Contacts of the strand formed by residues 249 - 254 (chain F) in PDB entry 5MQF
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 TYR 249 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F LEU* 4.3 1.4 - - - +
244F SER* 3.1 32.7 + - - +
246F GLU* 5.8 0.2 - - - +
247F GLY* 3.3 7.9 + - - +
248F SER* 1.3 79.7 - - - +
250F LEU* 1.3 62.3 + - - +
261F VAL* 6.1 0.9 - - + -
262F TRP 3.3 16.4 - - - +
263F ASP* 3.8 12.8 - - + -
264F VAL 4.8 1.1 - - - +
274F VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F ILE* 5.6 7.9 - - + -
242F SER 3.4 13.7 - - - +
243F LEU* 3.9 11.9 - - + +
244F SER* 4.1 0.4 - - - +
249F TYR* 1.3 76.9 - - - +
251F LEU* 1.3 60.5 + - - +
252F SER* 3.9 2.5 + - - -
260F ARG 3.9 1.6 - - - +
261F VAL* 3.6 1.6 - - - -
262F TRP* 2.9 36.9 + - + +
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Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F SER* 2.8 50.7 + - - +
243F LEU* 4.2 2.1 - - - +
244F SER* 4.6 4.8 - - - +
250F LEU* 1.3 70.4 - - - +
252F SER* 1.3 58.6 + - - +
253F ASN 4.4 0.2 + - - -
260F ARG 3.7 6.3 - - - +
261F VAL* 4.2 12.3 - - + +
291F CYS* 4.8 6.2 - - + +
293F TRP* 5.8 7.9 - - + -
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Residues in contact with SER 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F ILE* 6.3 3.1 - - - -
240F GLY 3.7 11.9 - - - -
241F LEU* 4.2 8.1 - - - -
242F SER 4.1 5.2 - - - +
250F LEU* 3.9 2.6 + - - -
251F LEU* 1.3 74.3 - - - +
253F ASN* 1.3 62.5 + - - +
259F VAL* 3.8 2.8 - - - +
260F ARG* 2.9 43.3 + - - +
291F CYS* 5.8 1.3 - - - -
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Residues in contact with ASN 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F SER 4.9 0.3 - - - +
238F VAL* 3.6 2.9 - - - -
239F THR* 2.5 50.8 + - - +
240F GLY* 2.9 21.8 + - - +
241F LEU* 4.5 0.2 - - - +
251F LEU 4.4 0.4 + - - -
252F SER* 1.3 74.0 - - - +
254F ALA* 1.3 53.7 + - - +
258F THR 4.4 1.1 - - - -
259F VAL* 4.7 5.8 - - + +
282F HIS* 5.4 4.9 - - + -
289F LEU* 4.7 9.0 - - + +
291F CYS* 4.8 14.5 - - + +
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Residues in contact with ALA 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F SER* 4.1 17.0 - - - +
238F VAL 4.4 0.7 - - - -
239F THR* 3.4 6.2 - - - +
253F ASN* 1.3 73.0 - - - +
255F MET* 1.3 53.9 + - - +
256F ASP* 2.9 4.2 + - + +
257F ASN* 2.8 27.5 + - - -
258F THR* 2.5 44.0 + - - +
260F ARG* 5.1 8.7 - - + -
282F HIS* 5.3 1.2 - - - +
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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
------------------------------------------------------------
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