Contacts of the strand formed by residues 422 - 431 (chain A) in PDB entry 2JKK
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 ILE 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A ILE* 4.1 9.6 - - + -
419A ARG 3.0 16.7 + - - +
420A GLU* 4.4 3.3 - - - +
421A ARG* 1.3 78.6 - - - +
423A GLU* 1.3 63.9 + - - +
424A LEU 4.0 1.4 + - - +
440A ILE 3.3 4.5 - - - +
441A TYR* 3.8 35.2 - - + -
442A MET* 4.6 2.9 - - - +
451A VAL* 4.5 2.2 - - + -
453A ILE* 3.8 26.7 - - + -
490A ILE* 4.1 21.5 - - + -
496A TRP* 3.7 27.4 - - + -
498A ILE* 4.1 24.5 - - + -
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Residues in contact with GLU 423 (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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421A ARG 4.1 0.4 + - - -
422A ILE* 1.3 74.1 - - - +
424A LEU* 1.3 69.9 + - - +
425A GLY* 4.6 0.2 - - - -
439A GLY* 3.2 4.0 - - - -
440A ILE* 3.0 50.4 + - + +
442A MET* 4.5 20.0 - - + +
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Residues in contact with LEU 424 (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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422A ILE* 4.0 2.6 + - - +
423A GLU* 1.3 77.9 - - - +
425A GLY* 1.3 61.5 + - - +
437A HIS* 3.7 39.3 - - + +
438A GLN 4.3 0.9 - - - -
453A ILE* 3.6 41.3 - - + -
455A THR* 4.6 4.5 - - + -
496A TRP* 3.7 34.0 - - + -
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Residues in contact with GLY 425 (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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423A GLU* 3.5 3.9 + - - -
424A LEU* 1.3 75.6 - - - +
426A ARG* 1.3 60.5 + - - -
437A HIS* 2.9 23.2 - - - -
438A GLN* 2.7 25.5 + - - -
439A GLY* 4.5 2.2 - - - -
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Residues in contact with ARG 426 (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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425A GLY* 1.3 71.4 - - - -
427A CYS* 1.3 70.7 + - - +
428A ILE* 3.5 5.3 + - + -
437A HIS* 3.3 1.1 - - - -
438A GLN* 2.9 64.3 + - + +
1686A BI9 6.2 2.5 - - - -
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Residues in contact with CYS 427 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A ARG* 1.3 80.5 - - - +
428A ILE* 1.3 59.8 + - - +
429A GLY* 3.4 29.4 - - - -
435A ASP* 4.2 17.0 - - - +
436A VAL 3.4 8.7 - - - -
437A HIS* 3.5 17.8 - - + +
1686A BI9 5.3 2.8 - - - +
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Residues in contact with ILE 428 (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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426A ARG* 3.5 16.8 + - + +
427A CYS* 1.3 77.3 - - - +
429A GLY* 1.3 57.1 + - - +
436A VAL* 2.8 25.9 + - + +
437A HIS 3.8 17.7 - - - +
438A GLN* 3.9 20.2 - - + +
452A ALA* 4.4 1.3 - - + -
501A LEU* 4.2 7.6 - - + -
1686A BI9 3.4 106.1 - - + +
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Residues in contact with GLY 429 (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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427A CYS* 3.4 17.6 - - - -
428A ILE* 1.3 82.2 - - - +
430A GLU* 1.3 64.6 + - - +
435A ASP* 3.6 1.6 - - - +
436A VAL* 2.9 23.2 + - - -
1686A BI9 4.0 11.9 - - - -
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Residues in contact with GLU 430 (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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429A GLY* 1.3 76.5 - - - +
431A GLY* 1.3 66.6 + - - +
434A GLY 3.5 10.8 - - - +
435A ASP* 4.4 10.4 - - - +
436A VAL* 4.0 8.9 - - - +
457A LYS* 6.0 0.2 + - - -
567A LEU* 4.1 5.9 - - - +
1686A BI9 4.9 6.4 - - - -
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Residues in contact with GLY 431 (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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430A GLU* 1.3 80.7 - - - +
432A GLN* 1.3 66.0 + - - -
433A PHE 3.2 4.2 + - - -
434A GLY 2.8 20.2 + - - +
567A LEU* 3.7 22.2 - - - +
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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