Contacts of the helix formed by residues 282 - 288 (chain C) in PDB entry 3GEB
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 PHE 282 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ASP* 3.2 10.8 + - - +
277C GLU* 3.3 6.7 + - - -
280C ILE* 3.8 13.5 - - + -
281C ILE* 1.3 76.1 - - - +
283C HIS* 1.3 97.9 + + - +
284C SER 3.0 0.9 - - - -
285C LEU* 2.9 32.6 + - + +
286C LEU* 3.7 13.0 + - + +
305C GLY* 3.9 7.4 - - - -
308C MET* 3.6 25.4 - - + -
309C GLU* 3.7 35.0 - - + -
312C ILE* 4.0 10.1 - - + -
457C LYS* 3.9 18.4 - - - -
461C TYR* 3.4 20.2 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ASP* 3.0 35.3 + - + +
277C GLU* 4.0 5.8 + - - +
282C PHE* 1.3 104.0 - + - +
284C SER* 1.3 55.3 + - - +
285C LEU 3.1 0.2 - - - -
286C LEU* 3.1 28.8 + - + +
287C THR* 3.1 22.9 + - + +
448C THR* 5.5 5.2 - - - -
449C THR* 4.7 6.5 - - - -
457C LYS* 4.0 8.4 + - - -
----------------------------------------------------------
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 GLU* 2.9 33.7 + - - +
281C ILE* 3.8 13.7 - - - -
282C PHE 3.0 0.2 - - - -
283C HIS* 1.3 78.4 - - - +
285C LEU* 1.3 59.2 + - - +
287C THR* 3.4 15.4 + - - -
288C GLY* 3.4 5.9 + - - -
289C THR* 2.7 21.5 + - - -
290C PHE* 3.2 33.9 + - - +
301C SER* 4.4 0.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
281C ILE* 3.7 29.8 - - + +
282C PHE* 2.9 17.3 + - + +
284C SER* 1.3 77.3 - - - +
286C LEU* 1.3 60.7 + - - +
288C GLY 3.9 2.5 + - - -
290C PHE* 5.1 3.1 - - + -
301C SER* 2.8 43.2 + - - +
302C VAL* 3.6 6.2 + - - +
304C ILE* 4.2 9.9 - - + +
305C GLY* 4.0 20.0 - - - -
308C MET* 5.6 2.0 - - + -
417C LEU* 3.4 27.4 - - + -
420C LEU* 3.2 35.7 - - + -
461C TYR* 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 4.2 23.3 - - + +
283C HIS* 3.1 14.0 + - + +
285C LEU* 1.3 77.4 - - - +
287C THR* 1.3 61.4 + - + +
288C GLY 3.3 1.8 - - - -
302C VAL* 3.7 18.1 - - + +
305C GLY* 3.3 44.0 - - - +
306C LEU* 3.4 17.5 - - + +
309C GLU* 4.6 16.8 - - - +
407D ARG* 5.0 6.3 - - - +
411D LEU* 3.7 39.8 - - + +
414D ARG* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C HIS* 3.1 20.9 + - + +
284C SER* 3.4 5.0 - - - -
286C LEU* 1.3 79.0 - - + +
288C GLY* 1.3 61.5 + - - +
289C THR* 3.2 32.3 + - + +
411D LEU* 5.8 0.2 - - - -
414D ARG* 4.1 20.8 + - - +
415D ALA* 3.7 15.4 + - - -
418D GLU* 4.0 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER 3.4 6.6 + - - -
285C LEU 3.9 6.2 + - - -
286C LEU 3.3 3.4 - - - -
287C THR* 1.3 78.8 + - - +
289C THR* 1.3 57.8 - - - +
290C PHE 3.4 2.5 - - - -
291C ALA* 3.7 5.3 + - - +
292C SER* 2.8 32.9 + - - -
298C THR* 4.7 1.5 - - - +
301C SER* 4.7 5.8 - - - -
415D ALA* 3.9 22.7 - - - +
418D GLU* 4.3 4.1 - - - +
----------------------------------------------------------
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