Contacts of the helix formed by residues 572 - 591 (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 572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571B GLU* 1.3 81.0 - - + +
573B ASP* 1.3 65.1 + - - +
574B ASP* 3.4 12.5 + - - +
575B GLU* 2.9 45.0 + - + +
576B LYS* 3.0 22.5 + - - +
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Residues in contact with ASP 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B GLU 3.8 1.3 + - - +
572B THR* 1.3 73.6 - - - +
574B ASP* 1.3 62.3 + - - +
576B LYS* 4.0 16.4 + - - +
577B ARG* 3.1 28.9 + - - +
602B VAL* 5.1 10.9 - - + +
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Residues in contact with ASP 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B THR* 3.0 10.3 + - - +
573B ASP* 1.3 83.2 + - - +
575B GLU* 1.3 60.7 + - + +
577B ARG* 3.3 7.3 + - - +
578B LEU* 3.0 29.4 + - - +
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Residues in contact with GLU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B THR* 3.1 27.4 + - + +
569B LYS* 3.0 35.3 + - - +
571B GLU* 3.1 20.6 + - - +
572B THR* 2.9 50.6 + - + +
574B ASP* 1.3 77.4 - - + +
576B LYS* 1.3 63.2 + - - +
578B LEU* 3.3 6.3 + - - +
579B ASN* 3.1 16.6 + - - -
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Residues in contact with LYS 576 (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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545B SER* 3.1 54.9 + - - +
546B SER* 4.4 6.9 - - - -
570B GLY* 3.2 32.1 - - - -
571B GLU 3.5 13.7 + - - +
572B THR 3.0 18.6 + - - +
573B ASP* 4.0 12.5 + - - +
575B GLU* 1.3 72.7 - - - +
577B ARG* 1.3 66.8 + - - +
579B ASN* 3.1 2.4 + - - +
580B ALA* 2.9 26.0 + - - +
602B VAL* 4.0 21.3 + - + +
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Residues in contact with ARG 577 (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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573B ASP 3.1 17.0 + - - +
574B ASP* 3.4 7.9 - - - +
576B LYS* 1.3 79.3 - - - +
578B LEU* 1.3 62.5 + - - +
580B ALA* 3.5 1.4 + - - +
581B THR* 3.1 51.0 + - - +
598B PRO* 4.0 17.1 - - - +
599B GLU* 3.0 34.8 + - + +
602B VAL* 4.0 14.5 - - + +
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Residues in contact with LEU 578 (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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566B LEU 5.0 6.3 - - - +
568B THR* 3.6 26.0 - - + -
574B ASP 3.0 13.1 + - - +
575B GLU* 3.5 11.2 - - - +
576B LYS 3.1 0.4 - - - -
577B ARG* 1.3 75.8 - - - +
579B ASN* 1.3 65.2 + - - +
581B THR* 3.6 5.8 + - - -
582B TYR* 3.2 21.2 + - + +
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Residues in contact with ASN 579 (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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546B SER 3.1 26.6 + - - +
547B GLY* 4.5 4.3 - - - -
548B LEU* 4.5 2.6 - - - +
551B LEU* 4.1 11.8 - - + +
566B LEU 4.7 0.9 - - - +
567B VAL* 3.7 14.5 - - - +
568B THR* 3.0 59.2 + - - +
569B LYS 3.9 3.6 + - - -
570B GLY 4.3 0.2 - - - +
575B GLU 3.1 5.8 + - - -
576B LYS 3.1 5.4 + - - +
578B LEU* 1.3 75.0 - - - +
580B ALA* 1.3 54.6 + - - +
582B TYR* 2.8 11.4 + - - +
583B ILE* 2.6 39.7 + - - +
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Residues in contact with ALA 580 (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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547B GLY* 5.6 0.4 - - - -
576B LYS 2.9 16.7 + - - +
577B ARG 3.6 4.7 - - - +
579B ASN* 1.3 77.2 - - - +
581B THR* 1.3 63.3 + - - +
583B ILE* 3.1 7.7 + - - +
584B VAL* 3.0 26.7 + - - +
598B PRO* 3.2 33.9 - - + +
601B ILE* 4.2 18.4 - - + -
602B VAL* 4.0 8.3 - - + -
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Residues in contact with THR 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B ARG* 3.1 40.9 + - - +
578B LEU* 4.0 7.2 - - - -
579B ASN 3.3 0.2 - - - -
580B ALA* 1.3 78.0 - - - +
582B TYR* 1.3 60.5 + - - +
584B VAL* 3.7 4.2 + - + +
585B SER* 3.3 26.6 + - - +
598B PRO* 3.5 16.7 - - + +
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Residues in contact with TYR 582 (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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551B LEU* 3.7 24.5 - - + -
561B VAL 3.8 7.6 + - - -
562B VAL* 4.5 2.7 - - + -
563B ASN* 3.0 36.0 + - - +
566B LEU* 3.9 29.3 - - + +
