Contacts of the strand formed by residues 214 - 224 (chain F) in PDB entry 1RFU
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 VAL 214 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F ARG* 3.5 29.8 - - + +
207F THR 3.0 8.7 - - - +
208F ARG* 3.5 44.9 - - + +
212F GLY 3.9 2.0 - - - +
213F SER* 1.3 72.8 - - - +
215F VAL* 1.3 63.3 + - - +
216F THR* 3.5 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F GLN 4.1 0.3 - - - +
206F ARG* 3.7 1.2 - - - -
207F THR* 2.7 68.1 + - + +
209F ALA* 5.1 7.4 - - + +
213F SER* 3.9 3.0 - - - +
214F VAL* 1.3 73.0 - - - +
216F THR* 1.3 67.7 + - - +
217F GLN* 4.3 11.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F SER* 5.0 2.5 - - - +
205F GLN 3.5 8.9 + - - +
206F ARG* 3.9 29.3 + - + +
214F VAL* 3.5 8.4 + - - +
215F VAL* 1.3 80.5 + - - +
217F GLN* 1.3 71.9 + - - +
218F ARG* 4.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLY 4.5 0.9 - - - -
204F SER* 3.4 4.0 + - - -
205F GLN* 2.6 72.4 + - + +
207F THR* 5.3 2.3 + - - -
215F VAL* 4.3 11.5 + - + +
216F THR* 1.3 76.0 - - - +
218F ARG* 1.3 65.9 + - - +
219F ILE* 4.4 4.2 - - + +
250F ASN* 3.6 24.1 + - - +
251F ASN* 3.6 4.2 + - - +
252F LEU* 3.2 31.2 - - + +
253F LYS* 4.3 4.9 - - - +
311F VAL* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 3.3 46.1 + - + +
172F MET* 5.4 0.2 - - - +
173F ASP* 2.8 36.4 + - - -
203F GLY 3.6 2.2 - - - -
204F SER* 3.5 27.9 + - - +
216F THR* 4.0 17.0 + - + +
217F GLN* 1.3 77.2 - - - +
219F ILE* 1.3 67.4 + - - +
311F VAL* 3.6 9.6 - - - +
312F LEU* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 6.1 0.2 - - - +
201F ALA 3.9 0.5 - - - +
202F LEU* 3.3 4.2 - - - +
203F GLY 2.7 53.7 + - - +
217F GLN* 5.2 3.6 - - + +
218F ARG* 1.3 84.8 - - - +
220F ARG* 1.3 58.8 + - - +
221F MET* 4.2 9.0 - - + -
252F LEU* 3.5 10.3 - - + +
253F LYS* 3.5 38.6 - - + +
256F CYS* 3.4 36.3 - - + -
309F ALA* 4.4 8.1 - - + -
310F THR 3.3 10.5 - - - +
311F VAL* 4.5 10.5 - - + -
312F LEU* 4.3 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F GLN* 2.6 31.8 + - - +
193F PRO* 3.1 29.1 - - - +
200F MET* 3.0 34.8 - - + +
201F ALA 3.4 3.6 - - - -
202F LEU* 3.2 23.6 - - + -
219F ILE* 1.3 73.2 - - - +
221F MET* 1.3 72.2 + - - +
222F GLU* 3.6 13.2 + - - -
310F THR* 2.8 55.1 + - - +
312F LEU* 3.7 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 221 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F VAL* 5.8 3.6 - - + -
199F LEU 3.5 0.9 - - - +
200F MET* 3.0 9.1 - - - +
201F ALA* 2.7 64.0 + - + +
202F LEU 5.2 0.7 - - - -
203F GLY* 4.9 2.9 - - - +
219F ILE* 4.2 15.5 - - + +
220F ARG* 1.3 80.2 - - - +
222F GLU* 1.3 67.3 + - - +
223F MET* 3.9 6.1 - - + -
237F PHE* 6.3 0.7 - - + -
256F CYS* 3.9 34.3 - - + +
257F GLU 4.7 0.2 - - - -
260F VAL* 4.0 22.7 - - + -
307F VAL* 4.7 11.0 - - + -
308F GLN 4.7 3.4 - - - +
309F ALA* 3.5 30.5 - - + +
310F THR* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F SER* 4.2 10.7 - - - +
193F PRO* 3.5 36.1 - - + +
194F ARG* 2.9 53.9 + - - +
198F TYR* 4.4 13.6 - - + -
199F LEU 3.4 3.8 - - - +
200F MET* 4.7 1.1 - - + -
220F ARG* 3.6 15.5 + - - -
221F MET* 1.3 77.2 - - - +
223F MET* 1.3 62.3 + - - +
307F VAL* 4.3 15.4 - - - +
308F GLN 5.4 3.0 + - - -
310F THR* 5.5 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 223 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F THR 3.4 23.6 - - - +
187F SER* 3.9 4.9 - - - -
198F TYR* 3.1 11.2 - - - -
199F LEU* 2.6 71.7 + - + +
201F ALA* 4.0 13.0 - - + -
221F MET* 4.5 9.0 - - + +
222F GLU* 1.3 77.9 - - - +
224F HIS* 1.3 61.5 + - - +
225F LYS 3.6 0.2 - - - -
260F VAL* 3.6 26.7 - - + -
307F VAL* 4.9 7.4 - - + -
5402F ADP 3.1 38.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 224 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F ASP* 3.5 17.3 + - + -
198F TYR* 3.3 40.7 - + + -
223F MET* 1.3 72.1 - - - +
225F LYS* 1.3 70.2 + - - +
226F VAL* 3.7 5.7 + - - +
264F HIS* 4.6 27.1 - - + +
268F GLN* 4.9 9.9 - - - +
5402F ADP 3.3 15.0 - - - -
----------------------------------------------------------
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