Contacts of the helix formed by residues 572 - 586 (chain B) in PDB entry 6HBU
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 SER 572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B MET* 3.2 40.6 + - - +
551B PHE* 3.4 20.4 - - - +
568B LEU 3.7 6.1 + - - -
569B GLN 3.7 3.5 + - - -
570B TYR 3.4 2.0 - - - -
571B PHE* 1.3 76.3 - - - +
573B ILE* 1.3 62.8 - - - +
575B ARG* 3.3 27.5 + - - +
576B TYR* 3.1 21.8 + - - -
636B MET* 5.1 0.2 - - - -
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Residues in contact with ILE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B CYS* 4.0 18.6 - - - -
516B VAL* 4.0 21.4 - - + +
519B SER* 3.5 33.7 - - - +
520B ALA* 3.9 9.2 - - + +
523B MET* 4.5 14.8 - - + -
545B PHE* 4.8 2.2 - - + -
548B MET* 3.5 14.8 - - - -
571B PHE 3.3 2.2 + - - -
572B SER* 1.3 70.8 - - - +
574B PRO* 1.4 69.6 - - + +
575B ARG 3.3 1.0 + - - -
576B TYR* 3.3 4.7 + - - +
577B GLY 3.3 16.1 + - - -
633B LEU* 3.8 19.9 - - + +
636B MET* 3.7 28.3 - - + -
640B PHE* 4.6 0.7 - - + -
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Residues in contact with PRO 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE* 5.7 0.4 - - + -
434B THR* 4.7 13.2 + - - +
435B THR* 5.0 11.7 - - + -
438B CYS* 3.7 25.6 - - + -
439B PHE* 6.3 1.8 - - + -
516B VAL* 5.6 0.2 - - + -
545B PHE* 5.0 6.3 - - + +
548B MET* 3.7 30.1 - - + +
549B MET* 4.7 5.2 - - + +
552B SER* 4.1 19.2 - - - -
572B SER 3.7 0.7 - - - -
573B ILE* 1.4 90.8 - - + +
575B ARG* 1.3 60.9 + - - +
577B GLY 4.0 1.1 - - - +
578B PHE* 3.2 28.2 + - - +
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Residues in contact with ARG 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B PHE 3.4 26.5 - - - +
552B SER* 3.9 14.9 - - - +
558B LEU* 4.1 19.1 - - + +
569B GLN* 3.3 36.3 + - - +
570B TYR* 4.5 14.3 + - - -
572B SER* 3.3 19.5 + - - +
573B ILE 3.2 1.4 - - - -
574B PRO* 1.3 78.8 - - - +
576B TYR* 1.3 89.4 + - - +
579B THR* 2.5 47.6 + - - +
618B GLY 5.3 7.3 + - - -
628B LYS* 5.5 10.5 - - - +
629B ASN* 4.4 6.4 + - - -
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Residues in contact with TYR 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLN 4.7 1.1 - - - -
570B TYR* 2.7 53.8 + + - +
572B SER 3.1 25.1 + - - -
573B ILE 3.3 2.7 + - - +
575B ARG* 1.3 98.2 - - - +
577B GLY* 1.3 64.5 + - - +
580B ALA* 3.3 10.9 + - - +
628B LYS* 5.0 4.3 - - + -
629B ASN* 3.3 56.6 - - + +
632B ALA* 3.6 28.8 - - + +
633B LEU* 3.9 15.4 - - + +
636B MET* 4.2 18.6 - - - -
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Residues in contact with GLY 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B THR* 3.8 9.6 - - - -
512B THR* 3.7 10.9 - - - +
516B VAL* 3.6 25.0 - - - +
573B ILE 3.3 8.6 + - - -
574B PRO 4.3 0.4 - - - -
576B TYR* 1.3 81.2 - - - +
578B PHE* 1.3 57.2 + - - +
580B ALA 3.3 1.6 + - - -
581B LEU* 3.0 32.6 + - - +
633B LEU* 4.7 1.1 - - - -
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Residues in contact with PHE 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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427B ALA 3.2 28.9 - - - -
430B LEU* 3.5 28.9 - - + -
431B PHE* 3.5 24.2 - + + -
434B THR* 3.7 14.6 - - + +
552B SER* 3.8 20.0 - - - +
553B GLY 4.3 7.4 - - - -
554B LEU* 3.7 27.6 - - + -
574B PRO 3.2 20.1 + - - +
575B ARG 4.7 0.4 - - - +
577B GLY* 1.3 73.6 - - - +
579B THR* 1.3 60.7 + - - +
581B LEU* 3.9 1.6 - - - +
582B GLN* 3.1 57.7 + - + +
617B GLN* 5.3 0.2 - - - -
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Residues in contact with THR 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B SER 5.0 3.1 + - - -
575B ARG* 2.5 42.3 + - - +
578B PHE* 1.3 78.6 - - - +
