Contacts of the strand formed by residues 578 - 582 (chain J) in PDB entry 3E20
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 578 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576J GLY 3.1 5.8 + - - -
577J TYR* 1.3 76.8 - - - +
579J CYS* 1.3 71.0 + - - +
589J GLU* 3.8 16.1 + - - -
590J VAL 3.2 10.0 + - - -
591J SER* 3.9 10.3 - - - +
647J ASP* 4.8 0.7 - - - +
396K GLN* 3.1 33.2 - - - +
399K MET* 5.2 8.3 - - - -
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Residues in contact with CYS 579 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577J TYR* 3.9 22.9 - - + -
578J SER* 1.3 81.3 + - - +
580J VAL* 1.3 63.0 + - - +
589J GLU* 3.7 3.8 - - - +
590J VAL* 2.6 48.9 + - - +
592J PHE* 4.8 1.6 - - - -
645J LEU* 3.7 36.6 - - - -
646J ARG 3.3 16.8 - - - +
647J ASP* 4.1 6.7 - - - +
652J VAL* 5.0 0.9 - - - -
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Residues in contact with VAL 580 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579J CYS* 1.3 77.4 - - - +
581J MET* 1.3 62.1 + - - +
582J HIS* 3.4 22.9 - - - +
587J VAL* 3.7 21.8 - - + -
588J GLU 3.7 7.0 - - - +
589J GLU* 5.6 2.9 - - + -
644J THR 3.8 0.3 - - - +
645J LEU* 3.4 1.7 - - - -
646J ARG* 2.6 48.8 + - + +
648J GLN* 3.3 32.3 - - + +
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Residues in contact with MET 581 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J PHE* 3.0 38.4 - - + -
579J CYS 3.9 1.0 + - - -
580J VAL* 1.3 71.8 - - - +
582J HIS* 1.3 68.1 + - - +
583J ILE* 3.2 30.0 + - + +
587J VAL* 3.4 3.3 - - - -
588J GLU* 2.7 48.4 + - + +
590J VAL* 3.9 21.1 - - + -
623J LEU* 4.3 4.9 - - + -
625J THR* 4.9 6.3 - - - -
629J VAL* 5.5 2.5 - - - -
631J MET* 5.2 1.3 - - - -
643J PHE* 3.5 37.0 - - + -
644J THR 3.6 3.6 - - - -
645J LEU* 4.1 5.6 - - + -
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Residues in contact with HIS 582 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580J VAL* 3.4 20.0 - - + +
581J MET* 1.3 80.3 - - - +
583J ILE* 1.3 60.3 - - - +
584J HIS 3.9 2.7 - - - +
586J ALA 3.7 6.1 - - - +
587J VAL* 3.2 23.3 - - + +
643J PHE* 3.2 5.0 - - - -
644J THR* 3.0 42.0 + - + +
646J ARG* 3.4 31.3 + - - -
648J GLN* 2.8 29.1 + - - -
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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