Contacts of the helix formed by residues 281 - 287 (chain X) in PDB entry 4HSC
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 ASP 281 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X GLY 4.1 2.2 + - - -
280X ILE* 1.3 69.7 - - - +
282X PHE* 1.3 62.8 + - - +
283X LYS* 3.3 15.7 + - - +
284X SER* 3.1 26.3 + - - -
285X ILE* 3.1 26.0 + - - +
290X LYS* 2.8 37.9 + - + +
292X VAL* 5.6 1.8 - - - +
353X GLU* 5.4 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257X VAL* 3.5 21.3 - - + -
258X TYR 3.5 20.3 - - - +
259X SER* 3.3 24.7 - - - -
260X LYS* 3.3 47.6 - - + -
263X ILE* 4.5 3.1 - - + -
271X SER* 5.7 1.3 - - - -
275X ASP* 4.2 7.2 - - + -
280X ILE* 3.1 54.4 + - + -
281X ASP* 1.3 72.5 + - - +
283X LYS* 1.3 62.9 + - - +
285X ILE* 3.3 7.5 + - + +
286X SER* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281X ASP* 3.1 13.1 + - - +
282X PHE* 1.3 77.4 - - - +
284X SER* 1.3 67.7 + - - +
286X SER* 2.6 24.3 + - - +
287X LYS* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281X ASP* 3.1 34.0 + - - -
283X LYS* 1.3 78.8 - - - +
285X ILE* 1.3 60.3 + - - +
287X LYS* 3.3 10.9 + - - +
289X GLU* 2.9 44.7 + - - +
290X LYS* 3.1 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 285 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257X VAL* 3.5 32.3 - - + +
258X TYR* 4.4 20.2 - - + +
280X ILE* 4.1 20.4 - - + -
281X ASP 3.1 15.9 + - - +
282X PHE* 3.5 11.9 - - + +
283X LYS 3.1 0.8 - - - -
284X SER* 1.3 74.3 - - - +
286X SER* 1.3 61.1 + - - +
288X GLY* 2.8 21.7 + - - -
290X LYS* 3.6 22.2 - - + +
291X LYS* 5.7 1.3 - - - -
292X VAL* 3.8 31.9 - - + +
455X THR* 4.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 286 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149X ILE* 5.4 0.2 - - - +
151X ARG* 4.7 14.0 + - - -
258X TYR 5.7 2.0 + - - -
282X PHE 3.0 14.0 + - - -
283X LYS* 2.6 28.9 + - - +
285X ILE* 1.3 77.3 - - - +
287X LYS* 1.3 61.1 + - - +
288X GLY 3.2 1.1 + - - -
455X THR* 4.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149X ILE* 3.6 20.5 - - - +
151X ARG* 6.1 0.4 - - - +
283X LYS* 3.0 46.2 + - + +
284X SER* 3.7 7.3 - - - +
285X ILE 3.0 0.6 - - - -
286X SER* 1.3 80.2 + - - +
288X GLY* 1.3 61.2 + - - +
289X GLU* 3.0 42.5 + - - +
----------------------------------------------------------
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