Contacts of the strand formed by residues 427 - 433 (chain A) in PDB entry 4BL8
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 HIS 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A ARG* 3.9 4.0 - - - +
416A ASN* 2.9 58.8 + - + +
418A GLY* 4.4 0.9 - - - -
424A ILE* 4.2 1.6 - - + -
425A PRO 2.8 21.8 + - - -
426A GLU* 1.3 75.3 - - - +
428A TRP* 1.3 78.5 + - - +
429A HIS 4.5 0.2 - - - -
463A ARG* 3.1 36.1 + - + -
464A LEU 3.1 21.8 - - - +
466A ARG* 3.8 4.5 - - - +
573A TRP* 3.7 16.8 - + - -
575A ILE* 3.2 32.1 - - + +
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Residues in contact with TRP 428 (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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413A MET* 6.0 0.4 - - + -
414A TYR 3.5 15.5 - - - +
415A ARG* 3.6 50.9 - - + -
427A HIS* 1.3 75.2 - - - +
429A HIS* 1.3 59.4 + - - +
430A TYR* 3.7 20.8 - - + +
462A PHE 3.3 1.6 - - - +
463A ARG* 3.2 6.8 - - - -
464A LEU* 2.9 47.7 + - + +
466A ARG* 3.9 22.2 - - + +
470A GLU* 3.3 35.3 + - + -
471A SER 3.9 0.7 - - - -
472A ALA* 3.4 28.9 - - - -
473A PRO* 3.4 32.8 - - + -
474A PRO* 3.6 18.2 - - + +
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Residues in contact with HIS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 4.5 2.7 - - + -
385A TYR* 2.8 31.8 + - + +
412A SER 3.6 1.9 - - - +
413A MET* 3.7 0.4 - - - -
414A TYR* 2.9 35.1 + - + +
416A ASN* 4.7 5.2 - - + -
427A HIS* 4.2 0.8 + - + -
428A TRP* 1.3 73.2 - - - +
430A TYR* 1.3 67.6 + - - +
431A ILE* 3.7 18.3 - - + +
461A THR* 3.7 9.3 - - - -
462A PHE 3.3 13.7 - - - -
463A ARG* 3.3 37.8 + - + +
522A ASP* 2.8 24.1 + - - -
525A MET* 3.7 19.5 - - + -
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Residues in contact with TYR 430 (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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411A VAL* 4.2 7.4 - - + -
412A SER 3.3 5.6 - - - +
413A MET* 3.5 37.9 - - + -
428A TRP* 3.7 24.0 - - + +
429A HIS* 1.3 74.1 - - - +
431A ILE* 1.3 61.9 + - - +
461A THR* 2.9 30.5 - - - -
462A PHE* 2.9 28.7 + + - +
464A LEU* 3.9 12.1 - - + +
473A PRO* 3.9 3.3 - - + +
474A PRO* 2.8 46.1 + - - +
477A PRO* 3.4 33.4 - - + +
478A ALA 4.7 1.6 - - - -
481A MET* 3.8 21.8 - - + -
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Residues in contact with ILE 431 (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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377A ILE* 4.1 22.4 - - + -
381A CYS* 4.0 13.9 - - - -
385A TYR* 4.8 1.6 - - + -
411A VAL* 3.3 5.5 - - - -
412A SER* 2.9 33.8 + - - +
414A TYR* 3.8 26.7 - - + -
429A HIS* 3.7 28.9 - - + +
430A TYR* 1.3 78.0 - - - +
432A SER* 1.3 73.4 + - - +
433A PHE* 3.7 7.0 - - + -
460A LEU 3.6 6.3 - - - +
461A THR* 4.1 8.1 - - + -
481A MET* 4.9 0.4 - - - -
525A MET* 3.8 25.1 - - + -
537A PHE* 4.3 6.7 - - + -
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Residues in contact with SER 432 (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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408A LEU* 3.7 31.7 - - - +
410A TYR 3.7 4.7 - - - -
411A VAL* 4.4 2.2 - - - +
431A ILE* 1.3 75.7 - - - +
433A PHE* 1.3 73.0 + - - +
435A LEU* 4.5 0.3 - - - +
459A GLU* 2.8 39.0 + - - +
460A LEU* 2.8 40.5 + - - +
481A MET* 4.4 5.8 - - - -
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Residues in contact with PHE 433 (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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374A LEU* 4.3 13.5 - - + -
377A ILE* 3.2 45.5 - - + -
378A TYR* 3.4 34.5 - + - -
381A CYS* 4.6 3.1 - - - -
408A LEU* 3.5 4.5 - - - +
409A ASP* 2.9 28.4 + - - +
410A TYR* 3.0 41.1 + + + +
412A SER* 3.4 24.5 - - - -
431A ILE* 3.7 18.4 - - + -
432A SER* 1.3 79.8 - - - +
434A GLY* 1.3 58.2 + - - +
435A LEU 3.9 0.2 - - - -
438A LEU* 3.8 18.4 - - + -
459A GLU* 3.5 3.1 - - - -
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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