Contacts of the helix formed by residues 214 - 219 (chain E) in PDB entry 3FFC
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 ALA 214 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ILE* 4.1 21.3 - - + -
155E GLN* 3.2 43.4 + - + +
156E LYS* 3.6 5.0 - - - +
157E ALA* 4.6 2.7 - - - +
213E SER* 1.3 72.6 - - - +
215E THR* 1.3 63.0 + - - +
217E TRP* 3.3 4.7 + - - +
218E GLN* 3.0 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E SER* 4.0 11.1 + - - -
214E ALA* 1.3 79.0 - - - +
216E PHE* 1.3 62.7 + - - +
218E GLN* 3.3 7.5 + - - +
219E ASN* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E VAL* 3.4 34.1 - - + -
178E ASN* 3.8 9.6 - - - -
212E VAL* 3.9 18.2 - - + -
213E SER* 3.3 20.2 + - - +
215E THR* 1.3 80.5 - - - +
217E TRP* 1.3 60.7 + - - +
219E ASN* 3.8 4.1 + - - +
222E ASN* 2.7 55.2 + - - +
224E PHE* 3.6 17.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ARG* 5.1 1.3 - - - -
145E GLU* 3.3 33.2 - - + -
146E PRO* 3.3 30.8 + - + +
148E GLU* 5.4 0.6 + - - -
151E ILE* 4.0 15.0 - - + +
157E ALA* 3.7 31.0 - - + -
159E LEU* 3.9 21.1 - - + -
212E VAL* 4.2 6.3 - - + +
213E SER 3.2 10.8 + - - +
214E ALA 3.3 2.7 + - - +
216E PHE* 1.3 76.8 - - - +
218E GLN* 1.3 69.9 + - + +
224E PHE* 3.5 33.4 - + - -
255E ALA* 4.7 2.0 - - + -
256E TRP 3.3 26.0 - - - -
257E GLY* 2.9 30.0 - - - -
258E ARG* 3.0 22.6 + - + +
260E ASP* 4.6 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ILE* 3.2 27.8 - - - +
214E ALA* 3.0 27.9 + - - +
215E THR* 3.3 7.7 + - - +
217E TRP* 1.3 82.5 - - + +
219E ASN* 1.3 64.0 + - - +
220E PRO* 3.3 6.9 - - - +
258E ARG 3.2 18.6 - - - +
259E ALA* 3.4 33.1 + - - +
260E ASP* 5.5 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E THR 3.3 11.9 + - - +
216E PHE* 3.8 10.3 - - - +
217E TRP 3.4 1.8 - - - +
218E GLN* 1.3 74.1 - - - +
220E PRO* 1.3 66.8 - - - +
221E ARG* 2.8 75.0 + - - +
222E ASN* 3.5 24.1 + - - +
257E GLY* 3.3 14.6 - - - -
----------------------------------------------------------
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