Contacts of the strand formed by residues 358 - 362 (chain B) in PDB entry 5F2R
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 GLU 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.8 35.3 - - + +
214B ARG* 2.9 32.4 + - - -
218B LYS* 5.0 13.4 - - + +
219B ASN 3.1 3.0 + - - -
220B ILE* 3.3 18.1 - - + +
221B LEU 2.9 26.2 + - - -
237B ILE* 6.3 0.2 - - + -
356B ILE* 3.3 4.5 - - - +
357B ASP* 1.3 97.5 - - + +
359B ILE* 1.3 64.0 + - - +
360B VAL* 4.1 0.7 - - + -
382B LYS* 4.4 2.7 + - - +
385B SER* 4.5 7.1 + - - +
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.4 12.6 - - + +
223B PHE* 5.4 0.7 - - + -
356B ILE* 4.0 13.2 - - + -
358B GLU* 1.3 78.5 + - - +
360B VAL* 1.3 66.9 + - - +
361B LEU* 4.8 1.8 - - + -
375B VAL* 3.9 25.4 - - + -
376B LYS* 5.9 0.2 - - - -
379B PHE* 3.3 46.2 - - + -
382B LYS* 4.0 36.2 - - + +
383B GLU 4.9 1.0 + - - +
384B PRO* 3.2 17.9 - - + +
385B SER* 2.9 28.5 + - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA* 4.0 27.6 - - + +
206B ALA* 4.8 4.5 - - - -
209B TYR* 4.0 21.5 - - + -
211B LEU* 3.6 30.3 - - + -
220B ILE* 4.0 13.0 - - + -
221B LEU 3.0 7.1 + - - +
222B VAL* 3.4 13.5 - - + +
223B PHE* 2.9 28.6 + - - +
359B ILE* 1.3 76.9 - - - +
361B LEU* 1.3 68.0 + - - +
362B VAL* 3.8 7.4 + - + -
385B SER* 4.3 9.9 - - - +
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Residues in contact with LEU 361 (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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209B TYR* 5.0 6.1 + - - -
223B PHE* 3.6 17.0 - - + -
359B ILE* 4.2 1.9 + - + -
360B VAL* 1.3 77.7 - - - +
362B VAL* 1.3 63.6 + - - +
366B THR* 3.9 20.9 - - + +
371B ILE* 5.6 0.2 - - + -
372B GLN* 3.8 33.9 - - + +
375B VAL* 3.9 37.9 - - + -
384B PRO* 3.9 30.0 - - + +
385B SER 5.1 7.9 + - - +
386B ARG* 6.2 1.1 - - - +
390B PRO* 3.6 15.3 - - + +
393B ALA* 5.0 3.1 - - - +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 6.1 0.9 - - + -
202B PRO* 5.4 0.4 - - + -
205B ALA* 3.5 23.1 - - + -
222B VAL* 3.5 26.2 - - + -
223B PHE 2.9 6.3 + - - -
224B ASP* 3.2 29.7 - - + +
225B LEU 3.0 21.7 + - - -
360B VAL* 4.0 2.9 - - + -
361B LEU* 1.3 79.3 - - - +
363B GLY* 1.3 66.3 + - - +
366B THR* 3.1 10.5 - - - +
390B PRO* 3.8 9.6 - - - +
393B ALA* 5.0 2.0 - - + -
394B VAL* 3.7 27.1 - - + +
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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