Contacts of the strand formed by residues 517 - 521 (chain E) in PDB entry 6M04
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 GLU 517 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493E ASP 3.8 0.8 + - - -
494E VAL* 3.3 45.4 - - + +
515E LEU* 3.3 18.4 - - - +
516E GLN* 1.3 82.4 - - + +
518E LEU* 1.3 66.3 + - - +
519E HIS* 2.9 39.9 + - - -
539E LEU* 3.7 2.7 - - - +
541E CYS* 3.2 35.7 - - + +
542E LEU 3.7 3.0 - - - +
543E HIS* 3.1 17.1 + - - -
564E GLU* 4.9 2.9 - - - +
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Residues in contact with LEU 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495E LEU* 3.3 43.5 - - + +
497E LEU* 4.2 24.5 - - + -
505E ILE* 5.1 16.2 - - + -
515E LEU* 4.8 11.2 - - + -
517E GLU* 1.3 78.1 + - - +
519E HIS* 1.3 76.3 + - - +
520E LEU* 3.8 17.6 + - + +
539E LEU* 4.8 12.1 - - + -
541E CYS 4.0 3.2 + - - -
542E LEU* 3.7 6.7 - - + +
543E HIS 3.1 18.4 + - - +
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Residues in contact with HIS 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471E LYS* 4.2 20.8 - - + +
494E VAL* 5.4 1.8 - - + +
495E LEU 2.9 11.5 + - - -
496E LYS* 3.5 29.3 - - + +
497E LEU* 2.7 35.9 + - - +
517E GLU* 2.9 41.9 + - - -
518E LEU* 1.3 74.1 - - - +
520E LEU* 1.3 57.1 + - - +
521E CYS* 5.6 4.9 - - - -
543E HIS* 3.2 38.0 + + + +
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Residues in contact with LEU 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497E LEU* 3.3 12.3 - - + -
518E LEU* 4.6 22.4 - - + +
519E HIS* 1.3 74.9 - - - +
521E CYS* 1.3 61.5 + - - +
523E CYS* 3.8 20.9 - - + +
525E ALA* 6.3 1.3 - - + -
542E LEU* 5.8 0.9 - - + -
543E HIS 2.6 20.2 + - - +
544E VAL* 3.3 41.2 - - + +
545E LYS 3.2 11.4 + - - +
547E THR* 5.7 1.8 - - + -
553E PRO* 3.7 28.3 - - + -
555E TRP* 4.6 19.5 - - + +
556E VAL* 5.2 4.0 - - + -
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Residues in contact with CYS 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E LYS* 6.4 0.4 - - - -
497E LEU 3.0 17.4 + - - -
498E GLU* 3.6 17.7 - - - -
499E LEU* 3.0 25.1 + - - +
519E HIS* 5.6 5.6 - - - -
520E LEU* 1.3 76.9 - - - +
522E HIS* 1.3 63.4 + - - +
523E CYS* 3.2 4.2 - - - +
545E LYS* 3.2 23.8 - - + +
546E PHE* 3.5 22.7 - - + -
547E THR* 5.2 0.4 - - - -
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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