Contacts of the strand formed by residues 570 - 575 (chain K) in PDB entry 2A07
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 GLY 570 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564K ARG* 5.1 1.8 - - - -
566K GLU* 3.3 10.0 - - - +
567K ASN* 2.9 31.3 + - - +
568K VAL 3.3 1.0 + - - -
569K LYS* 1.3 80.5 - - - +
571K ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 571 (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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9D A 3.7 11.6 + - - +
526K THR* 3.8 23.5 - - - +
527K LEU 4.8 1.0 + - - -
564K ARG* 3.5 41.3 - - + +
565K VAL 3.4 12.1 - - - +
566K GLU* 3.9 2.7 - - - -
567K ASN* 3.6 4.2 + - - -
570K GLY* 1.3 76.2 - - - +
572K VAL* 1.3 65.7 + - - +
573K TRP* 5.3 0.7 - - - -
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Residues in contact with VAL 572 (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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524K GLN* 3.7 44.9 - - + +
525K LEU* 3.5 11.9 - - - +
526K THR* 4.2 15.3 - - + +
529K GLU* 5.5 0.7 - - - +
564K ARG* 3.5 4.2 - - - +
565K VAL* 2.8 51.5 + - + +
567K ASN* 3.4 21.3 - - - +
571K ALA* 1.3 76.6 - - - +
573K TRP* 1.3 63.4 + - - +
574K THR* 4.4 2.9 - - + -
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Residues in contact with TRP 573 (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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9D A 2.8 46.7 + - + -
10D T 3.4 24.5 - - - -
517K ILE* 3.8 11.9 - - + +
524K GLN* 3.3 6.9 - - - -
525K LEU 2.6 38.9 + - - +
526K THR* 4.8 0.4 - - - -
527K LEU* 4.0 15.5 - - - +
530K ILE* 4.0 13.5 - - + -
556K LEU* 3.6 64.5 - - + +
557K SER 4.5 0.2 - - - -
562K PHE 3.8 11.2 - - - -
563K VAL 3.8 4.9 - - - -
564K ARG* 3.6 41.5 - - + -
571K ALA 5.3 0.7 - - - -
572K VAL* 1.3 76.8 - - - +
574K THR* 1.3 60.5 + - - +
606K MG 4.3 1.1 - - - -
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Residues in contact with THR 574 (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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517K ILE* 4.1 3.7 - - - +
523K ARG 4.0 18.2 - - - +
524K GLN* 4.2 11.7 - - + +
562K PHE* 3.4 8.3 - - - +
563K VAL* 2.8 49.4 + - - +
565K VAL* 3.6 27.2 - - + +
572K VAL* 4.4 1.8 - - + -
573K TRP* 1.3 80.1 - - - +
575K VAL* 1.3 68.3 + - - +
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Residues in contact with VAL 575 (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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514K ARG* 4.0 22.7 - - + +
517K ILE* 3.6 40.1 - - + +
518K MET* 5.0 3.6 - - - -
523K ARG* 3.2 28.9 + - - +
561K CYS 3.3 7.4 - - - +
562K PHE* 3.9 17.9 - - + -
563K VAL* 5.5 0.2 - - - -
574K THR* 1.3 79.6 - - - +
576K ASP* 1.3 71.4 + - - +
577K GLU* 3.2 18.7 + - - +
580K TYR* 4.4 8.1 - - + -
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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