Contacts of the helix formed by residues 559 - 576 (chain B) in PDB entry 1BHG
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 GLU 559 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A HIS* 2.7 37.0 + - - -
617A SER* 4.1 0.9 + - - -
545B THR* 3.6 18.1 - - + +
547B ALA* 2.3 33.1 - - - +
549B PHE 3.2 18.1 + - - +
550B HIS* 3.6 15.7 - - + -
558B THR* 1.3 71.0 - - - +
560B GLU* 1.3 71.0 + - - +
562B GLN* 3.2 10.7 + - - +
563B LYS* 3.2 17.8 + - - +
616B LYS* 5.0 5.5 - - + -
617B SER* 2.6 40.8 + - - +
618B ALA* 5.2 1.0 - - - +
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Residues in contact with GLU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A PRO* 4.9 1.1 - - + -
617A SER* 4.6 5.2 + - - -
620A PHE* 3.5 41.8 - - + -
550B HIS* 3.0 50.6 + - - -
551B GLN 3.6 13.9 - - - +
554B PRO* 4.4 9.5 - - + +
558B THR* 3.1 8.0 - - + -
559B GLU* 1.3 80.1 - - - +
561B TYR* 1.3 65.5 - - - +
563B LYS* 2.9 26.4 + - + +
564B SER* 2.9 13.4 + - - -
617B SER* 4.3 6.4 + - - -
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Residues in contact with TYR 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B SER* 3.1 29.5 + - - -
507B TRP* 3.6 28.9 - + - -
512B GLY* 3.1 25.1 + - - -
514B LEU* 3.0 34.0 - - + +
543B ALA* 4.2 6.7 - - + -
554B PRO* 3.5 19.2 - - + +
555B LEU* 2.7 31.4 - - - +
556B MET* 3.4 17.0 - - - +
558B THR* 2.9 11.5 + - - +
560B GLU* 1.3 78.4 - - - +
562B GLN* 1.3 50.9 + - - +
564B SER* 2.6 19.9 + - - -
565B LEU* 2.8 33.6 + - + +
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Residues in contact with GLN 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ALA* 3.6 21.8 + - + +
545B THR* 3.2 32.7 + - - +
558B THR 3.2 2.8 + - - +
559B GLU* 3.3 11.7 - - - +
560B GLU 3.1 0.4 - - - -
561B TYR* 1.3 78.1 - - - +
563B LYS* 1.3 58.3 + - - +
565B LEU* 4.5 5.4 - - - +
566B LEU* 2.9 54.0 + - + +
586B ILE* 6.0 0.4 - - - +
606B LYS 3.9 13.1 + - - -
607B GLY 4.4 6.7 + - - -
608B ILE* 4.4 11.0 - - - +
616B LYS* 4.6 13.4 - - - +
618B ALA* 2.9 28.6 + - + +
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Residues in contact with LYS 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A PHE* 4.2 33.5 - - + +
624A GLU* 5.3 5.3 + - - -
559B GLU 3.2 7.9 + - - +
560B GLU* 2.9 21.8 + - + +
562B GLN* 1.3 81.5 - - - +
564B SER* 1.3 54.8 + - - +
567B GLU* 3.1 34.6 + - - +
617B SER* 5.8 5.4 - - - +
618B ALA* 4.7 6.5 - - + +
621B LEU* 3.4 33.1 - - + +
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Residues in contact with SER 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 4.0 16.4 - - - -
554B PRO* 3.4 20.2 - - - +
560B GLU 2.9 11.8 + - - -
561B TYR* 2.6 26.2 + - - -
563B LYS* 1.3 75.3 - - - +
565B LEU* 1.3 61.9 + - - +
567B GLU* 3.6 9.3 + - - +
568B GLN* 3.1 30.2 + - - +
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Residues in contact with LEU 565 (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 TYR 4.5 9.6 - - - +
506B SER* 4.9 0.4 - - - -
507B TRP* 4.4 4.5 - - + -
514B LEU* 3.7 15.8 - - + +
517B ILE* 4.1 13.9 - - + -
541B TYR* 4.3 0.7 - - + -
542B GLY* 3.1 31.9 - - - +
543B ALA* 3.1 33.4 - - + -
561B TYR* 2.8 30.3 + - + +
562B GLN* 3.9 3.4 - - - +
564B SER* 1.3 70.3 - - - +
566B LEU* 1.3 72.2 + - + +
568B GLN* 2.9 16.5 + - - +
569B TYR* 3.0 34.2 + - + +
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B TYR* 4.1 10.3 - - + -
542B GLY* 4.2 15.7 - - - -
543B ALA 4.9 0.2 - - - +
562B GLN* 2.9 36.5 + - + +
565B LEU* 1.3 80.0 - - + +
567B GLU* 1.3 58.6 + - - +
569B TYR* 3.2 2.9 + - - +
570B HIS* 2.9 45.1 + - + +
586B ILE* 3.7 31.6 - - + -
608B ILE* 5.0 2.9 - - + -
618B ALA* 3.8 17.5 - - + +
621B LEU* 3.1 32.1 - - + -
622B LEU* 4.7 8.5 - - + -
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Residues in contact with GLU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LYS* 3.1 27.4 + - - +
564B SER* 3.7 8.2 - - - +
565B LEU 3.1 0.6 - - - -
566B LEU* 1.3 80.8 - - - +
568B GLN* 1.3 67.4 + - - +
570B HIS* 3.3 13.6 + - + +
571B LEU* 2.8 45.8 + - + +
621B LEU* 4.9 7.4 - - + +
