Contacts of the strand formed by residues 489 - 494 (chain K) in PDB entry 6D6Q
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 ALA 489 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475K ILE* 3.6 22.2 - - + -
477K SER* 4.2 11.7 - - - +
488K ASP* 1.3 79.1 - - - +
490K LEU* 1.3 69.8 + - - +
504K VAL* 3.3 5.9 - - - +
505K HIS* 2.9 45.3 + - + +
551K LEU* 4.5 13.7 - - + -
582K ILE* 4.6 2.2 - - + -
584K SER* 5.4 0.7 - - - -
667K MET* 4.9 0.2 - - - +
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Residues in contact with LEU 490 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475K ILE* 3.4 24.3 - - - +
476K CYS* 3.8 20.7 + - - +
478K VAL* 5.5 9.4 - - + +
488K ASP* 4.8 1.1 - - + -
489K ALA* 1.3 86.7 - - - +
491K HIS* 1.3 68.2 + - - +
502K VAL* 6.2 0.9 - - + -
503K GLY 3.4 6.5 - - - +
504K VAL* 4.4 11.0 - - + -
505K HIS* 4.9 0.7 - - - -
613K LEU* 3.9 21.8 - - + -
662K MET* 3.9 29.4 - - + -
663K VAL* 4.2 10.5 - - + -
666K PHE* 4.3 18.2 - - + -
667K MET* 3.7 22.4 - - + -
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Residues in contact with HIS 491 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470K LEU* 5.0 2.6 - - + +
473K LEU* 3.6 32.2 - - + +
474K CYS* 3.3 23.1 - - - +
475K ILE* 4.3 0.7 - - + -
476K CYS* 6.1 1.1 - - - -
490K LEU* 1.3 78.5 - - - +
492K CYS* 1.3 62.3 + - - +
493K ARG* 3.9 17.2 + - + +
501K GLU* 4.0 10.5 + - - +
502K VAL* 3.4 7.5 - - - +
503K GLY* 2.9 60.4 + - - +
505K HIS* 3.2 31.5 + + - -
563K ILE* 3.5 13.7 - - + +
609K SER* 4.2 6.3 - - - -
613K LEU* 4.2 4.7 - - - -
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Residues in contact with CYS 492 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474K CYS* 5.3 3.4 - - - -
491K HIS* 1.3 75.7 - - - +
493K ARG* 1.3 57.9 + - - +
494K GLU 3.8 1.9 + - - -
500K LEU* 3.5 39.7 - - - -
501K GLU 3.6 4.5 - - - -
502K VAL* 4.1 6.1 - - + +
609K SER* 3.3 32.3 + - - +
612K GLY* 4.1 21.5 - - - -
613K LEU* 3.9 19.3 - - + -
616K LEU* 4.4 1.3 - - - -
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Residues in contact with ARG 493 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472K HIS* 6.1 0.7 - - - -
473K LEU* 4.2 19.5 - - + +
474K CYS* 5.8 4.5 - - - -
491K HIS* 3.9 14.9 + - + -
492K CYS* 1.3 72.4 - - - +
494K GLU* 1.3 78.7 + - - +
495K LEU* 4.6 10.1 - - - +
500K LEU* 3.5 2.2 - - - -
501K GLU* 2.4 83.5 + - + +
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Residues in contact with GLU 494 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492K CYS* 3.8 4.0 + - - -
493K ARG* 1.3 93.5 + - - +
495K LEU* 1.3 71.0 + - - +
498K GLY* 3.0 26.4 - - - +
499K ASN 3.3 6.1 - - - +
500K LEU* 3.6 22.9 - - - +
568K HIS* 4.6 9.1 + - - -
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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