Contacts of the helix formed by residues 281 - 290 (chain C) in PDB entry 3OP5
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 ASN 281 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 3.0 12.5 + - + +
278C TYR 3.1 11.1 - - - +
280C GLU* 1.3 78.3 - - + +
282C ILE* 1.4 61.6 + - - +
283C ALA* 3.7 12.6 + - - +
284C SER* 2.7 53.9 + - - +
285C LEU 3.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TYR 3.4 15.7 - - - +
279C ARG* 3.5 18.4 - - + +
280C GLU 4.1 0.6 - - - -
281C ASN* 1.4 69.4 - - - +
283C ALA* 1.3 59.1 + - - +
285C LEU* 3.0 8.3 + - + +
286C MET* 2.9 41.4 + - + +
300C ALA* 4.1 16.2 - - + +
303C MET* 3.6 49.6 - - + +
304C GLU* 3.7 32.6 + - + +
307C LYS* 3.8 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ASN* 3.3 11.4 + - - +
282C ILE* 1.3 77.7 - - - +
284C SER* 1.4 55.3 + - - +
286C MET* 3.4 8.2 + - - +
287C ASP* 3.0 38.8 + - - +
304C GLU* 5.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 4.7 5.7 + - - +
278C TYR* 3.6 16.1 - - - -
281C ASN* 2.7 46.7 + - - +
283C ALA* 1.4 74.5 - - - +
285C LEU* 1.4 59.4 + - - +
287C ASP* 3.5 10.5 + - - +
288C LYS* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C TYR* 5.3 4.3 - - + -
252C ILE* 3.8 24.7 - - + -
260C PRO* 3.8 14.8 - - + -
261C TRP* 4.3 7.4 - - + -
278C TYR* 3.5 50.7 - - + +
281C ASN 3.4 0.6 + - - -
282C ILE* 3.0 12.7 + - + +
284C SER* 1.4 77.9 + - - +
286C MET* 1.4 72.1 + - + +
288C LYS* 3.3 1.0 + - - +
289C CYS* 3.0 52.2 + - - -
303C MET* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ILE* 4.2 6.7 - - + -
282C ILE* 2.9 27.7 + - + +
283C ALA* 3.7 9.6 - - - +
285C LEU* 1.4 100.2 - - + +
287C ASP* 1.4 57.3 + - - +
289C CYS* 6.0 0.2 - - + -
290C PHE* 2.9 59.7 + - + +
295C ALA* 4.2 20.1 - - + +
296C PRO 4.9 1.1 - - - +
299C ILE* 4.0 23.6 - - + -
300C ALA* 4.0 27.8 - - + -
303C MET* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ALA* 3.0 31.5 + - - +
284C SER* 3.7 9.5 - - - +
285C LEU 3.3 0.2 - - - -
286C MET* 1.4 78.6 - - - +
288C LYS* 1.3 57.9 + - - +
290C PHE 3.2 16.8 - - - +
292C ALA* 5.5 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PRO* 3.8 38.1 + - + -
278C TYR* 3.5 25.3 + - + +
284C SER 3.0 17.9 + - - +
285C LEU* 3.7 4.3 - - - +
287C ASP* 1.3 79.5 - - - +
289C CYS* 1.3 59.5 + - - +
290C PHE 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ILE* 3.6 32.1 - - + -
256C THR* 3.3 23.6 - - + +
258C HIS 5.3 1.3 - - - -
259C LEU* 5.4 0.2 - - - -
260C PRO* 3.7 32.8 - - - -
285C LEU* 3.0 27.9 + - - +
288C LYS* 1.3 76.6 - - - +
290C PHE* 1.3 74.1 + - + +
291C PRO* 4.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ILE* 4.4 16.8 - - + -
255C LEU* 4.1 24.5 - - + -
256C THR* 3.5 26.2 - - + -
286C MET* 2.9 39.9 + - - +
287C ASP* 3.2 20.1 - - - +
288C LYS 5.2 0.2 - - - -
289C CYS* 1.3 89.4 - - + +
291C PRO* 1.4 74.9 - - + +
292C ALA* 3.6 0.7 + - - -
294C ASN 4.4 3.4 - - - -
295C ALA* 3.7 29.6 - - + +
296C PRO* 3.5 28.7 - - + -
299C ILE* 4.5 3.6 - - + -
----------------------------------------------------------
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