Contacts of the strand formed by residues 506 - 511 (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 VAL 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A GLN* 3.2 4.3 - - - -
500A MET* 2.7 48.8 + - + -
503A ASN* 3.0 36.3 + - + +
504A GLU 3.4 0.2 - - - -
505A LEU* 1.3 81.8 - - - +
507A TYR* 1.3 61.4 + - - +
517A GLN* 3.5 36.6 - - + +
518A HIS 3.1 7.2 - - - +
519A GLN* 4.4 19.1 - - + +
949D MET* 4.8 11.2 - - + -
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Residues in contact with TYR 507 (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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472A ARG* 4.6 1.3 - - + -
479A VAL* 3.4 32.3 - - + +
481A LEU* 4.2 0.3 - - - +
497A ALA* 3.8 15.7 - - + -
498A PHE 3.2 16.8 - - - +
499A GLN* 3.1 36.6 + - + -
500A MET* 5.4 1.8 - - - -
504A GLU 3.6 13.0 - - - -
505A LEU 3.5 15.3 - - - -
506A VAL* 1.3 75.6 - - - +
508A LEU* 1.3 70.2 + - - +
509A CYS 3.4 0.5 + - - -
517A GLN* 3.6 4.6 - - - -
518A HIS* 2.6 41.9 + + + +
520A ALA* 3.9 8.7 - - + -
528A HIS* 2.8 32.0 - + - -
530A ILE* 3.9 15.0 - - + -
534A ALA* 4.3 13.9 - - + -
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Residues in contact with LEU 508 (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* 6.3 1.8 - - + -
408A LEU* 5.0 5.8 - - + -
457A LEU* 6.4 0.7 - - + -
466A LEU* 4.3 24.0 - - + -
467A PRO* 5.8 1.3 - - + -
469A LEU* 4.3 22.0 - - + +
498A PHE* 2.9 32.3 + - + +
500A MET* 5.6 3.4 - - - +
507A TYR* 1.3 71.4 - - - +
509A CYS* 1.3 61.0 + - - +
515A ILE* 3.6 30.7 - - + -
516A ILE 3.8 2.5 - - - +
517A GLN* 5.2 1.3 - - - +
534A ALA* 3.6 12.1 - - - +
536A TRP* 3.3 48.6 + - + +
947D PRO* 4.1 19.1 - - + -
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Residues in contact with CYS 509 (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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507A TYR 3.6 1.1 - - - +
508A LEU* 1.3 78.4 - - - +
510A LEU* 1.3 77.8 + - - +
515A ILE* 3.6 6.2 - - - +
516A ILE* 2.8 44.3 + - + +
518A HIS* 3.3 40.2 - - + -
531A ASN* 4.5 10.1 - - - -
533A GLY* 3.5 25.4 - - - +
534A ALA* 3.7 4.9 - - + -
536A TRP* 4.4 5.2 - - - +
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Residues in contact with LEU 510 (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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396A ASN* 3.7 38.1 - - + +
398A LEU* 5.8 5.4 - - + -
406A ARG* 3.7 21.1 - - + -
417A ALA* 3.6 24.2 - - + -
509A CYS* 1.3 87.0 - - - +
511A SER* 1.3 61.7 + - - +
512A HIS* 3.5 18.2 - - - +
514A LYS 3.4 6.5 - - - +
515A ILE* 4.4 1.6 - - + -
516A ILE* 4.4 0.8 - - - +
533A GLY* 3.0 22.5 + - - +
536A TRP* 4.2 12.8 - - + -
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Residues in contact with SER 511 (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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510A LEU* 1.3 73.7 - - - +
512A HIS* 1.3 63.8 + - - +
514A LYS* 2.8 52.1 + - - +
516A ILE* 4.2 22.6 - - - +
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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