Contacts of the strand formed by residues 427 - 433 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B ARG* 3.9 4.0 - - - +
416B ASN* 2.9 60.1 + - + +
418B GLY* 4.4 0.2 - - - -
424B ILE* 4.2 17.4 - - + +
425B PRO* 2.8 27.6 + - + +
426B GLU* 1.3 76.1 - - - +
428B TRP* 1.3 77.6 + - - +
429B HIS* 4.6 0.7 - - + -
463B ARG* 3.1 46.0 + - + -
464B LEU 3.1 22.7 - - - +
465B LYS* 4.1 3.8 - - - -
466B ARG* 3.8 4.7 - - - +
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B MET* 6.0 0.4 - - + -
414B TYR 3.5 14.8 - - - +
415B ARG* 3.6 51.4 - - + -
427B HIS* 1.3 77.4 - - - +
429B HIS* 1.3 60.2 + - - +
430B TYR* 3.8 19.3 - - + -
462B PHE 3.3 1.2 - - - +
463B ARG* 3.2 6.9 - - - -
464B LEU* 2.9 47.7 + - + +
466B ARG* 3.9 22.0 - - + +
470B GLU* 3.2 35.0 + - + -
471B SER 4.0 0.2 - - - -
472B ALA* 3.5 27.8 - - - -
473B PRO* 3.4 33.4 - - + -
474B PRO* 3.6 18.9 - - + +
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Residues in contact with HIS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 4.5 3.4 - - + -
385B TYR* 2.8 32.0 + - + +
412B SER 3.6 2.6 - - - +
413B MET* 3.7 0.6 - - - -
414B TYR* 3.0 35.8 + - + +
416B ASN* 4.6 5.2 - - + -
427B HIS* 4.2 1.3 + - + -
428B TRP* 1.3 72.7 - - - +
430B TYR* 1.3 68.2 + - - +
431B ILE* 3.8 17.1 - - + +
461B THR* 3.6 8.0 - - - +
462B PHE 3.3 13.9 - - - -
463B ARG* 3.3 38.3 + - + +
522B ASP* 2.8 24.9 + - - -
525B MET* 3.8 19.5 - - + -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 4.2 7.0 - - + -
412B SER 3.3 5.6 - - - +
413B MET* 3.4 38.1 - - + -
428B TRP* 3.8 23.2 - - + +
429B HIS* 1.3 75.1 - - - +
431B ILE* 1.3 61.2 + - - +
461B THR* 2.9 31.6 - - - -
462B PHE* 2.9 28.6 + + + +
464B LEU* 3.9 11.5 - - + +
473B PRO* 3.9 2.5 - - + +
474B PRO* 2.8 46.6 + - - +
477B PRO* 3.3 33.1 - - + +
478B ALA 4.7 1.6 - - - -
481B MET* 3.8 21.8 - - + -
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Residues in contact with ILE 431 (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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377B ILE* 3.9 22.7 - - + -
381B CYS* 4.0 13.2 - - - -
385B TYR* 4.8 1.8 - - + -
411B VAL* 3.3 5.5 - - - -
412B SER* 2.9 32.9 + - - +
414B TYR* 3.8 27.6 - - + -
429B HIS* 3.8 24.5 - - + +
430B TYR* 1.3 80.8 - - - +
432B SER* 1.3 74.6 + - - +
433B PHE* 3.7 5.2 - - + -
460B LEU 3.6 5.8 - - - +
461B THR* 4.1 6.5 - - + -
481B MET* 4.9 0.2 - - - -
525B MET* 3.8 30.1 - - + -
537B PHE* 4.4 6.7 - - + -
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Residues in contact with SER 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 4.6 0.5 - - - +
408B LEU* 3.6 31.0 - - - +
410B TYR 3.7 4.7 - - - -
411B VAL* 4.4 2.2 - - - +
431B ILE* 1.3 77.3 - - - +
433B PHE* 1.3 72.7 + - - +
435B LEU* 4.6 0.3 - - - +
459B GLU* 2.9 27.2 + - - +
460B LEU* 2.8 45.0 + - - +
481B MET* 4.5 5.6 - - - +
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Residues in contact with PHE 433 (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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374B LEU* 4.3 11.9 - - + -
377B ILE* 3.0 46.9 - - + -
378B TYR* 3.3 38.4 - + - -
381B CYS* 4.5 7.6 - - - -
408B LEU* 3.5 5.1 - - - +
409B ASP* 2.9 27.5 + - - +
410B TYR* 3.0 40.4 + + + +
412B SER* 3.4 24.5 - - - -
431B ILE* 3.7 15.0 - - + -
432B SER* 1.3 78.8 - - - +
434B GLY* 1.3 57.9 + - - +
435B LEU 3.9 0.2 - - - -
438B LEU* 3.8 13.2 - - + -
459B GLU* 3.5 3.8 - - - -
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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