Contacts of the strand formed by residues 268 - 280 (chain B) in PDB entry 5F0P
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 PHE 268 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 4.1 13.2 - - + -
78B LEU* 5.1 0.4 - - + -
121B TYR* 3.6 29.8 - + + -
126B VAL* 3.6 44.9 - - + -
128B LEU* 4.0 19.3 - - + -
215B GLU* 5.2 1.1 - - + -
216B ILE 3.2 12.8 - - - +
217B THR* 4.3 0.7 - - - -
261B MSE 4.3 15.7 - - + -
263B ASP 3.5 0.7 + - - -
264B VAL* 2.9 66.9 + - + +
267B LYS* 1.3 80.5 - - + +
269B SER* 1.3 63.1 + - - +
270B VAL* 4.2 11.7 - - + -
408B EDO 3.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LYS 4.3 0.2 - - - -
215B GLU* 3.4 1.7 - - - +
216B ILE* 2.7 50.2 + - - +
261B MSE 3.2 8.1 - - - -
262B ARG* 3.8 10.4 + - - -
263B ASP* 2.9 33.6 + - - -
268B PHE* 1.3 72.8 - - - +
270B VAL* 1.3 70.5 + - - +
271B ARG* 4.2 10.8 - - - -
408B EDO 3.7 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 3.7 24.5 - - + +
213B LYS* 4.0 16.8 - - + -
214B LYS 3.2 6.5 - - - +
215B GLU* 4.0 9.0 - - + -
258B THR* 3.9 5.4 - - - +
259B PRO 4.2 0.9 - - - +
260B THR* 3.4 6.6 - - - +
261B MSE 2.8 69.9 + - + +
268B PHE* 4.2 4.3 - - + -
269B SER* 1.3 79.9 - - - +
271B ARG* 1.3 64.9 + - - +
272B TYR* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LYS* 3.6 1.9 - - - -
214B LYS* 2.8 34.6 + - - +
216B ILE* 4.3 17.2 - - + +
260B THR* 4.6 5.6 - - + -
261B MSE 4.9 0.2 - - - +
262B ARG* 3.5 49.9 - - - +
269B SER* 4.4 8.5 - - - -
270B VAL* 1.3 84.3 - - - +
272B TYR* 1.3 66.4 + - - +
273B PHE* 3.7 27.9 - - + -
291B GLU* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 4.3 15.0 - - + -
212B ILE 3.3 6.3 - - - -
213B LYS* 3.4 37.8 - - + +
230B ILE* 3.9 7.0 - - + -
257B PRO* 3.7 16.9 - - + +
258B THR* 2.9 49.8 + - - -
259B PRO 3.8 11.9 - - - -
260B THR* 3.8 13.6 + - - -
270B VAL* 3.8 12.1 - - + -
271B ARG* 1.3 75.5 - - - +
273B PHE* 1.3 63.5 + - - +
291B GLU* 3.2 11.2 - - - +
292B ILE* 3.0 42.7 + - + +
294B LEU* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLN 3.5 0.5 - - - +
211B LEU* 3.5 8.0 - - - +
212B ILE* 2.8 42.8 + - + +
214B LYS* 3.6 33.0 - - + -
271B ARG* 3.7 41.3 - - + -
272B TYR* 1.3 75.7 - - - +
274B LEU* 1.3 61.8 + - - +
275B ASN 3.8 0.8 + - - -
289B GLN* 3.6 37.9 - - + -
290B GLN* 3.3 4.7 - - - -
291B GLU* 3.7 40.6 - - + -
292B ILE* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 4.0 37.9 + - + -
191B ILE* 4.0 28.5 - - + -
209B LEU* 4.1 21.3 - - + -
210B GLN 3.3 10.1 - - - +
211B LEU* 4.2 16.8 - - + -
250B LEU* 4.4 12.1 - - + -
273B PHE* 1.3 70.6 - - - +
275B ASN* 1.3 60.1 + - - +
276B LEU 3.8 1.1 + - - -
288B LYS 3.7 2.4 - - - +
289B GLN* 3.5 2.0 - - - -
290B GLN* 2.7 37.4 + - - +
292B ILE* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.7 1.9 - - - -
210B GLN* 2.8 63.2 + - + +
212B ILE* 3.4 29.4 - - + +
273B PHE 3.8 0.4 - - - -
274B LEU* 1.3 71.7 - - - +
276B LEU* 1.3 58.7 + - - +
277B VAL* 3.5 15.7 + - - +
287B PHE* 3.4 27.0 - - - +
288B LYS 3.4 14.8 - - - +
289B GLN* 3.9 13.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 3.7 29.4 - - + -
178B PHE* 4.2 17.0 - - + -
180B TYR* 3.9 10.1 - - - +
195B ILE* 3.9 31.0 - - + -
207B MSE 4.0 8.1 - - + -
208B GLU 3.7 13.0 - - - +
209B LEU* 4.1 12.7 - - + +
235B ILE* 4.0 16.8 - - + -
274B LEU 3.8 2.2 + - - -
275B ASN* 1.3 71.0 - - - +
277B VAL* 1.3 58.4 + - - +
278B LEU* 4.3 10.9 - - + +
287B PHE* 3.1 9.2 - - - +
288B LYS* 2.9 38.8 + - + +
557D MSE 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B HIS 4.2 0.3 - - - +
207B MSE 3.4 2.8 - - - -
208B GLU* 2.8 52.3 + - + +
210B GLN* 3.7 19.3 - - + +
275B ASN* 3.5 26.9 - - - +
276B LEU* 1.3 79.4 - - - +
278B LEU* 1.3 74.1 + - - +
279B VAL* 4.2 9.7 - - + +
285B ARG* 3.7 31.9 - - + +
286B TYR 3.4 5.6 - - - +
287B PHE* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.5 25.8 - - + -
176B ILE* 4.0 20.0 - - + -
197B PHE* 4.0 16.4 - - + -
204B ILE* 3.7 27.8 - - + -
206B HIS 3.8 5.4 - - - +
207B MSE 3.7 29.8 - - + +
276B LEU* 4.4 7.6 - - + -
277B VAL* 1.3 75.1 - - - +
279B VAL* 1.3 62.3 + - - +
280B ASP 4.4 0.2 - - - -
285B ARG* 3.4 3.6 - - - -
286B TYR* 2.8 50.9 + - + +
557D MSE 4.1 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 3.7 4.6 - - - +
205B GLN* 2.8 43.6 + - - +
206B HIS* 3.0 37.7 + - + +
208B GLU* 5.7 0.2 - - - +
277B VAL* 4.2 9.0 - - + +
278B LEU* 1.3 80.1 - - - +
280B ASP* 1.3 65.4 + - - +
283B ASP* 4.0 21.3 - - - +
284B ARG 3.3 9.2 - - - +
285B ARG* 4.1 28.9 - - + +
286B TYR* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.3 13.4 - - + +
203B LYS 3.2 20.2 - - - +
204B ILE* 4.1 0.9 - - - +
205B GLN* 3.9 7.0 - - - +
278B LEU 4.4 0.2 - - - -
279B VAL* 1.3 82.3 - - - +
281B GLU* 1.3 60.3 + - - +
282B GLU 3.4 7.8 + - - -
283B ASP* 3.0 16.6 + - - +
284B ARG* 2.7 74.8 + - - +
286B TYR* 3.2 21.3 + - + -
131C GLY 5.0 1.2 - - - +
----------------------------------------------------------
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