Contacts of the helix formed by residues 233 - 244 (chain E) in PDB entry 5FWP
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 CYS 233 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 5.7 1.6 - - - -
223E ALA* 3.8 13.0 - - - -
226E LEU* 4.7 3.8 - - + -
228E VAL* 3.4 33.4 - - + -
229E ASP 3.7 4.0 - - - -
230E PRO 3.7 8.5 - - - -
232E ALA* 1.3 82.9 - - + +
234E PHE* 1.3 60.0 + - - +
235E ARG 3.1 3.1 - - - -
236E GLN* 2.9 46.0 + - - +
237E PHE* 3.1 27.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E GLN* 3.8 10.8 - - + -
175E LEU* 3.5 27.8 - - + -
176E SER* 3.7 18.2 - - - -
179E VAL* 3.6 23.6 - - + -
182E VAL* 3.9 9.9 - - + -
219E ILE* 3.6 19.2 - - + +
230E PRO 2.8 14.3 + - - +
231E ARG 3.5 17.7 - - - -
232E ALA 5.4 0.2 - - - -
233E CYS* 1.3 76.8 - - - +
235E ARG* 1.3 109.4 + - + +
237E PHE* 3.1 25.2 + - - +
238E PHE* 3.3 27.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 6.0 0.8 - - - +
338B ARG* 4.6 14.1 - - - +
341B PHE* 3.5 44.4 - - + -
172E GLN* 3.7 24.9 + - + +
176E SER* 2.9 39.8 + - - +
179E VAL* 5.6 1.8 - - - +
231E ARG 4.9 3.0 + - - -
232E ALA 6.1 0.8 - - - -
233E CYS* 3.1 0.6 + - - -
234E PHE* 1.3 112.7 - - + +
236E GLN* 1.3 57.1 + - - +
238E PHE* 3.4 7.3 + - - +
239E THR* 2.8 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A THR* 3.9 18.4 + - + +
341B PHE* 3.9 23.2 - - + -
226E LEU* 4.1 15.1 - - + +
232E ALA 5.4 1.1 + - - -
233E CYS* 2.9 33.1 + - + +
235E ARG* 1.3 75.0 - - - +
237E PHE* 1.3 62.8 + - + +
239E THR* 3.5 9.9 - - - -
240E LYS* 2.8 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E VAL* 6.4 0.7 - - + -
218E PHE* 2.9 50.0 - + + -
219E ILE* 3.0 39.3 - - + -
222E LEU* 3.4 26.2 - - + -
223E ALA 3.6 12.8 - - - -
226E LEU* 5.2 3.8 - - + -
233E CYS* 3.1 37.5 - - + -
234E PHE* 3.1 15.0 + - - +
236E GLN* 1.3 78.0 - - + +
238E PHE* 1.3 62.9 + - + +
240E LYS* 3.3 8.6 + - + +
241E ILE* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E TRP* 3.5 54.5 - + + -
171E SER* 3.5 21.8 - - - -
172E GLN* 3.5 50.9 - - + +
175E LEU* 4.0 9.9 - - + -
215E VAL* 4.0 16.2 - - + -
219E ILE* 4.3 6.5 - - + -
234E PHE* 3.3 37.9 - + - -
235E ARG 3.4 2.4 + - - +
237E PHE* 1.3 77.9 - - + +
239E THR* 1.3 58.5 + - - +
241E ILE* 4.4 4.3 - - + +
242E LYS* 2.9 41.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
614A ASN* 3.9 21.9 + - - +
616A THR* 3.6 23.6 - - + -
617A MET* 4.2 9.9 - - + +
341B PHE* 4.1 14.8 - - + -
172E GLN* 4.9 3.5 + - - +
235E ARG 2.8 22.6 + - - -
236E GLN* 3.5 11.4 - - - -
237E PHE 3.2 0.2 - - - -
238E PHE* 1.3 78.1 - - - +
240E LYS* 1.3 52.6 + - - +
242E LYS* 3.7 3.9 + - - -
243E THR* 2.6 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A THR* 3.3 25.6 - - + +
619A TYR* 5.8 3.4 - - - -
620A MET* 3.7 26.1 - - + +
218E PHE* 4.9 8.7 - - + -
222E LEU* 3.6 35.1 - - + +
226E LEU* 4.9 14.8 - - - +
236E GLN* 2.8 27.3 + - - +
237E PHE* 3.6 10.8 - - + +
239E THR* 1.3 74.3 - - - +
241E ILE* 1.3 56.7 + - - +
243E THR* 3.1 5.4 + - - -
244E ALA* 2.8 39.0 + - - +
249E MET* 5.0 0.2 - - - -
252E PHE* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E TRP* 3.6 59.5 - - + +
215E VAL* 5.2 7.2 - - + -
218E PHE* 3.7 31.2 - - + -
237E PHE* 2.8 28.3 + - + +
238E PHE* 3.9 7.4 - - + +
240E LYS* 1.3 72.9 - - - +
242E LYS* 1.3 63.8 + - - +
243E THR 3.3 1.0 + - - -
244E ALA* 3.7 8.1 + - - +
249E MET* 3.6 34.4 - - + +
256E LEU* 6.4 0.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
621A MET* 5.3 1.6 - - - +
168E TRP* 3.5 35.7 - - + -
169E ASP* 2.6 35.3 + - - +
172E GLN* 2.7 27.6 + - - +
238E PHE* 2.9 26.4 + - - +
239E THR* 4.1 4.7 - - - +
241E ILE* 1.3 77.6 - - + +
243E THR* 1.3 62.6 + - + +
244E ALA 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A TYR* 5.7 0.5 - - - +
597A GLY* 5.2 3.5 + - - -
617A MET* 3.8 43.6 - - + -
620A MET* 3.2 37.1 - - - +
621A MET* 3.9 24.8 - - + +
239E THR* 2.6 25.8 + - + +
240E LYS* 3.3 0.5 + - - -
242E LYS* 1.3 84.5 - - + +
244E ALA* 1.3 66.8 + - - +
245E ASP 3.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A TYR* 5.1 4.4 - - - +
620A MET* 3.6 23.6 - - - -
240E LYS 2.8 18.2 + - - +
241E ILE 3.7 4.8 + - - +
242E LYS 5.3 0.3 - - - -
243E THR* 1.3 79.8 + - - +
245E ASP* 1.3 64.5 + - - +
246E ARG* 3.5 2.6 + - - -
249E MET* 3.7 32.6 - - + +
252E PHE* 4.2 10.1 - - + -
----------------------------------------------------------
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