Contacts of the helix formed by residues 576 - 592 (chain O) in PDB entry 5KHU
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 ASN 576 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575O LYS* 3.8 29.6 - - - +
577O THR* 3.8 29.4 - - - +
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Residues in contact with THR 577 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576O ASN* 3.8 29.8 - - - +
578O GLU* 3.8 28.3 - - - +
580O VAL* 4.6 15.5 - - - +
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Residues in contact with GLU 578 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577O THR* 3.8 26.5 - - - +
579O MET* 3.8 29.2 - - - +
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Residues in contact with MET 579 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578O GLU* 3.8 29.2 - - - +
580O VAL* 3.8 25.4 - - - +
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Residues in contact with VAL 580 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577O THR* 4.6 15.5 - - - +
579O MET* 3.8 28.3 - - - +
581O ILE* 3.8 29.4 - - - +
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Residues in contact with ILE 581 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580O VAL* 3.8 25.6 - - - +
582O SER* 3.8 28.7 - - - +
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Residues in contact with SER 582 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581O ILE* 3.8 29.6 - - - +
583O VAL* 3.8 28.0 - - - +
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Residues in contact with VAL 583 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582O SER* 3.8 25.6 - - - +
584O LEU* 3.8 30.3 - - - +
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Residues in contact with LEU 584 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583O VAL* 3.8 25.8 - - - +
585O LEU* 3.7 29.4 - - - +
587O VAL* 4.4 15.9 - - - +
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Residues in contact with LEU 585 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584O LEU* 3.7 29.8 - - - +
586O SER* 3.8 26.5 - - - +
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Residues in contact with SER 586 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585O LEU* 3.8 25.1 - - - +
587O VAL* 3.8 28.9 - - - +
589O GLU* 4.1 20.0 - - - +
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Residues in contact with VAL 587 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584O LEU* 4.4 17.3 - - - +
586O SER* 3.8 29.2 - - - +
588O ALA* 3.8 24.7 - - - +
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Residues in contact with ALA 588 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587O VAL* 3.8 29.2 - - - +
589O GLU* 3.8 26.7 - - - +
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Residues in contact with GLU 589 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586O SER* 4.1 18.4 - - - +
588O ALA* 3.8 24.7 - - - +
590O LEU* 3.8 29.4 - - - +
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Residues in contact with LEU 590 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589O GLU* 3.8 26.9 - - - +
591O TYR* 3.7 29.8 - - - +
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Residues in contact with TYR 591 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590O LEU* 3.7 29.6 - - - +
592O TRP* 3.8 26.0 - - - +
594O SER* 4.6 17.3 - - - +
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Residues in contact with TRP 592 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591O TYR* 3.8 30.1 - - - +
593O ARG* 3.8 24.9 - - - +
753O ASN* 4.6 15.3 - - - +
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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