Contacts of the helix formed by residues 581 - 585 (chain F) in PDB entry 6Q2J
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 581 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560F PRO* 5.5 0.2 - - + -
565F CYS* 2.0 64.6 - - + -
574F GLU* 3.9 26.8 + - + +
578F ILE* 5.7 1.3 - - - +
580F ILE* 1.3 81.9 - - + +
582F PRO* 1.3 65.8 - - - +
583F GLN* 4.4 1.8 - - - -
584F ASP* 3.6 14.8 - - - -
585F CYS* 3.3 23.7 + - - +
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Residues in contact with PRO 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518F SER* 5.5 0.9 - - - +
520F ALA* 3.7 32.1 - - + -
578F ILE* 4.8 8.1 - - + -
579F ASN 4.4 7.6 - - - +
580F ILE 3.9 5.1 - - - +
581F CYS* 1.3 83.8 - - - +
583F GLN* 1.3 58.4 + - + +
584F ASP 3.0 5.1 + - - -
585F CYS* 2.9 5.0 + - + +
586F LEU* 2.8 47.8 + - + +
611F CYS* 3.9 18.2 - - + +
613F PRO* 4.0 31.6 - - + -
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Residues in contact with GLN 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520F ALA* 4.4 13.2 - - - +
555F PHE* 4.4 12.0 - - + -
557F THR* 2.5 37.2 + - - +
558F CYS 4.0 6.9 + - - -
559F SER* 3.7 25.5 - - - +
565F CYS* 3.8 16.5 - - - -
566F PRO* 4.6 10.2 - - + +
581F CYS* 4.4 0.4 - - - -
582F PRO* 1.3 78.7 - - + +
584F ASP* 1.3 57.3 + - + +
586F LEU* 4.7 3.6 - - - -
601F GLY* 4.3 4.9 - - - -
602F ILE* 3.8 28.2 + - + +
609F CYS 3.3 13.2 - - - +
611F CYS* 4.0 21.1 - - - -
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Residues in contact with ASP 584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F CYS 3.4 12.8 - - - +
566F PRO* 5.0 1.1 - - + -
567F ASP* 1.9 35.1 - - - +
568F GLY* 3.2 12.9 - - - -
569F HIS* 2.1 35.2 + - - +
570F CYS* 3.3 13.6 - - - +
574F GLU* 4.4 0.2 - - - -
581F CYS* 3.6 13.1 + - - +
582F PRO 3.1 0.4 - - - -
583F GLN* 1.3 78.3 - - - +
585F CYS* 1.3 61.6 + - - +
586F LEU 4.0 0.2 - - - -
600F ARG* 4.3 9.4 - - - +
601F GLY* 4.1 10.7 - - - -
602F ILE 5.1 0.2 - - - +
711F CA 2.4 3.2 - - - -
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Residues in contact with CYS 585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570F CYS* 2.0 52.3 - - - -
574F GLU* 3.8 28.5 - - - +
575F THR* 5.4 1.6 - - - -
578F ILE* 4.8 17.5 - - + +
581F CYS 3.3 18.2 - - - +
582F PRO* 2.9 3.6 + - + -
583F GLN 3.7 0.2 - - - -
584F ASP* 1.3 82.4 - - - +
586F LEU* 1.3 66.0 + - - +
587F ARG* 4.0 1.2 + - - +
600F ARG* 3.3 21.6 + - - +
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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