Contacts of the strand formed by residues 245 - 251 (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 SER 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ARG* 3.1 39.3 + - - +
194B LYS* 4.8 7.2 - - - +
195B ILE 3.4 6.3 - - - -
196B TYR* 3.4 22.5 - - - -
243B GLY 3.8 1.7 + - - -
244B GLU* 1.3 76.8 + - - +
246B ILE* 1.3 70.9 + - - +
13C THR* 3.9 25.2 - - - -
14C LYS 4.0 8.5 + - - -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ARG* 3.2 26.7 - - - +
139A GLY* 4.7 0.7 - - - -
141A GLN* 3.7 10.5 - - + +
194B LYS* 3.2 7.7 - - - +
195B ILE* 2.8 31.9 + - + +
197B PHE* 3.8 26.9 - - + -
207B MSE 4.0 17.9 - - + -
235B ILE* 3.3 31.0 - - + +
236B MSE 3.7 22.4 - - + -
244B GLU* 4.5 2.9 - - + -
245B SER* 1.3 81.2 - - - +
247B PRO* 1.3 73.3 - - + +
248B ILE* 4.4 1.2 - - - +
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Residues in contact with PRO 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU 3.9 15.5 - - - +
136A MET* 3.8 40.7 - - + +
138A ARG* 3.7 31.4 - - + +
139A GLY* 4.3 6.9 - - - +
193B GLY 3.8 5.4 - - - +
194B LYS* 4.6 3.4 - - + -
235B ILE* 4.6 8.3 - - - +
246B ILE* 1.3 94.7 - - + +
248B ILE* 1.3 62.4 + - - +
249B ARG 4.3 0.5 + - - -
10C ARG* 4.9 10.3 - - + -
11C LEU 6.2 0.2 - - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A MET* 5.0 0.8 - - - +
180B TYR* 3.9 22.2 - - + -
191B ILE* 3.9 15.0 - - + +
192B VAL* 3.6 7.1 - - - +
193B GLY 2.9 33.1 + - - +
194B LYS* 4.1 12.3 - - - +
195B ILE* 3.8 27.6 - - + -
209B LEU* 3.7 26.7 - - + -
235B ILE* 3.9 31.6 - - + -
246B ILE 4.4 2.0 - - - +
247B PRO* 1.3 77.3 - - - +
249B ARG* 1.3 66.7 + - - +
250B LEU* 4.3 6.3 - - + +
9C ARG 5.1 0.9 - - - +
10C ARG* 5.7 1.2 - - - -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 4.6 0.4 - - - -
99A GLN* 3.0 32.4 + - - +
111A LEU* 4.8 1.8 - - - +
132A ASP* 2.6 41.6 + - - -
136A MET* 3.6 27.5 - - + +
190B VAL* 3.7 18.8 - - + -
191B ILE 3.3 4.0 - - - +
192B VAL* 4.7 4.3 - - + -
233B TYR* 3.3 25.0 + - - -
247B PRO 4.2 0.8 + - - -
248B ILE* 1.3 75.9 - - - +
250B LEU* 1.3 58.3 + - - +
251B PHE* 3.5 32.7 + - + -
7C ASP* 3.5 18.2 + - - -
8C THR 3.5 6.7 - - - -
9C ARG* 3.1 30.5 + - - +
10C ARG* 3.6 6.1 - - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B VAL* 4.1 0.9 - - - -
191B ILE* 2.9 53.6 + - + +
209B LEU* 3.7 29.4 - - + +
211B LEU* 5.2 9.4 - - + +
231B ALA* 5.3 2.0 - - + -
233B TYR* 3.7 41.3 - - + -
248B ILE* 4.5 6.3 - - + -
249B ARG* 1.3 73.0 - - - +
251B PHE* 1.3 63.2 + - - +
252B LEU* 3.4 9.1 + - + -
255B TYR* 3.6 32.5 - - + +
274B LEU* 4.4 8.1 - - + -
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.7 42.0 - - + +
99A GLN* 3.8 31.2 - - + -
100A TYR* 3.6 25.3 - + + +
189B ASP 4.0 2.5 - - - -
190B VAL* 3.4 30.3 - - + -
233B TYR* 5.6 0.8 + - - -
249B ARG* 3.5 40.6 - - + -
250B LEU* 1.3 71.6 - - - +
252B LEU* 1.3 63.7 + - - +
253B ALA* 3.4 2.9 + - + +
254B GLY* 3.5 8.5 + - - -
255B TYR* 3.6 16.6 - - - -
7C ASP* 4.2 19.3 - - + -
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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