Contacts of the helix formed by residues 245 - 259 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243D ASN 4.4 2.0 - - - +
244D THR* 1.3 87.8 - - - +
246D GLU* 1.3 68.6 + - - +
248D ILE* 3.5 3.1 + - + +
249D ALA* 2.9 31.2 + - - +
281D VAL* 3.8 27.6 - - + -
282D ASN* 3.4 25.2 - - - +
285D ALA* 3.7 15.3 - - + +
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D THR* 3.1 10.4 - - - +
245D PRO* 1.3 96.2 - - - +
247D GLU* 1.3 59.7 + - + +
249D ALA* 3.5 5.8 + - - +
250D LEU* 3.0 30.0 + - - +
285D ALA* 4.6 9.7 - - + +
289D VAL* 5.6 0.2 - - - +
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 3.8 18.2 - - + +
242D LYS 4.9 0.2 - - - +
243D ASN* 3.4 16.5 + - + +
244D THR* 3.0 48.4 + - - +
246D GLU* 1.3 76.2 - - + +
248D ILE* 1.3 62.6 - - - +
250D LEU* 3.5 4.8 + - - +
251D ALA* 3.1 25.8 + - - +
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Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 4.9 0.9 - - + -
232D MET* 4.3 11.7 - - + -
233D VAL 3.4 23.0 - - - +
234D THR* 3.9 23.3 - - + -
242D LYS* 6.3 1.1 - - - +
243D ASN* 3.7 31.9 - - + +
244D THR 3.0 19.4 + - - +
245D PRO* 3.8 4.5 - - + +
247D GLU* 1.3 77.5 - - - +
249D ALA* 1.3 57.9 + - - +
251D ALA* 3.8 0.8 - - - +
252D THR* 2.8 40.7 + - - +
282D ASN* 3.8 35.0 - - + +
286D ILE* 5.3 1.8 - - + -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PRO 2.9 18.4 + - - +
246D GLU* 3.8 6.1 - - - +
247D GLU 3.3 0.2 - - - -
248D ILE* 1.3 77.3 - - - +
250D LEU* 1.3 63.3 + - - +
252D THR* 3.4 0.9 + - - -
253D VAL* 3.0 29.8 + - - +
285D ALA* 3.6 12.3 - - + +
286D ILE* 3.6 39.0 - - + +
289D VAL* 3.7 8.1 - - + -
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D GLU 3.0 18.9 + - - +
247D GLU* 4.0 5.4 - - - +
248D ILE 3.4 0.2 - - - -
249D ALA* 1.3 75.8 - - - +
251D ALA* 1.3 58.1 + - - +
253D VAL* 3.8 0.5 - - - -
254D GLN* 2.8 64.3 + - + +
289D VAL* 4.0 14.8 - - + +
290D PRO* 6.1 0.9 - - + -
291D LEU* 4.1 17.7 - - + -
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 4.0 15.9 - - + -
202D GLN* 3.6 29.4 + - - +
233D VAL* 3.7 21.7 - - + +
247D GLU 3.1 18.0 + - - +
248D ILE 3.8 2.5 - - - +
250D LEU* 1.3 77.5 - - - +
252D THR* 1.3 62.5 + - - +
254D GLN* 4.5 1.8 - - - +
255D ALA* 3.0 26.2 + - - +
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Residues in contact with THR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ASN 4.9 1.1 - - - +
232D MET* 3.7 11.2 - - - +
233D VAL* 2.8 33.1 + - + +
248D ILE* 2.8 24.4 + - - +
249D ALA 3.9 2.9 - - - -
251D ALA* 1.3 76.1 - - - +
253D VAL* 1.3 58.1 + - - +
255D ALA* 3.3 4.0 + - - +
256D LEU* 3.0 33.4 + - + +
269D PHE* 3.4 39.7 - - + -
286D ILE* 4.0 13.7 - - + -
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Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ALA 3.0 19.7 + - - +
250D LEU 4.1 0.4 - - - +
252D THR* 1.3 73.0 - - + +
254D GLN* 1.3 60.7 + - - +
256D LEU* 3.5 7.4 + - + +
257D ARG* 2.9 49.0 + - + +
286D ILE* 3.7 38.8 - - + +
