Contacts of the helix formed by residues 245 - 259 (chain A) in PDB entry 1FBA
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 PRO 245 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASN 4.5 1.1 - - - +
244A THR* 1.3 89.1 - - - +
246A GLU* 1.3 70.4 + - - +
248A ILE* 3.5 2.6 + - + +
249A ALA* 2.8 31.5 + - - +
281A VAL* 3.7 28.5 - - + -
282A ASN* 3.5 23.7 - - - +
285A ALA* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 3.1 10.3 + - - +
245A PRO* 1.3 94.5 - - - +
247A GLU* 1.3 59.0 + - + +
249A ALA* 3.9 5.5 - - - +
250A LEU* 3.1 30.3 + - - +
285A ALA* 4.6 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.9 13.9 - - + +
243A ASN* 2.8 42.3 + - + +
244A THR* 3.1 34.6 + - - +
246A GLU* 1.3 76.5 - - + +
248A ILE* 1.3 63.8 + - - +
250A LEU* 3.9 4.6 - - - +
251A ALA* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.7 1.8 - - + -
232A MET* 4.4 11.2 - - + -
233A VAL 3.4 23.3 - - - +
234A THR* 4.0 24.9 - - + -
243A ASN* 4.0 28.0 - - + +
244A THR 3.1 16.9 + - - +
245A PRO* 3.7 4.3 - - + +
247A GLU* 1.3 74.1 - - - +
249A ALA* 1.3 60.5 + - - +
251A ALA 3.3 1.0 + - - -
252A THR* 2.8 41.8 + - - +
282A ASN* 3.7 35.4 - - + +
286A ILE* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO 2.8 18.8 + - - +
246A GLU* 3.9 5.4 - - - +
248A ILE* 1.3 76.1 - - - +
250A LEU* 1.3 57.2 + - - +
252A THR* 3.8 0.7 - - - -
253A VAL* 2.9 35.7 + - - +
282A ASN 4.8 0.4 - - - +
285A ALA* 3.5 37.2 - - + +
286A ILE* 3.6 15.7 - - + +
289A VAL* 3.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU 3.1 18.9 + - - +
247A GLU* 3.9 5.4 - - - +
249A ALA* 1.3 74.8 - - - +
251A ALA* 1.3 61.2 + - - +
253A VAL* 3.9 0.5 - - - +
254A GLN* 2.9 56.3 + - - +
289A VAL* 4.1 14.7 - - + +
290A PRO* 5.9 1.3 - - + -
291A LEU* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.0 17.3 - - + -
202A GLN* 3.6 29.5 + - - +
233A VAL* 3.8 21.1 - - + -
247A GLU 3.1 15.8 + - - +
248A ILE 3.8 2.9 - - - +
250A LEU* 1.3 79.5 - - - +
252A THR* 1.3 56.7 + - - +
254A GLN* 3.4 2.6 + - - +
255A ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN 4.9 1.1 - - - +
232A MET* 3.7 10.1 - - - +
233A VAL* 2.8 33.4 + - + +
248A ILE* 2.8 25.1 + - - +
249A ALA 3.8 3.6 - - - -
251A ALA* 1.3 73.9 - - - +
253A VAL* 1.3 66.3 + - + +
255A ALA* 3.4 3.1 + - - +
256A LEU* 3.1 32.8 + - + +
269A PHE* 3.4 40.4 - - + -
286A ILE* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 2.9 20.2 + - - +
250A LEU 4.2 0.4 - - - +
252A THR* 1.3 74.4 - - + +
254A GLN* 1.3 61.0 + - - +
256A LEU* 3.9 5.5 - - + +
257A ARG* 2.9 48.3 + - + +
286A ILE* 3.7 39.5 - - + +
289A VAL* 3.7 22.4 - - + -
291A LEU* 4.4 3.1 - - + -
293A ARG* 3.8 24.2 - - + -
295A TRP* 4.7 2.4 - - + -
297A LEU* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN* 3.2 29.7 + - - +
250A LEU* 2.9 47.6 + - + +
251A ALA* 4.4 1.4 - - - +
253A VAL* 1.3 77.4 - - - +
255A ALA* 1.3 64.3 + - - +
257A ARG* 3.2 8.8 + - - +
258A ARG* 3.0 56.0 + - - +
291A LEU* 4.2 12.9 - - + +
224D GLU* 5.1 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN* 4.3 3.4 - - + -
205A THR* 4.3 12.8 - - + -
206A GLU* 3.6 28.4 + - + +
209A LEU* 4.9 0.9 - - - -
233A VAL* 4.0 17.7 - - + -
251A ALA 3.0 18.8 + - - +
252A THR 3.7 4.7 - - - +
253A VAL 3.3 0.2 - - - -
254A GLN* 1.3 77.0 - - - +
256A LEU* 1.3 61.3 + - + +
258A ARG* 3.4 5.9 + - - +
259A THR* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A THR* 5.6 2.0 - - + -
209A LEU* 3.6 25.8 - - + -
228A LEU* 4.4 9.2 - - + -
230A PRO* 4.5 9.6 - - + -
231A ASN 5.9 0.7 - - - +
252A THR* 3.1 20.0 + - + +
253A VAL* 4.0 4.0 - - + +
255A ALA* 1.3 73.6 - - + +
257A ARG* 1.3 63.7 + - - +
259A THR* 3.9 2.5 - - - -
260A VAL* 2.9 36.9 + - + +
267A VAL* 4.1 9.4 - - + -
269A PHE* 3.6 32.8 - - + -
295A TRP* 3.5 26.0 - - + -
297A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 2.9 36.2 + - + +
254A GLN* 3.5 7.0 - - - +
256A LEU* 1.3 76.0 - - - +
258A ARG* 1.3 58.5 + - + +
259A THR 3.6 0.2 + - - -
260A VAL 4.9 1.0 + - - +
291A LEU* 3.7 33.5 - - - +
292A ILE* 2.9 54.9 + - - +
295A TRP* 3.8 15.0 - - + -
224D GLU* 4.7 11.1 + - - +
261D PRO* 3.3 5.4 - - - +
262D ALA* 3.3 33.5 + - + +
263D ALA* 3.0 47.7 + - + +
294D PRO 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN* 3.3 12.9 - - - +
206A GLU* 3.0 34.2 + - + +
254A GLN* 3.0 43.7 + - - +
255A ALA 3.7 5.2 - - - +
256A LEU 3.1 0.4 - - - -
257A ARG* 1.3 79.3 - - - +
259A THR* 1.3 65.0 + - + +
6D TYR* 4.0 16.7 - - - -
12D GLN* 4.7 5.5 + - - -
222D TYR* 3.8 18.4 + - - -
223D LEU* 3.4 24.8 - - + +
224D GLU* 2.8 38.9 + - - +
261D PRO* 3.6 9.5 - - - +
263D ALA* 3.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 3.4 36.3 - - + +
209A LEU* 3.3 31.2 - - + +
210A ALA* 4.0 15.1 - - + +
213A TYR* 3.5 15.0 - - - +
255A ALA 2.9 18.9 + - - +
256A LEU 3.1 0.6 + - - -
257A ARG 3.3 0.8 - - - -
258A ARG* 1.3 88.8 - - + +
260A VAL* 1.3 63.6 + - - +
261A PRO* 3.2 12.2 - - - +
261D PRO* 4.8 6.9 - - - +
----------------------------------------------------------
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