Contacts of the strand formed by residues 585 - 589 (chain C) in PDB entry 3A8P
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 VAL 585 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C TRP* 4.3 13.9 - - + -
576C VAL* 2.8 53.0 + - + +
577C PRO* 6.0 0.2 - - - +
579C HIS* 4.2 13.7 - - + -
582C LYS* 3.7 35.2 - - + +
583C GLU 3.2 3.6 - - - +
584C HIS* 1.3 78.3 - - - +
586C PHE* 1.3 69.5 + - - +
597C LEU* 4.2 12.3 - - + -
598C PHE 3.1 13.2 - - - +
599C GLN* 4.2 9.0 - - + -
606C LEU* 3.5 7.9 - - - +
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Residues in contact with PHE 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C LEU* 3.9 22.7 - - + -
573C VAL* 3.5 26.0 - - + -
574C GLN 3.3 12.1 - - - +
575C SER* 4.0 3.1 - - - +
576C VAL* 4.1 3.6 - - - +
584C HIS 4.1 9.4 - - - -
585C VAL* 1.3 76.8 - - - +
587C CYS* 1.3 61.1 + - - +
588C LEU* 5.1 0.9 - - + -
597C LEU* 3.6 2.4 - - - -
598C PHE* 2.7 74.9 + + + +
600C ALA* 4.1 9.2 - - + -
606C LEU* 4.0 21.8 - - + -
609C TRP* 3.7 32.3 - + + -
610C VAL* 4.7 4.0 - - + -
613C ILE* 4.3 12.1 - - + -
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Residues in contact with CYS 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LEU* 5.2 1.8 - - - -
572C ILE 3.6 1.6 - - - +
573C VAL* 3.2 5.9 - - - -
574C GLN* 2.5 45.8 + - + +
576C VAL* 3.7 16.4 - - + -
586C PHE* 1.3 75.0 - - - +
588C LEU* 1.3 59.5 + - - +
595C VAL* 3.3 31.4 - - - -
596C TYR 3.4 9.2 - - - -
597C LEU* 3.9 11.9 - - + -
731C SER* 3.3 28.0 + - - +
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Residues in contact with LEU 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C LEU* 4.0 26.5 - - + -
566C LEU* 4.4 7.9 - - + -
568C ALA* 4.3 15.0 - - + -
571C SER* 3.8 16.4 - - - +
572C ILE 3.4 5.2 - - - +
573C VAL* 4.4 7.4 - - + +
586C PHE* 5.5 0.2 - - + -
587C CYS* 1.3 76.0 - - - +
589C SER* 1.3 75.8 + - - +
590C ASN* 3.6 8.7 - - + +
595C VAL* 3.5 1.4 - - - +
596C TYR* 2.8 51.6 + - + +
598C PHE* 4.1 20.7 - - + -
613C ILE* 4.4 20.0 - - + -
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Residues in contact with SER 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C SER* 3.2 2.9 - - - -
572C ILE* 3.0 41.3 + - - +
587C CYS 4.1 0.2 + - - -
588C LEU* 1.3 77.1 - - - +
590C ASN* 1.3 62.7 + - - +
594C ASP 3.3 10.8 - - - -
595C VAL* 4.2 3.4 - - - +
731C SER* 3.6 35.1 + - - -
734C HIS* 2.9 30.4 + - - +
735C ALA* 4.9 2.0 - - - -
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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
------------------------------------------------------------
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