Contacts of the strand formed by residues 405 - 411 (chain A) in PDB entry 3BRF
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 THR 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A CYS* 4.0 0.7 - - - -
395A PHE* 3.9 14.1 - - + -
396A ASN 3.4 15.5 - - - +
397A ARG* 3.2 34.9 + - - +
398A LEU* 5.1 0.9 - - - -
403A VAL 4.4 2.8 + - - -
404A SER* 1.3 79.4 + - - +
406A ARG* 1.3 72.5 + - - +
407A TYR* 3.7 40.7 - - + +
419A SER* 4.2 9.9 - - - +
7B T 4.9 2.9 + - - -
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Residues in contact with ARG 406 (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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395A PHE* 3.3 5.5 - - - +
396A ASN* 2.9 33.8 + - - +
398A LEU* 5.5 8.1 - - + +
404A SER* 5.2 10.1 + - - -
405A THR* 1.3 79.7 - - - +
407A TYR* 1.3 64.4 + - - +
417A ALA* 2.8 33.9 + - + -
418A SER 3.3 9.2 - - - +
419A SER* 3.8 23.0 - - - +
510A LEU* 3.7 24.2 - - + -
512A HIS* 3.2 42.8 + - - +
513A ASP* 3.4 14.5 - - - +
536A TRP* 4.8 0.8 - - - -
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Residues in contact with TYR 407 (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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237A CYS* 3.8 15.8 - - - -
238A PRO* 4.0 12.8 - - + -
239A PRO* 3.4 38.4 - - + +
328A LYS* 5.6 3.2 - - + +
394A LEU 3.6 4.3 - - - +
395A PHE* 3.4 15.9 - - + -
405A THR* 3.7 36.7 - - + +
406A ARG* 1.3 74.1 - - - +
408A LEU* 1.3 64.7 + - - +
409A HIS* 3.3 2.1 + - - +
417A ALA* 3.2 6.8 - - - -
418A SER 2.8 47.5 + - - -
419A SER 4.0 19.5 - - - -
420A THR* 4.5 3.1 - - - -
421A LYS 3.5 22.2 - - - +
422A TRP* 3.5 15.9 - - + -
536A TRP* 4.9 0.7 - - - -
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Residues in contact with LEU 408 (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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394A LEU* 2.8 47.4 + - + +
407A TYR* 1.3 71.0 - - - +
409A HIS* 1.3 53.0 + - - +
415A PHE* 4.0 14.4 - - + -
416A HIS 3.7 14.8 - - - +
417A ALA* 4.8 0.2 - - - +
422A TRP* 3.7 1.4 - - - +
423A GLY 2.7 30.0 + - - +
425A PHE* 3.3 33.3 - - + -
457A LEU* 4.9 1.1 - - + -
466A LEU* 4.1 22.9 - - + -
508A LEU* 5.0 8.3 - - + -
515A ILE* 3.8 24.9 - - + -
536A TRP* 4.2 11.8 - - + -
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Residues in contact with HIS 409 (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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243A TYR* 4.8 3.4 + - - -
407A TYR 3.8 4.5 - - - +
408A LEU* 1.3 79.4 - - - +
410A VAL* 1.3 78.4 + - - +
411A GLU* 4.1 10.8 - - + -
415A PHE* 4.5 1.6 - - - -
416A HIS* 2.7 73.8 + + + +
418A SER* 3.9 2.1 - - - -
421A LYS* 3.7 53.6 - - + +
422A TRP 4.1 6.3 - - - -
423A GLY* 4.0 15.3 - - - +
425A PHE* 4.0 4.7 - - - -
459A ASP* 6.0 0.4 - - - -
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Residues in contact with VAL 410 (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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409A HIS* 1.3 88.7 + - - +
411A GLU* 1.3 65.5 + - - +
413A ASN 4.7 2.9 - - - +
414A ALA 3.2 20.2 - - - +
415A PHE* 3.9 17.0 - - + -
425A PHE* 3.6 14.7 - - + -
459A ASP* 3.3 35.7 + - + +
462A THR* 3.3 36.0 - - + +
464A ILE* 4.4 9.0 - - + -
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Residues in contact with GLU 411 (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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409A HIS* 3.9 9.8 + - + -
410A VAL* 1.3 74.9 - - - +
412A GLY* 1.3 70.4 + - - +
414A ALA* 2.9 18.4 + - - +
416A HIS* 3.0 46.8 + - + +
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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