Contacts of the helix formed by residues 579 - 589 (chain B) in PDB entry 2O8C
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 CYS 579 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554B ARG* 3.2 26.2 - - - -
556B TYR* 3.1 27.6 - - - +
575B ASP* 3.4 13.5 - - - +
576B ASP 3.3 7.5 + - - -
577B ARG 3.2 4.4 - - - -
578B HIS* 1.3 80.9 - - - +
580B SER* 1.3 65.5 + - - +
581B ARG 3.2 2.9 - - - -
582B PHE* 3.0 5.3 + - + -
583B ARG* 2.9 21.7 + - - +
604B GLU* 4.5 5.4 - - - -
605B THR* 4.2 1.6 - - - -
608B ILE* 3.7 28.3 - - + -
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Residues in contact with SER 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ASP* 3.4 2.2 + - - -
576B ASP* 2.9 32.1 + - - +
578B HIS* 3.2 8.3 - - - -
579B CYS* 1.3 75.2 - - - +
581B ARG* 1.3 58.0 + - - +
583B ARG* 3.7 7.5 + - - +
584B THR* 2.7 33.3 + - - -
713B ASP* 5.6 0.2 + - - -
736B ASP* 4.9 4.3 - - - +
737B ALA* 5.6 0.2 - - - +
1172B ARG* 5.1 13.4 + - - -
1199B SER* 5.2 12.1 - - - -
1203B HIS* 4.7 4.5 + - - -
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Residues in contact with ARG 581 (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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552B HIS* 4.7 11.0 - - - -
573B PHE* 3.7 22.2 - - + +
574B SER* 3.3 37.7 + - - +
575B ASP* 3.0 18.5 + - - +
576B ASP* 4.9 7.2 + - - +
580B SER* 1.3 81.2 - - - +
582B PHE* 1.3 62.0 + - - +
584B THR* 3.5 8.0 - - - -
585B LEU* 3.3 20.8 + - - +
709B TYR* 4.3 4.3 + - - -
711B PRO* 4.0 21.1 - - + +
713B ASP* 3.3 49.4 + - - +
714B SER* 4.8 8.1 + - - +
717B VAL* 4.1 21.8 - - - +
718B SER 4.7 7.3 + - - -
1203B HIS* 6.2 1.0 - - - -
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Residues in contact with PHE 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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540B LEU* 4.0 19.3 - - + -
542B LEU* 3.6 42.0 - - + -
556B TYR* 3.6 27.6 - + + -
558B VAL* 4.8 8.1 - - + -
573B PHE* 4.4 5.4 - + - -
575B ASP* 2.9 18.2 + - - +
579B CYS* 3.0 4.0 + - + +
581B ARG* 1.3 76.2 - - - +
583B ARG* 1.3 65.3 + - - +
584B THR 3.2 0.2 - - - -
585B LEU* 3.5 6.3 + - + +
586B VAL* 3.3 35.9 + - + +
605B THR* 4.0 15.5 - - + -
608B ILE* 4.2 32.3 - - + -
609B LEU* 4.8 11.7 - - + -
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Residues in contact with ARG 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B HIS* 3.2 24.8 + - - +
579B CYS 2.9 14.8 + - - +
580B SER* 4.1 6.5 - - - +
582B PHE* 1.3 76.3 - - - +
584B THR* 1.3 59.0 + - - +
586B VAL* 3.5 6.1 + - - +
587B ALA* 3.0 23.6 + - - +
607B THR* 5.9 0.2 + - - -
608B ILE* 4.0 44.2 - - + +
612B SER* 5.6 3.6 + - - -
737B ALA* 3.3 22.4 - - + +
738B VAL* 5.9 8.9 - - - +
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Residues in contact with THR 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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580B SER 2.7 20.8 + - - -
581B ARG* 3.5 9.3 - - - +
582B PHE 3.2 0.4 - - - -
583B ARG* 1.3 78.4 - - - +
585B LEU* 1.3 57.3 + - - +
587B ALA* 3.2 1.9 + - - +
588B HIS* 2.9 57.6 + - + +
709B TYR* 4.8 5.8 - - - +
712B LEU* 6.6 0.4 - - + -
734B VAL* 5.7 6.1 - - + -
735B LEU 4.1 7.6 - - - +
736B ASP* 3.4 22.0 - - - +
737B ALA* 3.6 9.0 + - - +
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Residues in contact with LEU 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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540B LEU* 4.0 29.8 - - + -
558B VAL* 3.7 32.5 - - + -
560B PHE* 3.8 18.2 - - + -
573B PHE* 4.3 3.6 - - + -
581B ARG 3.3 8.6 + - - +
582B PHE* 3.7 11.9 - - + +
583B ARG 3.4 0.4 - - - -
584B THR* 1.3 78.0 - - - +
586B VAL* 1.3 60.8 + - + +
588B HIS* 3.3 4.2 + - - +
589B TYR* 2.7 45.1 + - + +
709B TYR* 3.4 44.6 + - + +
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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
----------------------------------------------------------
540B LEU* 4.2 9.2 - - + -
582B PHE* 3.3 44.1 + - + +
583B ARG* 3.8 6.5 - - - +
584B THR 3.3 0.4 - - - -
585B LEU* 1.3 84.5 - - + +
587B ALA* 1.3 62.3 + - - +
589B TYR 4.2 4.0 - - - -
590B PRO* 3.3 23.4 - - - +
591B PRO* 3.7 15.3 - - + -
608B ILE* 5.9 0.9 - - + -
612B SER* 5.4 2.5 - - - +
613B LEU* 3.7 33.4 - - + -
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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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583B ARG 3.0 18.3 + - - +
584B THR 3.2 4.7 + - - +
586B VAL* 1.3 77.5 - - - +
588B HIS* 1.3 62.5 + - + +
590B PRO* 4.0 10.8 - - - +
737B ALA* 3.7 26.5 - - + +
740B LEU* 3.9 22.0 - - + +
741B ASN* 5.3 4.3 - - - +
746B PHE* 4.3 10.0 - - - -
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Residues in contact with HIS 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B THR* 2.9 43.3 + - + +
585B LEU* 4.6 0.9 - - - -
587B ALA* 1.3 79.9 - - + +
589B TYR* 1.3 82.3 + - + +
590B PRO* 3.5 6.8 - - - +
709B TYR* 5.9 0.4 - - - +
712B LEU* 5.7 7.6 - - + +
735B LEU* 2.7 29.9 + - + -
736B ASP 5.4 0.2 - - - -
740B LEU* 4.6 9.3 - - + +
746B PHE* 5.8 0.9 - - - -
775B LYS* 3.1 29.1 + - - +
779B CYS* 3.2 52.2 - - + +
780B ALA* 5.8 0.4 - - + -
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Residues in contact with TYR 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B TYR* 3.4 45.9 - + + +
560B PHE* 3.4 33.7 - + + -
569B PHE* 4.2 20.4 - + - -
585B LEU* 2.7 27.0 + - + +
586B VAL* 3.4 5.4 - - - +
588B HIS* 1.3 93.2 - - + +
590B PRO* 1.4 67.1 - - - +
591B PRO* 3.1 11.1 - - - +
709B TYR* 3.9 26.2 - + - -
775B LYS* 5.1 1.8 - - - -
776B GLN* 3.8 29.2 + - - -
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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