Contacts of the helix formed by residues 230 - 243 (chain E) in PDB entry 6C3P
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 TYR 230 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E GLN* 3.8 20.4 + - - -
226E SER 2.5 19.7 + - - -
227E LYS 4.8 5.0 + - - -
228E GLY* 3.9 16.8 - - - -
229E THR* 1.3 76.3 - - - +
231E TRP* 1.3 59.7 + - - +
232E TRP* 3.3 28.0 - + - +
233E MET* 3.6 14.6 - - + -
234E ASN 2.9 21.0 + - - -
374E GLN* 4.4 9.6 + - + -
375E ALA* 5.7 0.3 - - - -
378E TYR* 3.1 44.1 - + - +
1242E ALA* 4.3 10.8 - - - -
1245E ARG* 3.6 27.4 - - + +
1246E TRP* 3.1 22.8 - - + -
1249E VAL* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E SER* 3.9 17.5 - - - -
229E THR* 3.4 11.2 + - + -
230E TYR* 1.3 73.9 - - - +
232E TRP* 1.3 69.9 + - - +
234E ASN* 3.0 13.8 + - + +
235E ALA* 3.0 22.6 + - + +
1250E ARG* 3.6 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E PHE* 3.3 42.0 - + - -
218E LEU* 4.7 19.1 - - - +
219E GLN* 3.8 33.5 - - + +
222E VAL* 3.8 29.2 - - + -
226E SER* 3.9 17.6 + - - -
230E TYR* 3.8 32.3 - + - +
231E TRP* 1.3 80.5 - - - +
233E MET* 1.3 77.4 + - + +
235E ALA* 3.2 10.3 + - - +
236E PHE* 2.9 26.6 + - + +
378E TYR* 5.6 5.2 - + - -
1242E ALA* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E TYR* 3.3 24.4 + - + +
231E TRP 3.2 0.6 - - - -
232E TRP* 1.3 98.0 - - + +
234E ASN* 1.3 61.4 + - - +
236E PHE* 3.2 6.7 + - - +
237E ILE* 2.9 29.8 + - - +
1242E ALA* 4.1 25.4 - - + +
1243E ALA* 5.4 1.6 - - - -
1246E TRP* 4.4 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E TYR 2.9 8.8 + - - +
231E TRP* 3.0 27.1 + - + +
233E MET* 1.3 75.7 - - - +
235E ALA* 1.3 60.8 + - - +
237E ILE* 3.2 4.6 + - - +
238E LYS* 2.9 21.5 + - - +
1180E TYR* 5.1 0.3 + - - -
1246E TRP* 3.2 43.3 - - + +
1250E ARG* 4.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E TRP* 3.0 14.4 + - + +
232E TRP* 3.2 12.3 + - - +
234E ASN* 1.3 75.1 - - - +
236E PHE* 1.3 64.9 + - - +
238E LYS* 2.9 24.0 + - - +
239E THR* 3.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E PHE* 4.1 25.1 - - + -
232E TRP* 2.9 13.8 + - + +
233E MET* 3.2 13.4 + - - +
235E ALA* 1.3 78.1 - - - +
237E ILE* 1.3 61.2 + - - +
239E THR* 3.7 10.4 + - - -
240E ALA* 4.1 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E MET 2.9 15.8 + - - +
234E ASN 3.8 3.8 - - - +
236E PHE* 1.3 76.7 - - - +
238E LYS* 1.3 65.4 - - - +
240E ALA* 2.8 24.3 + - - +
241E HIS 3.7 0.9 + - - -
1180E TYR* 2.9 18.2 + - + -
1181E PHE* 6.2 1.3 - - + -
1184E ALA* 4.9 12.3 - - + +
1243E ALA* 5.9 8.3 - - + -
1246E TRP* 4.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ASN 2.9 12.4 + - - +
235E ALA* 2.9 20.2 + - - +
237E ILE* 1.3 77.3 - - - +
239E THR* 1.3 60.3 + - - +
241E HIS* 3.7 9.7 + - - +
242E LYS* 4.2 4.7 + - - +
1180E TYR* 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E ALA 3.8 3.2 + - - -
236E PHE 3.7 8.1 + - - -
237E ILE 3.2 0.8 - - - -
238E LYS* 1.3 75.1 - - - +
240E ALA* 1.3 56.4 - - - +
241E HIS 3.0 6.1 + - - -
242E LYS* 3.1 7.6 + - - +
243E LYS* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E PHE 4.1 3.2 + - - +
237E ILE* 2.8 20.2 + - - +
239E THR* 1.3 76.9 - - - +
241E HIS* 1.3 60.1 + - - +
243E LYS 3.4 17.2 - - - +
244E PRO* 4.9 1.9 - - - +
245E ILE* 5.4 12.5 + - + +
1183E VAL* 4.6 12.1 - - - +
1184E ALA* 4.1 27.8 - - + +
1187E ASP* 5.6 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E ILE 3.7 1.8 + - - -
238E LYS 3.7 7.3 + - - +
239E THR 3.0 0.8 - - - -
240E ALA* 1.3 80.0 - - - +
242E LYS* 1.3 64.6 + - - +
243E LYS 3.2 1.7 + - - -
244E PRO* 5.7 0.3 - - - +
1180E TYR* 3.4 34.0 - - + -
1183E VAL* 5.1 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E LYS 4.2 4.2 + - - +
239E THR* 3.1 10.0 + - - +
241E HIS* 1.3 78.4 - - - +
243E LYS* 1.3 60.8 + - + +
244E PRO* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E THR* 2.9 20.4 + - - +
240E ALA* 3.4 14.3 - - - +
241E HIS 3.2 2.5 + - - -
242E LYS* 1.3 83.5 - - + +
244E PRO* 1.3 76.3 - - + +
245E ILE* 3.4 2.8 + - - -
----------------------------------------------------------
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