Contacts of the strand formed by residues 238 - 242 (chain H) in PDB entry 6NR8
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 LYS 238 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H ASP 5.1 2.5 - - - +
237H ALA* 1.3 73.3 - - - +
239H ILE* 1.3 61.5 + - - +
240H ALA 3.6 0.2 + - - -
286H THR 4.4 10.9 + - - -
287H GLY* 4.1 21.2 + - - +
288H ALA* 3.3 33.0 - - + +
289H ASN 3.4 5.9 + - - -
290H VAL* 3.5 7.1 - - - +
341H LEU* 3.8 32.1 - - + +
344H MET* 6.0 0.7 - - - +
345H GLY* 3.7 21.5 - - - +
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Residues in contact with ILE 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H ALA 3.6 13.9 - - - +
238H LYS* 1.3 72.9 - - - +
240H ALA* 1.3 60.7 + - - +
241H VAL* 3.7 23.5 + - + +
288H ALA* 5.1 0.2 - - - -
290H VAL* 3.7 15.9 - - + -
292H VAL* 4.4 5.4 - - + -
324H LEU* 4.8 0.2 - - + -
328H VAL* 3.7 28.7 - - + +
341H LEU* 5.1 0.4 - - - -
343H GLU* 3.3 22.0 - - - +
345H GLY* 3.3 6.3 - - - -
346H HIS 3.5 25.4 - - - +
347H CYS* 3.7 21.8 - - + +
350H VAL* 5.1 4.3 - - + -
363H PHE* 4.1 31.6 - - + -
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Residues in contact with ALA 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H LYS 3.6 0.6 + - - -
239H ILE* 1.3 71.6 - - - +
241H VAL* 1.3 56.5 + - - +
242H TYR* 3.5 33.6 + - + +
283H ILE* 4.7 3.4 - - + -
288H ALA* 4.1 16.2 - - + -
290H VAL 3.1 18.1 + - - +
291H VAL* 3.5 3.8 - - - +
292H VAL* 2.7 35.0 + - - +
341H LEU* 5.1 0.2 - - + -
343H GLU* 4.1 10.3 - - - +
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Residues in contact with VAL 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H ILE* 3.7 21.6 + - + -
240H ALA* 1.3 75.6 - - - +
242H TYR* 1.3 65.2 + - - +
292H VAL* 3.7 4.3 - - + -
321H LEU* 3.7 33.7 - - + +
324H LEU* 3.6 41.3 - - + +
325H CYS* 4.4 6.1 - - - -
328H VAL* 5.3 0.7 - - + -
330H ALA* 3.7 20.6 - - + -
331H THR 2.9 25.6 - - - +
332H ALA* 3.7 3.6 - - + -
343H GLU* 4.0 5.9 - - - +
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Residues in contact with TYR 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H ALA* 3.5 23.4 - - + +
241H VAL* 1.3 83.5 - - - +
243H SER* 1.3 60.3 + - - +
245H PRO* 3.7 26.0 - - + -
283H ILE* 3.6 27.3 - - + +
291H VAL* 3.6 19.5 - - + -
292H VAL 2.9 22.8 + - - +
294H GLY 3.2 14.7 + - - -
321H LEU* 3.6 9.9 - - - +
331H THR 4.6 1.3 - - - -
332H ALA* 4.9 0.4 - - - -
333H LEU* 3.8 11.0 - - + +
335H ARG* 3.8 20.9 - - + -
339H PRO* 3.3 25.2 - - + +
340H VAL 3.6 14.4 + - - -
341H LEU* 5.2 0.2 - - - -
343H GLU* 3.1 28.0 + - - -
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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
------------------------------------------------------------
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