Contacts of the strand formed by residues 353 - 357 (chain B) in PDB entry 5FWP
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 ILE 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B LEU* 4.0 22.9 - - + -
351B ASN 4.4 0.2 - - - -
352B ASN* 1.3 76.2 - - + +
354B LYS* 1.3 65.5 + - - +
364B ASP* 4.0 8.5 - - - +
366B CYS* 3.1 20.9 - - - -
369B LEU* 3.6 25.5 - - + +
370B ILE* 3.8 30.3 - - + -
377B ILE* 3.2 31.0 - - + +
379B GLY* 3.3 26.9 - - - +
380B VAL 4.1 0.4 - - - +
381B VAL* 3.8 20.9 - - + -
408B ILE* 5.1 2.5 - - + -
412B CYS* 6.2 0.2 - - - -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS 5.3 4.2 + - - -
207B GLN* 5.1 5.5 - - - +
308B LEU* 6.0 5.8 - - + -
351B ASN* 4.0 21.5 - - - +
352B ASN 5.2 0.9 - - - +
353B ILE* 1.3 76.4 - - - +
355B LEU* 1.3 63.8 + - - +
356B TYR* 3.5 35.3 + - + +
361B PHE* 3.8 15.3 - - + -
363B MET 4.1 2.5 - - - -
364B ASP* 3.8 23.8 - - + -
378B ARG* 5.5 7.0 - - - +
379B GLY 3.1 11.1 + - - +
380B VAL* 3.6 2.6 - - + -
381B VAL* 2.9 26.3 + - - +
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE 4.9 0.7 - - - +
354B LYS* 1.3 72.1 - - - +
356B TYR* 1.3 63.1 + - - +
361B PHE* 3.6 4.3 - - - -
362B ILE* 3.0 26.3 + - + -
363B MET* 2.8 49.5 + - + +
364B ASP* 5.0 0.9 - - - -
365B SER 5.1 4.3 - - - +
369B LEU* 3.7 32.5 - - + -
381B VAL* 3.5 30.7 - - + +
386B LEU* 6.2 5.6 - - + -
395B LEU* 5.9 4.3 - - + -
401B LEU* 3.6 27.8 - - + -
404B ILE* 5.5 4.5 - - + -
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Residues in contact with TYR 356 (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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207B GLN* 3.0 34.8 + - - +
208B PHE* 3.5 28.1 - + - -
289B TRP* 5.5 0.4 - + - -
354B LYS* 3.5 38.1 + - + +
355B LEU* 1.3 77.3 - - - +
357B VAL* 1.3 60.5 + - - +
359B ARG* 3.7 13.2 - - - -
360B VAL 3.2 10.3 - - - +
361B PHE* 3.4 31.4 - + + -
380B VAL* 3.5 31.9 - - + +
381B VAL 2.8 8.9 + - - +
382B ASP* 3.6 15.3 - - - +
383B SER* 2.8 34.1 + - - -
386B LEU* 5.1 0.7 - - - +
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Residues in contact with VAL 357 (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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126B ILE* 5.1 3.2 - - + +
356B TYR* 1.3 73.6 - - - +
358B ARG* 1.3 85.1 + - + +
360B VAL* 2.9 25.4 + - - +
362B ILE* 3.6 22.9 - - + +
383B SER* 3.3 23.1 - - - +
384B GLU 4.4 7.4 - - - +
385B ASP* 4.9 0.7 - - - -
386B LEU* 3.9 28.0 - - + +
388B LEU* 4.1 21.3 - - + -
392B ARG* 5.7 2.7 - - - +
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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
------------------------------------------------------------
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