Contacts of the helix formed by residues 228 - 241 (chain B) in PDB entry 1FFT
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 ARG 228 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 3.7 52.4 + - - +
127B ILE* 4.5 5.0 - - - +
156B PRO* 3.3 23.0 - - + +
159B THR* 3.0 36.4 - - - +
227B ASP* 1.3 73.9 + - - +
229B ALA* 1.3 56.7 + - - +
230B ALA 3.1 2.2 - - - -
231B PHE* 2.8 43.9 + - + +
232B ASP* 2.3 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 2.7 31.5 + - - +
228B ARG* 1.3 73.5 - - - +
230B ALA* 1.3 58.2 + - - +
232B ASP* 3.5 17.8 + - - +
233B GLN* 3.6 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 4.3 21.1 + - + +
226B PRO* 5.4 3.6 - - + -
227B ASP* 3.2 13.7 + - - +
228B ARG 3.1 0.2 - - - -
229B ALA* 1.3 77.7 - - - +
231B PHE* 1.3 59.8 + - - +
232B ASP 3.4 0.4 - - - -
233B GLN* 3.1 30.3 + - - +
234B TRP* 3.6 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.8 23.6 - - + -
142B TYR* 3.9 16.4 - + - -
154B ALA* 3.3 16.2 - - + -
155B PHE* 3.3 29.8 - - + -
156B PRO* 3.1 32.3 - - + -
225B THR* 4.5 7.2 - - - +
227B ASP 3.7 4.3 + - - +
228B ARG* 2.8 34.4 + - + +
230B ALA* 1.3 76.5 - - - +
232B ASP* 1.3 65.1 + - - +
233B GLN 2.9 2.0 - - - -
234B TRP* 3.0 33.4 + + + +
235B VAL* 3.7 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 2.3 49.4 + - - +
229B ALA* 3.7 11.8 + - - +
231B PHE* 1.3 78.3 - - - +
233B GLN* 1.3 62.7 + - + +
235B VAL* 3.8 10.1 + - - +
236B ALA* 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA* 3.6 14.7 - - - +
230B ALA* 3.1 29.1 + - - +
231B PHE 2.9 0.2 - - - -
232B ASP* 1.3 79.0 - - + +
234B TRP* 1.3 59.0 + - - +
235B VAL 3.1 2.2 - - - -
236B ALA* 3.0 11.7 - - + +
237B LYS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 3.4 39.5 - + - -
147B ILE* 4.8 4.7 - - + -
149B THR* 3.4 24.5 - - + -
152B GLU* 3.0 42.3 + - - -
153B ILE* 3.6 2.7 - - - -
154B ALA* 3.2 37.2 - - + +
223B ILE* 5.1 3.3 - - + +
225B THR* 6.6 0.2 - - + -
230B ALA 3.6 7.1 + - - +
231B PHE* 3.0 25.2 + + + +
233B GLN* 1.3 79.5 - - - +
235B VAL* 1.3 65.6 + - + +
237B LYS* 3.8 8.5 + - + +
238B ALA* 3.6 14.0 + - - +
265B TYR* 2.7 35.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 5.3 2.7 - - + -
145B GLN* 4.1 29.2 - - + +
147B ILE* 3.2 35.2 - - + -
231B PHE* 3.8 21.1 - - + +
232B ASP* 3.8 9.6 - - - +
233B GLN 3.1 0.2 - - - -
234B TRP* 1.3 81.1 - - + +
236B ALA* 1.3 56.6 + - - +
238B ALA* 3.0 5.7 + - - +
239B LYS* 2.7 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ASP 3.4 5.6 + - - +
233B GLN* 3.0 25.7 + - + +
235B VAL* 1.3 78.3 - - - +
237B LYS* 1.3 56.7 + - - +
239B LYS* 2.8 37.7 + - - +
240B GLN* 3.2 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLN 2.9 16.4 + - - +
234B TRP* 4.0 9.9 - - + +
236B ALA* 1.3 71.6 - - - +
238B ALA* 1.3 62.4 + - - +
240B GLN* 3.2 31.4 - - - +
241B SER* 3.5 3.3 + - - -
265B TYR* 4.6 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.5 24.2 - - + -
234B TRP 3.6 3.4 + - - +
235B VAL 3.0 9.0 + - - +
237B LYS* 1.3 74.4 - - - +
239B LYS* 1.3 56.5 + - - +
240B GLN 2.8 4.9 - - - -
241B SER* 2.5 39.4 + - - +
265B TYR* 3.6 44.8 - - + -
266B PHE 4.3 1.8 - - - +
267B SER* 3.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN 3.0 24.6 + - - +
146B GLY* 3.3 19.2 + - - -
147B ILE* 3.0 27.1 - - + +
235B VAL* 2.7 43.3 + - + +
236B ALA* 2.8 18.4 + - - +
238B ALA* 1.3 69.6 - - - +
240B GLN* 1.3 56.8 + - + +
241B SER 3.9 0.2 - - - +
267B SER* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ALA 3.8 9.4 - - - +
237B LYS* 3.2 24.9 - - - +
238B ALA 2.7 1.4 + - - -
239B LYS* 1.3 76.1 - - + +
241B SER* 1.3 68.1 + - - +
242B PRO* 3.1 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LYS 3.5 2.8 + - - -
238B ALA* 2.5 27.4 + - - -
240B GLN* 1.3 73.9 - - - +
242B PRO* 1.3 64.3 - - - +
243B ASN* 3.0 16.7 + - - -
265B TYR* 3.9 19.1 - - - -
266B PHE 2.9 3.5 - - - -
267B SER* 2.3 58.2 + - - -
----------------------------------------------------------
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