Contacts of the strand formed by residues 577 - 580 (chain C) in PDB entry 2A2N
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 THR 577 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C ARG 4.1 2.9 + - - +
572C HIS* 3.9 18.0 - - + -
574C ARG 2.9 19.1 + - - -
576C TYR* 1.3 77.2 - - - +
578C LEU* 1.3 62.2 + - - +
579C SER* 3.6 14.1 + - - +
593C PHE 3.5 1.9 - - - +
594C ILE* 3.1 5.6 - - - -
595C THR* 3.0 33.6 + - - +
608C VAL* 3.5 31.6 - - + -
610C GLY 3.8 4.9 - - - +
611C ARG* 2.9 24.0 + - - +
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Residues in contact with LEU 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C ILE* 5.0 1.1 - - + -
505C THR* 4.2 18.8 - - + +
507C LEU* 3.8 21.3 - - + -
519C PHE* 4.7 6.5 - - + -
576C TYR 3.8 1.4 + - - +
577C THR* 1.3 69.9 - - - +
579C SER* 1.3 64.1 + - - +
592C PHE* 3.3 37.2 - - + -
593C PHE 3.4 8.7 - - - +
594C ILE* 3.7 17.7 - - + -
608C VAL* 3.6 0.9 - - - -
609C PHE* 2.9 54.8 + - + -
610C GLY* 2.9 24.6 + - - +
611C ARG* 4.1 1.8 - - - +
612C VAL* 5.6 0.4 - - + +
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Residues in contact with SER 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C HIS* 2.9 27.5 + - - -
577C THR* 3.6 4.4 - - - +
578C LEU* 1.3 76.9 + - - +
580C MET* 1.3 61.3 + - - +
592C PHE* 3.2 4.7 - - - +
593C PHE* 2.9 61.1 + - - -
606C HIS* 4.2 2.5 - - - -
607C THR 3.0 14.1 + - - -
608C VAL* 3.6 5.2 - - - -
609C PHE* 3.5 6.1 - - - -
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Residues in contact with MET 580 (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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515C THR* 3.6 28.3 - - + +
518C ASN* 4.4 5.6 - - - +
519C PHE* 6.1 1.8 - - - -
528C TYR* 5.7 0.7 - - - -
562C PHE* 4.3 5.6 - - + -
579C SER* 1.3 72.3 - - - +
581C ALA* 1.3 60.7 + - - +
582C ASN* 4.1 1.7 + - - +
588C ASN* 3.0 33.9 - - + +
589C GLY 3.8 36.3 - - - +
590C SER 4.2 5.2 - - - +
591C GLN 3.3 20.0 - - - +
592C PHE* 4.2 4.0 - - - -
593C PHE* 3.3 4.8 - - - -
606C HIS* 2.9 25.1 + - - +
607C THR* 2.9 20.7 + - - +
609C PHE* 3.5 22.9 - - + -
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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