Contacts of the strand formed by residues 423 - 428 (chain B) in PDB entry 3U1K
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 PHE 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LYS* 3.4 19.0 - - - +
420B ASP 3.5 9.7 + - - +
421B LYS* 4.0 8.5 - - + +
422B ASN* 1.3 78.8 - - - +
424B MET* 1.3 71.3 + - - +
425B LEU* 4.9 3.6 - - + -
455B GLU* 3.5 37.9 - - + +
458B LEU* 3.8 27.4 - - + -
459B TYR* 4.0 16.7 - + - -
462B ILE* 3.5 44.2 - - + -
470B ILE* 3.4 20.6 - - + -
472B VAL* 3.7 24.5 - - + -
495B LEU* 4.2 3.1 - - + -
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Residues in contact with MET 424 (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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419B LYS* 3.9 21.1 - - + -
423B PHE* 1.3 82.3 - - - +
425B LEU* 1.3 65.2 + - - +
426B HIS* 3.8 22.0 - - + +
455B GLU* 3.3 14.8 - - - +
469B THR* 5.5 2.2 - - + -
470B ILE 3.0 8.0 + - - +
471B ARG* 3.2 51.8 - - + +
472B VAL* 2.9 28.6 + - - +
473B THR* 5.5 0.7 - - - +
115C ASN* 5.0 3.1 - - - +
116C TYR* 3.6 31.0 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.9 2.0 - - + -
424B MET* 1.3 79.6 - - - +
426B HIS* 1.3 70.3 + - - +
427B TYR* 4.1 4.3 + - + -
451B GLY* 3.6 35.1 - - - +
454B ALA* 3.9 21.3 - - + -
455B GLU* 3.0 27.3 + - + +
458B LEU* 3.8 28.3 - - + -
472B VAL* 3.1 28.9 - - + +
474B SER* 3.9 16.4 - - - +
487B SER 4.6 3.1 - - - +
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Residues in contact with HIS 426 (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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424B MET* 3.8 19.5 - - + +
425B LEU* 1.3 75.3 - - - +
427B TYR* 1.3 70.7 + - - +
428B GLU* 2.7 33.4 + - + -
447B GLU* 5.5 1.8 - - - -
472B VAL 2.8 10.0 + - - +
473B THR* 3.4 8.2 - - + +
474B SER 2.8 26.9 + - - +
115C ASN* 3.0 47.5 + - - +
116C TYR* 4.0 14.0 + - + -
118C ARG 6.2 0.4 - - - -
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Residues in contact with TYR 427 (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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425B LEU* 4.1 5.9 + - + +
426B HIS* 1.3 83.2 + - - +
428B GLU* 1.3 69.2 + - - +
429B PHE* 3.2 29.8 - + + -
446B ARG* 5.8 0.4 - - + -
447B GLU* 3.4 37.9 + - + +
450B HIS* 2.9 41.1 + - + -
451B GLY* 3.4 23.7 - - - +
474B SER 3.3 6.7 - - - +
476B VAL* 3.7 16.2 - - + -
483B SER* 2.6 26.2 + - - -
484B SER* 4.1 5.8 - - - -
487B SER* 3.5 29.8 - - - -
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Residues in contact with GLU 428 (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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426B HIS* 2.7 30.8 + - + +
427B TYR* 1.3 81.9 - - - +
429B PHE* 1.3 60.1 + - - +
430B PRO* 3.5 11.0 - - + +
447B GLU* 3.5 17.9 - - - +
473B THR* 6.2 0.2 - - - -
474B SER 2.8 13.2 + - - +
475B GLU* 3.5 22.0 - - + +
476B VAL* 2.9 31.2 + - - +
103C ARG* 2.5 36.8 + - - -
115C ASN* 4.3 7.1 + - - +
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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