Contacts of the strand formed by residues 437 - 442 (chain A) in PDB entry 1JD7
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 ASP 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ARG* 3.9 8.4 + - - +
286A LEU* 3.8 9.2 - - - +
341A TYR* 2.7 28.6 + - - -
382A ASN 3.0 25.8 + - - +
406A LYS* 2.9 27.6 + - - -
433A ILE* 3.4 10.4 - - + +
434A GLY* 3.3 21.4 + - - +
435A ALA 3.3 3.1 - - - +
436A TRP* 1.3 78.3 - - - +
438A ALA* 1.3 83.2 + - - +
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Residues in contact with ALA 438 (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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286A LEU* 4.1 10.1 - - + -
289A VAL* 4.5 3.6 - - + -
341A TYR* 4.4 5.2 - - + -
380A ALA 3.1 16.4 - - - +
381A ILE* 3.8 16.2 - - + -
403A ASN* 3.4 12.1 + - - +
405A LEU* 3.9 19.0 - - + +
406A LYS* 4.2 3.6 - - - -
419A GLU* 4.6 0.5 - - - +
433A ILE* 3.6 10.1 - - - +
437A ASP* 1.3 96.6 + - - +
439A MET* 1.3 62.3 + - - +
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Residues in contact with MET 439 (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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289A VAL* 5.3 0.7 - - - +
378A HIS* 3.9 17.0 - - + +
379A MET* 3.3 33.1 - - - +
380A ALA* 3.0 30.1 + - + +
403A ASN* 3.3 21.8 - - - +
405A LEU* 3.6 4.9 - - - +
419A GLU* 4.4 1.3 - - - +
421A ILE* 4.3 16.6 - - + -
429A ILE* 4.1 18.8 - - + -
431A LEU* 4.2 16.4 - - + -
433A ILE* 3.8 23.5 - - + +
438A ALA* 1.3 76.7 - - - +
440A ALA* 1.3 75.3 + - - +
441A ILE* 4.2 11.7 - - + -
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Residues in contact with ALA 440 (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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289A VAL* 5.3 2.5 - - + -
293A ALA* 6.2 0.9 - - + -
348A PHE* 4.0 16.8 - - + -
378A HIS 3.4 7.9 - - - +
379A MET* 4.4 6.1 - - + -
403A ASN* 3.4 6.3 + - - -
404A VAL* 3.0 36.3 + - + +
405A LEU* 3.5 29.2 - - + -
439A MET* 1.3 79.1 - - - +
441A ILE* 1.3 66.2 + - - +
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Residues in contact with ILE 441 (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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348A PHE* 3.2 7.1 - - - -
377A GLY* 3.0 2.8 - - - -
378A HIS* 2.9 46.8 + - + +
396A MET* 4.3 9.4 - - - -
401A TYR* 3.6 35.7 - - + -
402A CYS 3.3 17.7 - - - +
404A VAL* 4.7 2.7 - - - -
421A ILE* 3.8 26.9 - - + -
423A VAL* 4.0 11.0 - - + -
429A ILE* 3.9 27.1 - - + -
439A MET* 4.3 3.8 - - - -
440A ALA* 1.3 80.7 - - - +
442A HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 442 (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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347A ASP* 2.8 30.7 + - - -
348A PHE* 3.9 22.7 - - + -
351A ASN* 3.4 30.9 + - + +
352A THR* 4.3 9.0 - - + -
376A SER 3.1 13.2 - - - +
377A GLY* 3.8 2.9 - - - -
396A MET* 3.9 4.7 - - - -
401A TYR* 3.6 12.7 - - - -
404A VAL* 3.9 12.3 - - + -
441A ILE* 1.3 77.0 - - - +
443A LYS* 1.3 58.7 + - - +
444A ASN* 2.9 53.5 + - + +
445A ALA* 2.9 26.2 + - + +
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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