Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 5JAJ
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 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN 3.9 9.2 - - - +
214A PRO* 1.3 79.0 - - - +
216A LYS* 1.3 62.6 + - - +
217A GLN* 5.0 1.6 + - - -
474A ASN* 6.4 0.2 - - - -
475A SER 3.0 12.2 + - - +
476A MET* 3.7 16.6 - - - +
477A TYR* 2.8 29.2 + - - +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 1.3 78.4 - - - +
217A GLN* 1.3 68.8 + - - +
218A TYR* 4.0 11.0 - - + -
463A MET* 3.8 0.6 - - - -
467A GLN* 3.2 15.3 - - - +
477A TYR* 3.2 36.6 - - + +
479A VAL* 3.7 9.4 - - - -
491A GLU* 2.7 26.3 + - - -
495A GLU* 2.7 40.5 + - - +
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Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 5.0 1.9 + - - -
216A LYS* 1.3 76.0 - - - +
218A TYR* 1.3 67.3 + - - +
219A ASP* 2.9 30.7 + - - +
355A ILE* 4.9 4.9 - - - +
358A GLU* 5.9 1.6 + - - -
359A HIS* 4.6 6.6 + - - -
476A MET* 3.6 39.4 - - + +
477A TYR 2.9 13.6 + - - +
478A SER* 3.3 1.4 - - - -
479A VAL* 2.9 28.1 + - - +
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Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LYS* 4.0 12.3 - - + -
217A GLN* 1.3 77.4 - - - +
219A ASP* 1.3 63.0 + - - +
220A LEU* 3.6 32.4 + - + +
479A VAL* 3.7 15.7 - - + -
488A VAL* 4.2 19.7 - - + -
491A GLU* 3.2 32.5 - - + +
492A GLN* 3.5 18.5 - - + +
495A GLU* 2.6 36.0 + - - -
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN* 2.9 32.6 + - - +
218A TYR* 1.3 74.2 - - - +
220A LEU* 1.3 63.5 + - - +
351A LYS* 4.0 20.4 + - + +
355A ILE* 3.5 23.5 - - + +
478A SER* 2.7 25.0 + - - +
479A VAL 2.8 13.3 + - - +
480A LEU* 3.3 26.0 - - + +
481A ALA 3.4 2.6 + - - -
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A TYR* 3.6 35.6 + - + +
219A ASP* 1.3 75.7 - - - +
221A CYS* 1.3 60.3 + - - +
222A GLN* 5.3 3.4 - - - +
351A LYS* 3.6 17.1 + - - +
479A VAL 4.7 2.7 - - - +
481A ALA* 3.2 11.2 - - + +
483A ALA* 4.2 23.6 - - + +
484A ASN 5.5 0.9 - - - +
488A VAL* 3.8 33.0 - - + -
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Residues in contact with CYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP 3.9 0.2 + - - -
220A LEU* 1.3 75.4 - - - +
222A GLN* 1.3 67.5 + - - +
347A PRO* 3.9 23.3 - - + +
348A ARG* 3.6 35.2 - - - -
351A LYS* 4.5 9.9 - - + +
480A LEU* 4.2 6.5 - - + -
481A ALA 3.0 24.9 + - - -
482A LYS* 3.4 14.2 - - - +
483A ALA* 2.9 26.0 + - - +
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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
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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