580B ALA* 1.3 57.3 + - - +
582B GLN* 3.3 8.8 + - - +
583B HIS* 2.9 28.4 + - - +
619B ILE* 3.8 34.9 - - + +
625B GLY 4.9 0.4 - - - +
629B ASN* 3.5 24.9 - - - +
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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
----------------------------------------------------------
512B THR* 3.8 13.9 + - + -
576B TYR 3.3 17.4 + - - +
577B GLY 3.3 0.4 + - - -
579B THR* 1.3 79.8 - - - +
581B LEU* 1.3 60.5 + - - +
583B HIS* 4.0 0.4 - - - -
584B ASN* 3.3 25.1 + - - +
626B LEU* 3.3 12.8 - - + +
629B ASN* 3.6 15.4 - - + +
630B HIS* 3.7 29.4 - - + -
633B LEU* 6.3 0.4 - - + -
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 3.4 44.4 - - + +
433B LEU* 4.4 5.4 - - + -
434B THR* 3.7 28.0 - - + -
509B MET* 4.0 22.2 - - + -
512B THR* 3.9 22.2 - - + +
513B LEU* 3.7 26.7 - - + -
577B GLY 3.0 15.2 + - - +
578B PHE* 4.2 3.4 - - - +
580B ALA* 1.3 78.2 - - - +
582B GLN* 1.3 63.1 + - - +
584B ASN* 3.9 6.1 - - + +
585B GLU* 3.2 19.4 + - - +
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Residues in contact with GLN 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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427B ALA* 3.9 2.6 - - + +
430B LEU* 4.0 8.1 - - + -
554B LEU* 5.3 0.2 - - - +
578B PHE* 3.1 55.4 + - + +
579B THR* 3.3 5.8 + - - +
581B LEU* 1.3 75.4 - - - +
583B HIS* 1.3 60.0 + - - +
586B PHE* 2.9 55.3 + - + +
613B TYR* 3.7 31.1 + - - -
614B LEU* 3.9 5.1 - - + +
617B GLN* 4.1 13.4 + - - +
619B ILE* 3.3 27.1 - - + +
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Residues in contact with HIS 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B THR 2.9 17.4 + - - +
582B GLN* 1.3 75.7 - - - +
584B ASN* 1.3 63.8 + - - +
585B GLU 3.6 0.2 + - - -
587B LEU* 3.3 42.3 + - + +
614B LEU* 3.5 19.3 - - + +
619B ILE* 4.0 7.5 - - + +
620B ASP 3.1 28.8 + - - -
621B LEU* 3.7 13.9 + - - -
622B SER 3.2 22.7 + - - -
623B PRO* 4.6 3.2 - - - +
625B GLY 4.4 4.0 - - - +
626B LEU* 3.4 42.2 - - + +
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Residues in contact with ASN 584 (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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500B LYS* 3.3 22.5 + - - +
505B ALA* 3.1 41.8 + - - +
508B VAL* 3.4 20.1 - - + +
509B MET* 3.2 25.7 - - - +
580B ALA 3.3 19.1 + - - +
581B LEU* 3.9 8.8 - - + +
582B GLN 3.3 0.6 - - - -
583B HIS* 1.3 81.5 - - - +
585B GLU* 1.3 58.0 + - + +
587B LEU* 4.5 4.2 + - - +
626B LEU* 4.4 7.5 - - + +
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Residues in contact with GLU 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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426B ARG* 3.2 39.1 + - - +
430B LEU* 3.3 34.5 - - + +
499B LEU* 3.3 30.0 - - + +
500B LYS* 3.3 24.8 - - + +
581B LEU 3.2 13.1 + - - +
582B GLN 4.4 0.4 - - - +
584B ASN* 1.3 80.1 - - + +
586B PHE* 1.3 64.2 + - + +
587B LEU 3.2 7.0 + - - +
589B GLN* 2.9 28.7 + - - +
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Residues in contact with PHE 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ILE* 3.9 20.9 - - + -
426B ARG* 3.5 32.3 - - + -
427B ALA* 3.8 14.8 - - + -
430B LEU* 4.4 7.6 - - + -
582B GLN* 2.9 47.2 + - + +
583B HIS 4.6 0.4 - - - -
585B GLU* 1.3 80.8 - - + +
587B LEU* 1.3 62.5 + - - +
589B GLN* 4.1 2.5 - - + -
591B PHE* 3.7 35.7 - + - -
610B GLY* 3.2 32.1 - - - +
611B GLU* 3.8 1.7 + - - -
613B TYR* 4.1 21.5 - + - -
614B LEU* 3.6 15.9 - - + +
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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
------------------------------------------------------------
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