Contacts of the helix formed by residues 515 - 529 (chain B) in PDB entry 3BYH
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 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502B LEU* 1.8 39.6 + - - +
503B LYS 3.6 0.2 - - - +
506B ARG* 3.7 24.7 - - + +
513B GLU 3.8 3.8 - - - +
514B MET* 1.3 78.7 - - - +
516B ASP* 1.3 55.5 + - - +
517B ALA* 3.6 10.1 + - - +
518B ASP* 2.9 42.9 + - - +
519B ILE* 3.5 3.5 + - - +
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Residues in contact with ASP 516 (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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4A ASP* 3.2 25.9 - - + +
498B MET 3.5 8.5 - - - +
499B LEU* 3.2 20.7 - - - +
502B LEU* 1.1 105.8 - - + +
515B THR* 1.3 68.8 - - - +
517B ALA* 1.3 63.1 + - - +
519B ILE* 3.1 5.2 + - - +
520B LEU 3.0 17.5 + - - -
539B PHE* 3.6 12.3 - - + -
610B LEU* 3.4 21.3 - - + +
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Residues in contact with ALA 517 (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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515B THR* 3.1 10.2 - - - +
516B ASP* 1.3 80.5 - - - +
518B ASP* 1.3 58.5 + - - +
520B LEU* 3.2 9.0 + - - +
521B SER* 2.9 30.4 + - - -
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Residues in contact with ASP 518 (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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505B LEU* 4.0 23.9 - - + +
506B ARG* 4.5 1.2 - - - -
513B GLU 3.9 5.0 - - - +
514B MET* 3.8 8.2 - - + -
515B THR* 2.9 36.8 + - - +
517B ALA* 1.3 76.9 - - - +
519B ILE* 1.3 58.3 + - - +
521B SER* 3.5 7.4 + - - -
522B TRP* 3.0 27.5 + - - +
525B ARG* 5.1 1.7 + - - -
617B MET* 4.2 0.3 - - - +
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Residues in contact with ILE 519 (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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498B MET* 4.0 2.2 - - + -
501B LEU 4.9 1.8 - - - -
502B LEU* 2.2 48.9 - - + +
505B LEU* 3.3 20.2 - - + -
516B ASP 3.1 6.5 + - - +
518B ASP* 1.3 75.7 - - - +
520B LEU* 1.3 64.0 + - - +
522B TRP 3.3 0.7 + - - -
523B ALA* 3.1 22.9 + - - +
539B PHE* 3.7 15.7 - - + -
610B LEU* 3.6 15.5 - - + +
613B THR* 3.8 4.5 - - + -
614B ALA* 3.6 33.7 - - + +
617B MET* 3.2 23.3 - - + +
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Residues in contact with LEU 520 (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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516B ASP 3.0 12.1 + - - +
517B ALA* 3.5 13.5 - - - +
519B ILE* 1.3 78.5 - - - +
521B SER* 1.3 64.8 + - - +
523B ALA* 3.5 2.5 + - - +
524B ASN* 3.0 48.6 + - - +
536B ILE* 3.6 39.9 - - + +
537B GLU 4.5 6.3 - - - +
538B SER* 3.8 24.9 - - - -
539B PHE* 3.5 19.4 - - + -
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Residues in contact with SER 521 (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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517B ALA 2.9 17.2 + - - -
518B ASP* 3.7 8.3 - - - -
520B LEU* 1.3 82.2 - - - +
522B TRP* 1.3 57.3 + - - +
524B ASN* 3.5 3.7 + - - +
525B ARG* 2.9 53.3 + - - +
528B ARG* 4.8 1.0 + - - -
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Residues in contact with TRP 522 (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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518B ASP 3.0 12.4 + - - +
519B ILE 3.3 0.2 + - - -
521B SER* 1.3 77.1 - - - +
523B ALA* 1.3 72.0 + - + +
