Contacts of the helix formed by residues 276 - 284 (chain A) in PDB entry 4M5X
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 THR 276 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 4.2 13.9 - - + -
217A LYS 5.2 2.9 + - - +
219A GLN* 2.8 21.2 + - - +
222A THR* 5.4 0.5 - - - +
225A MET* 3.4 25.4 - - + +
226A ASN* 4.2 7.3 + - - +
229A LEU* 3.8 28.0 - - + -
263A VAL* 4.6 4.3 - - + -
274A VAL 4.5 1.8 - - - +
275A GLY* 1.3 77.3 - - - +
277A LYS* 1.3 64.9 + - - +
278A LYS 3.2 2.7 - - - -
279A LEU* 3.0 16.2 + - + +
280A THR* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLN* 3.6 37.0 + - + +
275A GLY 3.8 0.2 - - - -
276A THR* 1.3 77.3 - - - +
278A LYS* 1.3 62.5 + - + +
280A THR* 3.2 9.1 + - - -
281A LYS* 3.2 25.5 + - - +
602A BR 3.7 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 3.8 10.1 + - - +
253A SER* 3.6 29.2 + - - +
259A ALA* 4.2 2.9 - - - +
262A ARG* 3.2 44.9 - - - +
276A THR 3.2 0.6 - - - -
277A LYS* 1.3 78.0 - - + +
279A LEU* 1.3 58.9 + - - +
281A LYS* 3.7 7.1 - - + +
282A SER* 2.9 28.9 + - - -
547A GLU* 4.1 7.4 + - - -
551A GLU* 3.3 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 4.8 4.5 - - - -
229A LEU* 3.7 41.1 - - + -
256A VAL* 4.6 4.5 - - + +
259A ALA* 3.7 25.3 - - + +
260A LEU* 4.4 14.1 - - + +
262A ARG* 4.8 0.4 - - - +
263A VAL* 4.1 22.2 - - + +
276A THR* 3.0 16.3 + - + +
278A LYS* 1.3 76.5 - - - +
280A THR* 1.3 66.4 + - - +
282A SER* 2.8 21.8 + - - +
283A PHE* 3.2 32.6 - - + -
303A LEU* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 4.6 4.9 - - + -
225A MET* 3.7 35.0 - - + -
276A THR* 3.0 16.5 + - - +
277A LYS* 3.2 14.4 + - - +
279A LEU* 1.3 75.2 - - - +
281A LYS* 1.3 59.0 + - - +
283A PHE* 3.4 8.4 + - + -
284A GLY 3.0 23.4 + - - -
285A TRP 3.2 25.3 + - - -
286A GLU* 4.0 6.1 - - - +
291A PHE* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A SER* 3.8 31.8 - - - +
277A LYS 3.2 16.9 + - - +
278A LYS* 3.7 6.3 - - + +
280A THR* 1.3 80.8 + - - +
282A SER* 1.3 62.5 + - - +
284A GLY* 3.3 11.1 + - - -
286A GLU* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A SER 3.9 12.8 - - - -
254A LYS* 4.1 9.6 - - - +
255A SER 3.8 13.9 - - - -
256A VAL* 3.3 42.3 - - - +
259A ALA* 3.7 5.2 - - - +
278A LYS 2.9 17.2 + - - -
279A LEU* 2.8 19.3 + - - +
281A LYS* 1.3 76.6 - - - +
283A PHE* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 4.4 3.6 - - - -
256A VAL* 3.7 13.7 - - + -
279A LEU* 3.2 47.4 + - + -
280A THR* 4.1 6.3 - - + -
282A SER* 1.3 81.0 + - - +
284A GLY* 1.3 61.9 + - - +
285A TRP* 3.4 58.7 + + + -
291A PHE* 3.6 21.3 - + - -
299A LEU* 3.6 17.0 - - + -
302A VAL* 4.0 23.4 - - + +
303A LEU* 3.9 22.4 - - + -
306A ASN* 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR 3.0 7.2 + - - -
281A LYS 3.3 12.0 + - - -
282A SER 3.4 0.4 + - - -
283A PHE* 1.3 78.3 - - - +
285A TRP* 1.3 64.2 + - - +
286A GLU* 3.4 13.5 + - - +
----------------------------------------------------------
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