAL 4.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273J GLY* 3.4 28.7 + - - -
274J SER 3.1 16.6 + - - +
275J GLY* 3.7 10.3 - - - +
276J SER 3.5 0.2 - - - -
277J ALA* 1.4 74.9 - - + +
279J ALA* 1.3 60.0 + - - +
280J GLY* 3.4 1.4 + - - -
332J ASP* 4.8 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J GLY 2.9 18.2 + - - +
276J SER 3.9 3.1 - - - +
277J ALA 3.2 0.4 - - - -
278J LYS* 1.3 75.0 - - - +
280J GLY* 1.3 60.5 + - - +
327J VAL* 3.4 28.0 - - + +
328J GLU 3.3 25.8 - - - +
329J VAL* 3.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276J SER 3.2 0.2 + - - -
277J ALA 2.9 16.4 + - - -
278J LYS 3.2 1.1 - - - -
279J ALA* 1.3 80.2 - - - +
281J VAL* 1.4 56.3 + - - +
282J LYS* 4.1 5.6 - - - +
320J ARG* 2.7 32.2 + - - -
327J VAL* 5.0 4.4 - - - +
----------------------------------------------------------
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