525B ARG* 3.7 23.6 - - - +
526B LYS* 2.7 54.4 + - + +
553B LEU* 3.9 33.7 - - + -
557B VAL* 4.2 8.7 - - + -
613B THR* 4.2 4.0 - - + -
616B ILE* 4.2 1.1 - - + -
617B MET* 3.1 74.2 - - + +
620B SER* 3.5 31.8 + - - -
621B LEU* 4.1 18.8 - - + +
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Residues in contact with ALA 523 (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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519B ILE 3.1 16.1 + - - +
520B LEU* 3.8 6.1 - - - +
521B SER 3.3 0.2 - - - -
522B TRP* 1.3 85.6 - - - +
524B ASN* 1.3 62.0 + - - +
526B LYS* 3.3 2.6 + - - +
527B VAL* 3.1 27.9 + - - +
536B ILE* 5.2 3.4 - - + -
539B PHE* 5.2 0.2 - - + -
549B PHE* 4.1 19.3 - - + -
553B LEU* 3.6 10.7 - - + +
613B THR* 3.7 24.5 - - + -
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Residues in contact with ASN 524 (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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520B LEU* 3.0 42.7 + - - +
521B SER* 3.9 4.0 - - - +
523B ALA* 1.3 79.0 - - - +
525B ARG* 1.3 62.7 + - - +
527B VAL* 3.4 0.5 + - - +
528B ARG* 3.2 15.0 + - - +
535B GLN* 2.8 49.2 + - - +
536B ILE* 2.8 45.3 + - - +
549B PHE* 3.9 5.1 - - - -
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Residues in contact with ARG 525 (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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518B ASP 5.1 1.0 + - - -
521B SER* 2.9 43.7 + - - +
522B TRP* 3.7 32.4 + - - +
524B ASN* 1.3 76.8 - - - +
526B LYS* 1.3 63.2 + - - +
528B ARG* 3.2 40.7 + - - +
529B THR* 3.2 21.4 + - + +
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Residues in contact with LYS 526 (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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522B TRP* 2.7 42.1 + - + +
523B ALA 3.3 4.9 + - - +
525B ARG* 1.3 74.9 - - - +
527B VAL* 1.3 57.7 + - - +
529B THR* 2.8 36.2 + - + +
530B MET 4.2 0.2 + - - -
553B LEU* 3.8 19.7 - - + -
556B ALA* 3.8 34.3 + - + +
557B VAL* 3.9 11.9 + - + +
620B SER* 3.8 20.9 + - - -
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Residues in contact with VAL 527 (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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523B ALA 3.1 15.0 + - - +
524B ASN 3.8 6.5 - - - +
525B ARG 3.2 0.2 - - - -
526B LYS* 1.3 72.5 - - - +
528B ARG* 1.3 62.0 + - - +
529B THR 3.1 4.7 - - - -
530B MET* 3.1 19.7 + - + +
532B ARG* 3.8 29.4 + - + +
534B LEU* 3.9 22.7 - - + +
535B GLN* 4.3 3.8 - - - +
549B PHE* 3.8 18.6 - - + +
552B ASN* 4.4 9.0 - - + +
553B LEU* 3.9 32.1 - - + +
556B ALA* 4.5 5.8 - - - -
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Residues in contact with ARG 528 (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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521B SER* 4.8 1.2 + - - -
524B ASN* 3.2 6.9 + - - +
525B ARG* 3.2 47.9 + - - +
527B VAL* 1.3 77.4 - - - +
529B THR* 1.3 60.9 + - - +
530B MET 3.2 0.2 - - - -
531B GLY* 3.4 12.8 + - - -
532B ARG 3.6 15.4 - - - +
533B LYS* 5.3 11.4 - - + +
535B GLN* 3.2 35.2 + - + +
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Residues in contact with THR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ARG* 3.2 22.9 - - + +
526B LYS* 2.8 31.5 + - + +
528B ARG* 1.3 77.6 - - - +
530B MET* 1.3 69.4 + - - +
531B GLY 3.3 1.9 + - - -
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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