567B VAL* 3.9 24.5 - - + -
578B LEU* 3.2 13.7 + - + +
579B ASN* 2.8 11.5 + - - +
581B THR* 1.3 77.1 - - - +
583B ILE* 1.3 58.8 + - - +
585B SER* 3.3 6.0 + - - -
586B VAL* 2.9 53.5 + - + +
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Residues in contact with ILE 583 (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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547B GLY* 3.4 37.0 - - - +
550B PHE* 3.5 29.4 - - + -
551B LEU* 3.8 21.8 - - + -
554B LEU* 4.1 14.3 - - + +
579B ASN 2.6 23.2 + - - +
580B ALA* 3.1 7.4 + - - +
582B TYR* 1.3 72.9 - - - +
584B VAL* 1.3 58.5 + - - +
586B VAL* 3.3 1.0 + - - +
587B ALA* 2.9 31.4 + - + +
601B ILE* 3.8 22.4 - - + -
612B LEU* 4.1 15.5 - - + -
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Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ALA 3.0 20.6 + - - +
581B THR* 4.0 7.0 - - + +
583B ILE* 1.3 76.3 - - + +
585B SER* 1.3 62.8 + - - +
587B ALA* 3.8 4.8 + - - +
588B ARG* 3.3 60.8 + - - +
594B VAL* 4.8 3.4 - - + +
596B LEU* 4.4 24.0 - - + +
598B PRO* 4.4 22.0 - - + -
601B ILE* 4.3 15.3 - - + -
612B LEU* 5.6 1.6 - - + -
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Residues in contact with SER 585 (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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581B THR* 3.3 18.9 + - - +
582B TYR* 3.3 8.6 + - - -
583B ILE 3.2 0.4 - - - -
584B VAL* 1.3 78.9 - - - +
586B VAL* 1.3 61.7 + - - +
588B ARG* 3.3 11.5 + - - +
589B LYS* 2.9 27.1 + - - +
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Residues in contact with VAL 586 (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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551B LEU* 5.3 0.7 - - + -
554B LEU* 4.0 19.7 - - + -
561B VAL* 3.3 44.0 - - + +
562B VAL* 4.2 4.0 - - + -
582B TYR* 2.9 58.0 + - + +
583B ILE* 3.9 3.4 - - - +
585B SER* 1.3 76.9 - - - +
587B ALA* 1.3 64.6 + - - +
589B LYS* 3.0 21.3 + - + +
590B LEU* 3.1 13.4 + - - +
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Residues in contact with ALA 587 (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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554B LEU* 4.4 11.8 - - + +
583B ILE 2.9 18.8 + - - +
584B VAL* 3.9 6.3 - - - +
586B VAL* 1.3 77.2 - - - +
588B ARG* 1.3 61.4 + - - +
590B LEU* 3.1 8.8 + - - +
591B GLY 3.2 0.7 + - - -
592B CYS* 3.0 36.7 + - + +
594B VAL* 4.7 3.8 - - + -
612B LEU* 4.1 12.3 - - + -
616B ILE* 3.9 22.9 - - + -
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Residues in contact with ARG 588 (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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400B LEU* 6.2 2.0 - - - +
584B VAL* 3.3 41.0 + - - +
585B SER* 3.7 10.4 + - - +
586B VAL 3.2 0.2 - - - -
587B ALA* 1.3 75.0 - - - +
589B LYS* 1.3 65.3 + - - +
591B GLY* 3.2 13.0 + - - -
592B CYS 3.5 20.6 - - - +
593B SER* 5.5 0.2 - - - -
594B VAL* 3.3 29.6 + - + +
595B PHE* 4.2 12.3 - - - +
596B LEU 4.3 5.7 + - - -
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Residues in contact with LYS 589 (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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560B ARG 5.2 2.4 + - - -
561B VAL* 4.6 36.0 + - + +
585B SER 2.9 14.2 + - - +
586B VAL* 3.1 18.6 - - + +
588B ARG* 1.3 78.3 - - - +
590B LEU* 1.3 57.7 + - - +
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Residues in contact with LEU 590 (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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554B LEU* 3.6 29.8 - - + -
557B VAL* 4.1 20.9 - - + -
558B GLU* 4.0 14.8 - - + -
561B VAL* 3.9 31.9 - - + -
586B VAL 3.1 11.8 + - - +
587B ALA* 3.4 9.4 - - - +
588B ARG 3.1 0.2 - - - -
589B LYS* 1.3 79.8 - - - +
591B GLY* 1.3 56.0 + - - +
592B CYS* 4.6 5.6 - - - -
616B ILE* 5.0 7.6 - - + +
619B TRP* 4.5 9.3 - - + -
623B ARG* 2.9 45.8 + - - +
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Residues in contact with GLY 591 (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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588B ARG 3.2 12.4 + - - -
589B LYS 4.6 0.2 - - - -
590B LEU* 1.3 79.1 - - - +
592B CYS* 1.3 65.1 + - - +
593B SER* 3.2 6.2 + - - -
619B TRP* 2.9 35.3 + - - -
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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