Contacts of the strand formed by residues 363 - 367 (chain A) in PDB entry 5F6K
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 363 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A MET* 5.0 3.0 - - - +
346A TRP 3.3 14.4 - - - -
347A SER* 3.9 6.5 - - - -
351A GLY* 5.4 0.7 - - - -
356A PRO 4.8 0.3 + - - -
357A LEU* 3.5 20.8 - - - +
358A GLY* 2.6 37.6 + - - -
359A TYR 3.9 0.2 + - - -
360A ASP* 3.7 13.2 + - - +
361A LYS 3.3 2.0 + - - -
362A PHE* 1.3 81.0 - - - +
364A TYR* 1.3 68.5 + - - +
375A HIS* 2.9 20.4 + - - -
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Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLY* 3.4 3.8 - - - -
346A TRP* 3.0 30.5 + - - +
357A LEU* 3.9 1.5 - - - +
361A LYS 4.6 3.8 - - - -
363A SER* 1.3 78.0 - - - +
365A SER* 1.3 61.5 + - - +
374A PHE 3.5 3.6 - - - -
375A HIS* 3.3 40.7 + + - -
447A ILE* 3.7 27.6 - - + -
449A PHE* 4.6 2.8 - - - -
460A TYR* 3.5 36.3 - + + -
463A ILE* 3.2 21.1 - - + +
464A PHE* 3.2 37.1 + - - -
468A TYR* 3.5 31.0 - + - -
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 3.8 11.8 - - - +
344A LEU 3.3 6.5 - - - -
357A LEU* 2.7 47.7 + - - -
358A GLY* 4.4 0.2 - - - -
364A TYR* 1.3 75.4 - - - +
366A TRP* 1.3 61.1 + - - +
373A LYS* 3.3 9.0 - - - +
374A PHE* 2.9 45.8 + - - +
449A PHE* 4.1 6.1 - - - -
460A TYR* 4.4 1.6 + - - -
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 3.3 2.0 - - - -
344A LEU 2.7 26.8 + - - +
365A SER* 1.3 75.8 - - - +
367A ARG* 1.3 57.1 + - - +
371A GLY* 3.5 15.8 + - - -
372A THR 3.6 13.5 - - - -
373A LYS* 4.8 0.7 - - - -
382A TYR* 3.5 15.8 - + - -
383A SER* 3.1 30.0 + - - -
384A SER 4.4 4.0 - - - -
386A TYR* 2.7 47.4 + + - -
392A LEU* 3.7 26.2 - - + -
393A GLY 4.7 0.7 - - - -
394A PHE* 4.3 8.7 - + + -
449A PHE* 3.5 37.5 - + + -
450A TYR 3.5 24.9 - - - -
451A LYS* 4.0 14.6 - - + -
456A GLN* 4.0 14.4 - - + -
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Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 4.3 6.1 - - - +
341A ALA* 5.2 1.3 - - + -
342A ALA 3.3 10.3 - - - +
343A ARG* 3.7 43.2 - - + +
365A SER 4.2 0.4 - - - -
366A TRP* 1.3 72.3 - - - +
368A SER* 1.3 67.7 + - - +
369A LYS* 2.8 45.4 + - + +
370A LYS* 4.0 18.0 - - - +
371A GLY* 3.3 21.7 + - - -
372A THR* 2.7 45.1 + - - +
374A PHE* 3.7 18.1 - - + -
386A TYR* 3.6 5.9 - - - -
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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