Contacts of the strand formed by residues 514 - 519 (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 LYS 514 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A HIS* 4.8 2.2 - - - -
510A LEU* 3.4 5.7 - - - +
511A SER* 2.8 51.2 + - - +
512A HIS* 3.4 2.7 - - + -
513A ASP* 1.3 109.6 + - - +
515A ILE* 1.3 68.2 + - - +
516A ILE* 3.9 8.9 + - + +
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Residues in contact with ILE 515 (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* 3.8 21.5 - - + -
415A PHE* 3.6 20.5 + - + +
416A HIS* 3.6 31.4 - - - +
417A ALA* 4.0 9.2 - - + -
466A LEU* 4.9 1.8 - - + -
508A LEU* 3.6 31.4 - - + -
509A CYS 3.6 7.6 - - - +
510A LEU* 4.4 1.1 - - + -
513A ASP 4.0 0.2 + - - -
514A LYS* 1.3 76.3 - - - +
516A ILE* 1.3 63.8 + - - +
536A TRP* 3.9 21.8 - - + -
945D TRP* 3.6 20.0 - - + -
947D PRO* 4.0 1.8 - - + -
948D PRO* 3.3 23.2 - - - +
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Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TYR 3.8 0.3 - - - +
508A LEU* 3.8 6.1 - - - +
509A CYS* 2.8 61.1 + - + +
511A SER* 4.2 25.6 - - - +
514A LYS* 4.7 13.7 - - + +
515A ILE* 1.3 79.9 - - - +
517A GLN* 1.3 65.2 + - - +
947D PRO* 4.0 3.8 - - - -
948D PRO* 3.6 18.8 - - + +
950D GLU* 3.8 46.9 - - + +
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Residues in contact with GLN 517 (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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500A MET* 3.6 35.2 - - - +
502A ASP* 5.5 1.2 - - - +
506A VAL* 3.5 17.3 - - + +
507A TYR 3.6 4.9 - - - +
508A LEU* 5.9 1.3 - - - -
516A ILE* 1.3 73.9 - - - +
518A HIS* 1.3 60.1 + - - +
946D MET* 4.0 18.6 - - - +
947D PRO* 2.8 38.9 + - + +
948D PRO 3.0 9.9 + - - +
949D MET* 3.8 31.3 - - + +
950D GLU* 3.3 26.3 + - - +
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Residues in contact with HIS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU 3.5 0.9 - - - +
506A VAL* 3.1 4.6 - - - -
507A TYR* 2.6 40.2 + - + +
509A CYS* 3.3 28.7 - - + -
516A ILE* 4.7 0.9 - - + -
517A GLN* 1.3 74.2 - - - +
519A GLN* 1.3 82.1 + - - +
520A ALA* 3.8 2.8 + - - -
529A GLN 4.6 0.6 + - - -
530A ILE* 3.9 13.4 - - + -
531A ASN* 3.2 47.8 + - + -
534A ALA* 4.1 16.2 - - + -
950D GLU* 2.4 31.1 + - - +
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Residues in contact with GLN 519 (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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503A ASN* 4.9 5.2 + - - +
505A LEU* 3.2 21.0 - - + +
506A VAL* 4.3 15.4 - - + +
517A GLN 4.2 0.8 + - - -
518A HIS* 1.3 89.7 + - - +
520A ALA* 1.3 72.0 + - - +
521A THR* 5.3 3.2 - - + +
949D MET* 5.4 8.6 - - + +
950D GLU* 3.9 12.2 + - - +
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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