Contacts of the strand formed by residues 336 - 341 (chain H) in PDB entry 5FHX
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 THR 336 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249H GLY* 3.5 10.3 - - - -
250H PRO* 3.8 34.8 - - + +
329H VAL* 4.7 0.4 - - + -
330H ASN* 3.1 5.1 - - - +
331H HIS* 2.8 34.9 + - - +
334H SER* 2.7 29.7 + - - -
335H ASN* 1.4 74.8 - - - +
337H LYS* 1.3 58.9 + - - +
338H VAL* 4.3 18.4 - - + -
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Residues in contact with LYS 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H ASN* 6.1 3.8 - - - -
329H VAL 3.4 6.3 - - - +
330H ASN* 3.4 31.6 - - + +
335H ASN 3.5 7.1 + - - +
336H THR* 1.3 76.0 - - - +
338H VAL* 1.4 66.4 + - - +
339H ASP* 5.1 10.5 - - - +
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Residues in contact with VAL 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H PRO* 5.1 4.5 - - + +
252H VAL* 4.3 28.1 - - + +
327H CYS 3.9 0.9 - - - +
329H VAL* 2.9 36.6 + - + +
336H THR* 4.5 17.9 - - + -
337H LYS* 1.4 79.0 - - - +
339H ASP* 1.3 65.5 + - - +
340H LYS* 4.3 0.6 + - + -
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Residues in contact with ASP 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H SER* 4.8 2.9 + - - -
326H ILE* 3.8 15.9 - - + +
327H CYS 3.2 4.3 - - - -
328H ASN* 3.2 36.9 + - - +
329H VAL 4.3 1.0 + - - +
337H LYS* 5.1 9.3 - - - -
338H VAL* 1.3 81.7 + - - +
340H LYS* 1.3 63.3 + - - +
341H LYS 4.2 0.3 + - - -
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Residues in contact with LYS 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H VAL* 4.0 34.7 - - + +
254H PRO* 4.3 25.1 - - + -
271H CYS* 4.1 8.5 - - - -
326H ILE* 3.3 3.8 - - - -
327H CYS* 2.8 37.5 + - - -
338H VAL* 4.2 1.7 + - + -
339H ASP* 1.3 74.9 - - - +
341H LYS* 1.3 71.7 + - - +
342H VAL* 3.8 4.2 + - - +
246L GLU* 2.8 36.8 + - - -
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Residues in contact with LYS 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H PRO* 4.6 5.5 - - - +
324H THR* 4.7 11.5 - - - +
325H TYR 3.4 15.3 - - - +
326H ILE* 3.8 20.4 - - + +
339H ASP 4.2 1.4 + - - -
340H LYS* 1.3 87.0 - - - +
342H VAL* 1.3 59.0 + - - +
343H GLU* 3.4 37.0 + - + +
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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