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Residues in contact with GLN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 4.0 28.5 - - + +
515B GLU* 5.2 3.2 - - - -
517B ILE* 3.9 22.5 - - + +
518B GLN* 2.9 37.3 + - + +
521B LEU* 4.8 0.2 - - - +
564B SER 3.1 15.3 + - - +
565B LEU 2.9 10.1 + - - +
567B GLU* 1.3 85.6 + - - +
569B TYR* 1.3 66.3 + - - +
571B LEU* 3.2 14.2 + - - +
572B GLY* 3.0 19.1 + - - -
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Residues in contact with TYR 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B SER* 2.7 32.6 + - - -
504B TYR* 3.3 2.0 - - - -
505B TYR* 2.9 21.6 + + + -
517B ILE* 3.6 29.2 - - + -
521B LEU* 3.9 29.5 - - + +
538B GLN* 3.7 18.4 - - + -
541B TYR* 3.3 48.0 - + + -
542B GLY 5.2 0.2 - - - -
565B LEU* 3.0 32.1 + - + +
566B LEU 3.4 8.5 - - - +
568B GLN* 1.3 77.3 - - - +
570B HIS* 1.3 56.7 + - - +
572B GLY* 3.2 1.9 + - - -
573B LEU* 2.8 36.8 + - + +
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Residues in contact with HIS 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B TYR* 2.6 32.0 + + - -
566B LEU* 2.9 41.1 + - + +
567B GLU* 3.5 11.2 - - + +
569B TYR* 1.3 72.5 - - - +
571B LEU* 1.3 65.6 + - - +
572B GLY 3.0 2.0 - - - -
573B LEU* 4.5 2.6 - - - +
574B ASP* 3.2 25.5 + - - +
584B GLU* 4.1 4.3 + - - -
621B LEU* 4.6 13.0 - - + +
622B LEU* 4.4 12.4 - - + +
625B ARG* 3.5 56.5 + - + +
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Residues in contact with LEU 571 (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 GLN* 3.5 27.9 - - - +
567B GLU* 2.8 40.8 + - + +
568B GLN* 3.2 18.6 + - - +
570B HIS* 1.3 76.6 - - - +
572B GLY* 1.3 60.6 + - - +
574B ASP* 3.7 13.6 - - + +
575B GLN* 3.6 17.5 + - - +
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Residues in contact with GLY 572 (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 GLN* 4.4 13.6 + - - -
521B LEU* 4.5 11.4 - - - -
522B ALA 6.4 0.2 - - - -
525B PHE* 5.8 1.6 - - - -
568B GLN 3.0 12.9 + - - -
569B TYR 3.5 3.4 - - - -
570B HIS 3.0 0.2 - - - -
571B LEU* 1.3 73.8 - - - +
573B LEU* 1.3 67.5 + - - +
574B ASP 3.0 1.8 - - - -
575B GLN* 2.8 28.3 + - - +
576B LYS* 3.7 2.6 + - - +
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Residues in contact with LEU 573 (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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344B TYR* 4.7 1.6 - - - +
521B LEU* 4.6 6.0 - - + +
525B PHE* 3.4 37.5 - - + -
538B GLN* 3.9 24.0 - - + +
541B TYR* 4.4 12.3 - - + +
569B TYR* 2.8 28.4 + - + +
570B HIS* 4.3 4.9 - - - +
572B GLY* 1.3 69.7 - - - +
574B ASP* 1.3 50.3 + - - +
576B LYS* 2.8 9.3 + - - +
577B ARG* 2.7 41.0 + - + +
581B VAL* 4.5 10.9 - - + +
584B GLU* 3.6 42.6 - - + +
625B ARG* 4.8 0.9 - - - +
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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
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570B HIS 3.2 14.4 + - - +
571B LEU* 3.7 16.0 - - + +
572B GLY 3.0 0.2 - - - -
573B LEU* 1.3 75.4 - - - +
575B GLN* 1.3 61.4 + - + +
576B LYS 3.3 0.2 - - - -
577B ARG* 2.8 53.1 + - - +
579B LYS* 4.8 2.4 + - - -
625B ARG* 2.6 30.1 + - - -
628B LYS* 4.7 8.1 + - - -
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Residues in contact with GLN 575 (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 GLN* 5.9 0.7 - - - +
522B ALA* 6.5 0.7 - - + -
571B LEU 3.6 14.9 + - - +
572B GLY* 2.8 23.2 + - - +
574B ASP* 1.3 74.5 + - - +
576B LYS* 1.3 74.8 + - + +
579B LYS* 3.0 23.2 + - - +
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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
----------------------------------------------------------
522B ALA* 4.3 26.9 + - - +
525B PHE* 3.8 26.5 - - + -
526B GLU* 4.8 7.7 - - - +
572B GLY 3.7 1.3 + - - +
573B LEU 2.8 7.9 + - - +
575B GLN* 1.3 94.4 - - + +
577B ARG* 1.3 63.8 + - - +
579B LYS* 2.9 24.6 - - + +
580B TYR* 2.9 51.5 + - + +
581B VAL* 3.2 27.0 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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