Contacts of the strand formed by residues 395 - 397 (chain A) in PDB entry 4K9P
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 TYR 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASP* 4.9 1.0 - - - +
237A ALA 3.3 22.3 + - - -
239A ARG* 3.3 29.0 - - - +
240A CYS* 3.6 20.9 + - + +
372A TYR* 3.2 9.9 - - + -
374A ASN* 2.9 41.2 + - + -
380A THR* 3.9 5.0 - - - +
383A MET* 4.2 17.5 - - + -
384A TRP* 3.4 42.0 + + - -
389A MET* 3.8 20.2 - - + -
393A GLY 3.6 1.4 - - - -
394A SER* 1.3 81.0 - - - +
396A TYR* 1.3 75.5 + - - +
397A PHE* 3.5 19.8 - - + +
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 6.2 0.7 - - - -
59A GLN* 3.6 30.1 - - + -
60A ALA* 3.5 23.7 - - + +
62A ARG* 5.5 0.2 + - - -
238A PRO 3.2 4.5 - - - -
239A ARG* 3.4 42.6 + - + -
371A ILE* 3.8 19.1 - - + -
372A TYR 3.0 7.3 + - - -
373A LEU* 3.3 27.7 - - + +
374A ASN* 2.8 27.9 + - - +
393A GLY* 3.7 32.6 + - - -
395A TYR* 1.3 84.9 - - - +
397A PHE* 1.3 61.0 + - - +
405A PHE* 4.3 12.1 - + + -
406A ALA* 5.7 0.2 - - - +
413A VAL* 4.2 17.7 - - + -
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Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 4.4 17.0 - - - -
237A ALA 3.4 29.2 - - - +
238A PRO* 2.9 19.3 + - - +
374A ASN* 3.4 39.5 - - - -
375A GLU* 5.2 1.3 - - - -
377A THR* 4.8 16.4 - - + -
380A THR* 4.2 12.8 - - + -
395A TYR* 3.5 12.3 - - + +
396A TYR* 1.3 75.1 - - - +
398A CYS* 1.3 105.2 + - - +
399A ALA* 3.0 4.5 + - - +
401A GLY* 4.9 6.3 - - - -
405A PHE* 4.0 8.1 - - - -
109C LEU* 5.1 11.2 - - + -
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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