289D VAL* 3.7 27.1 - - + -
291D LEU* 4.4 1.8 - - + -
293D ARG* 3.9 22.4 - - + -
295D TRP* 5.4 2.2 - - + -
297D LEU* 4.8 2.9 - - + -
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Residues in contact with GLN 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 5.2 3.4 - - - +
202D GLN* 3.1 29.2 + - - +
250D LEU* 2.8 48.5 + - + +
251D ALA* 4.5 2.4 - - - +
253D VAL* 1.3 76.1 - - - +
255D ALA* 1.3 62.4 + - - +
257D ARG* 3.2 9.1 + - - +
258D ARG* 3.0 55.4 + - - +
291D LEU* 4.3 11.4 - - + +
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Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLN* 4.4 3.4 - - + +
205D THR* 4.2 12.8 - - + -
206D GLU* 3.7 29.8 + - + +
209D LEU* 4.7 1.5 - - - +
233D VAL* 4.0 17.0 - - + -
251D ALA 3.0 18.4 + - - +
252D THR 3.3 4.5 + - - +
254D GLN* 1.3 76.7 - - - +
256D LEU* 1.3 55.7 + - + +
258D ARG* 3.4 6.9 + - - +
259D THR* 2.8 30.9 + - - +
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Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D THR* 5.7 1.8 - - + -
209D LEU* 3.8 16.2 - - + -
228D LEU* 4.3 9.4 - - + -
230D PRO* 4.4 10.5 - - + -
231D ASN 5.9 0.4 - - - +
252D THR* 3.0 24.4 + - + +
253D VAL* 4.0 5.2 - - + +
254D GLN 3.3 0.2 - - - -
255D ALA* 1.3 71.1 - - + +
257D ARG* 1.3 67.5 + - - +
258D ARG 3.0 2.0 + - - -
259D THR* 4.0 2.7 - - - -
260D VAL* 2.9 46.2 + - + +
267D VAL* 4.2 9.2 - - + -
269D PHE* 3.7 31.4 - - + -
295D TRP* 3.6 21.0 - - + -
297D LEU* 3.9 17.3 - - + -
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Residues in contact with ARG 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 4.9 10.9 + - - +
261A PRO* 3.4 2.8 - - - +
262A ALA* 3.3 33.1 + - + +
263A ALA* 3.1 47.4 + - + +
253D VAL* 2.9 36.4 + - + +
254D GLN* 3.6 6.5 - - - +
256D LEU* 1.3 75.7 - - - +
258D ARG* 1.3 61.5 + - - +
260D VAL 4.9 1.0 + - - +
291D LEU* 3.8 31.6 - - - +
292D ILE* 2.9 48.4 + - - +
295D TRP* 3.7 15.7 - - + -
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Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.9 16.7 + - - -
12A GLN* 4.9 4.8 + - - -
222A TYR* 3.8 17.7 + - - -
223A LEU* 3.4 27.5 - - + +
224A GLU* 2.8 32.0 + - - +
261A PRO* 3.5 9.3 - - - +
263A ALA* 3.7 20.6 - - + -
202D GLN* 3.4 12.7 - - - +
206D GLU* 3.0 35.1 + - + +
254D GLN* 3.0 42.1 + - - +
255D ALA* 3.8 4.9 - - - +
256D LEU 3.0 0.4 - - - -
257D ARG* 1.3 79.3 - - - +
259D THR* 1.3 65.7 + - + +
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Residues in contact with THR 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PRO* 4.9 6.9 - - - +
206D GLU* 3.3 37.2 - - + +
209D LEU* 3.4 29.1 - - - +
210D ALA* 4.0 16.5 - - + +
213D TYR* 3.6 15.1 - - - +
255D ALA 2.8 22.3 + - - +
256D LEU 3.1 0.6 + - - -
257D ARG 3.3 0.8 - - - -
258D ARG* 1.3 87.8 - - + +
260D VAL* 1.3 64.3 + - - +
261D PRO* 3.3 11.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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