Contacts of the strand formed by residues 242 - 253 (chain F) in PDB entry 5YUS
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 SER 242 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240F ARG* 3.2 24.3 - - - +
241F LYS* 1.3 79.5 - - - +
243F VAL* 1.3 66.4 + - - +
335F HIS* 3.5 23.4 + - - -
336F VAL 3.3 13.9 - - - -
337F THR* 4.7 2.0 - - - -
338F LEU* 4.1 2.7 - - - +
843G G 3.6 16.3 - - - +
844G T 2.6 28.6 + - - +
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Residues in contact with VAL 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F ARG* 4.1 22.2 - - - +
242F SER* 1.3 82.8 - - - +
244F GLY* 1.3 61.5 + - - +
270F LEU* 3.9 22.8 - - + +
273F ARG* 3.9 33.7 - - + +
274F LEU* 4.7 13.5 - - + +
277F VAL* 6.1 0.7 - - + -
335F HIS* 3.6 4.2 - - - -
336F VAL* 2.8 37.0 + - + +
338F LEU* 4.1 23.1 - - + -
843G G 3.6 7.4 - - - +
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Residues in contact with GLY 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F VAL* 1.3 75.3 - - - +
245F VAL* 1.3 64.0 + - - -
246F GLU* 5.6 2.7 - - - -
270F LEU* 4.8 0.4 - - - -
273F ARG* 2.8 22.3 + - - -
334F LEU 3.4 10.3 - - - -
335F HIS* 4.2 11.0 - - - -
842G G 3.5 11.9 + - - +
843G G 2.8 14.7 + - - -
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Residues in contact with VAL 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F GLY* 1.3 80.3 - - - +
246F GLU* 1.3 61.0 + - - +
247F ARG* 4.8 5.6 - - - +
266F LEU* 3.7 35.8 - - + +
269F GLU* 4.2 12.3 - - + -
270F LEU* 3.7 38.6 - - + +
273F ARG* 3.5 21.1 - - - +
333F GLY* 3.3 0.7 - - - -
334F LEU* 2.7 40.0 + - + +
842G G 3.4 9.9 - - - +
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F GLY* 5.6 1.7 - - - -
245F VAL* 1.3 77.5 + - - +
247F ARG* 1.3 85.6 + - - +
266F LEU* 4.1 3.1 - - - -
289F LYS* 2.7 40.9 + - - +
331F LEU* 4.0 17.5 - - + +
332F VAL 3.3 6.7 - - - +
333F GLY* 3.5 16.6 - - - +
334F LEU 5.5 1.2 - - - +
840G A 5.7 0.2 - - - +
841G G 3.7 36.2 + - + +
842G G 2.8 18.6 + - - +
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Residues in contact with ARG 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ARG* 4.4 18.6 - - - +
245F VAL* 4.8 6.5 - - - +
246F GLU* 1.3 89.3 + - - +
248F THR* 1.3 64.6 + - - +
249F MET* 3.8 11.2 - - - +
262F ILE* 5.2 4.5 - - + -
266F LEU* 4.0 17.2 - - + +
331F LEU* 3.3 3.6 - - - -
332F VAL 2.9 32.3 + - - +
841G G 3.0 32.9 + - - -
842G G 3.7 18.6 + - - -
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Residues in contact with THR 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ARG* 4.6 20.3 + - - +
38F ARG* 4.3 11.0 - - + +
247F ARG* 1.3 73.6 - - - +
249F MET* 1.3 73.9 + - - +
250F ALA 4.0 0.9 + - - -
291F LYS* 5.1 0.7 + - - -
330F ARG* 3.1 43.4 + - - +
331F LEU* 3.5 15.4 - - - +
840G A 3.8 16.2 + - - +
841G G 2.7 33.2 + - - -
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Residues in contact with MET 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ARG 5.1 1.3 - - - -
38F ARG* 2.6 32.9 + - - +
247F ARG* 3.8 15.3 - - - +
248F THR* 1.3 77.7 - - - +
250F ALA* 1.3 58.1 + - - +
251F GLU 3.2 19.1 - - - +
253F ILE* 4.3 20.0 - - + -
262F ILE* 3.8 37.2 - - + -
329F VAL 3.9 9.9 - - - +
330F ARG 2.9 35.1 + - - +
331F LEU* 3.9 7.2 - - - +
332F VAL* 4.2 14.8 - - + -
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Residues in contact with ALA 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLU 3.4 24.7 - - - +
37F ARG* 4.5 18.3 + - - +
38F ARG* 3.2 24.1 + - - +
248F THR 4.0 0.8 + - - -
249F MET* 1.3 73.9 - - - +
251F GLU* 1.3 74.0 + - + +
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Residues in contact with GLU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F GLU 5.8 0.2 - - - +
38F ARG* 3.4 7.4 - - - +
249F MET* 3.2 19.3 - - - +
250F ALA* 1.3 89.1 - - + +
252F ASP* 1.3 71.1 + - - +
253F ILE* 4.1 3.5 - - - +
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Residues in contact with ASP 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ARG* 2.7 40.6 + - - +
251F GLU* 1.3 81.3 + - - +
253F ILE* 1.3 61.7 + - - +
254F HIS* 3.7 24.5 + - + -
258F GLU* 5.3 1.0 - - - +
293F ASP* 3.2 30.2 - - - +
328F GLY* 4.1 0.8 - - - -
329F VAL 3.3 20.0 - - - +
330F ARG* 3.4 10.3 + - - +
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Residues in contact with ILE 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F MET* 4.3 24.2 - - + -
251F GLU 4.1 7.4 - - - +
252F ASP* 1.3 77.9 - - - +
254F HIS* 1.3 60.7 + - - +
258F GLU* 3.5 31.9 - - + +
259F CYS* 3.6 41.7 - - + +
262F ILE* 4.8 4.0 - - + -
320F TRP* 3.9 12.2 - - + -
327F ARG 4.4 0.3 - - - +
328F GLY* 3.6 4.0 - - - -
329F VAL* 2.9 53.8 + - + +
332F VAL* 4.4 3.6 - - + -
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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