Contacts of the helix formed by residues 283 - 289 (chain C) in PDB entry 3EGC
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 LEU 283 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 4.4 24.9 - - + -
254C HIS* 3.8 41.5 - - + +
281C ASP* 3.3 18.1 + - + +
282C ASN* 1.3 83.1 - - - +
284C PRO* 1.3 76.4 - - + +
285C TRP* 3.2 34.7 + - + +
286C MET* 3.2 24.1 + - + +
287C ALA* 4.1 1.7 + - - +
333C HIS* 5.4 0.9 + - - -
283D LEU* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASN* 4.0 6.7 - - - +
283C LEU* 1.3 92.9 - - + +
285C TRP* 1.3 63.1 + - + +
287C ALA* 3.0 18.6 + - + +
288C PHE* 3.6 19.7 - - + -
258D GLU* 3.7 39.3 - - + +
262D GLN* 4.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C HIS* 4.5 4.0 + - + +
257C THR* 4.1 19.5 - - + -
258C GLU* 4.2 25.0 + - + -
261C MET* 4.6 3.4 - - + -
283C LEU* 3.6 29.4 - - + +
284C PRO* 1.3 80.8 - - + +
286C MET* 1.3 87.1 + - + +
288C PHE* 2.9 37.0 + - + +
289C LEU* 3.6 31.4 + - + +
293C LEU* 4.9 0.7 - - + -
258D GLU* 4.9 3.1 + - - +
285D TRP* 3.2 66.4 - + + -
288D PHE* 3.9 26.5 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
254C HIS* 3.6 26.7 - - + -
257C THR* 4.2 4.9 - - + -
279C SER* 3.4 27.1 - - - +
281C ASP 3.3 24.7 - - - +
283C LEU* 3.4 17.7 - - + +
284C PRO 3.1 0.2 - - - -
285C TRP* 1.3 111.8 - - + +
287C ALA* 1.3 59.2 + - - +
288C PHE 3.2 1.3 + - - -
289C LEU* 3.7 8.7 + - - +
292C PRO* 3.6 1.7 - - - +
293C LEU* 2.9 48.3 + - + +
295C VAL* 3.6 17.9 - - + -
333C HIS* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU 4.1 0.6 + - - -
284C PRO* 3.0 15.3 + - + +
286C MET* 1.3 78.4 - - - +
288C PHE* 1.3 64.3 + - + +
289C LEU 3.3 1.7 - - - +
292C PRO* 4.0 22.5 - - + +
333C HIS* 4.0 27.5 - - + +
265D ASN* 4.9 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C PRO 3.6 17.3 - - - -
285C TRP* 2.9 31.7 + - + +
287C ALA* 1.3 82.6 - - + +
289C LEU* 1.3 69.8 + - + +
290C ASP* 5.5 0.2 - - - +
258D GLU* 3.5 33.2 - - + -
261D MET* 3.7 39.7 - - + +
262D GLN* 3.9 29.4 - - + -
265D ASN* 5.1 11.7 - - - +
285D TRP* 3.9 28.3 - + - -
289D LEU* 5.3 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C MET* 4.3 17.3 - - + -
271C TYR* 3.6 15.9 - - + -
285C TRP* 3.6 39.9 - - + +
286C MET* 3.8 11.7 - - - +
287C ALA 3.3 1.7 - - - +
288C PHE* 1.3 86.3 - - - +
290C ASP* 1.3 60.9 + - - +
291C PRO 3.2 14.6 - - - +
292C PRO* 3.1 21.3 - - - +
293C LEU* 3.9 22.4 - - + -
288D PHE* 5.5 5.4 - - + +
289D LEU* 4.6 18.6 - - + -
----------------------------------------------------------
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