Contacts of the strand formed by residues 422 - 430 (chain B) in PDB entry 2J0M
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B ILE* 3.8 19.5 - - + -
419B ARG* 2.9 18.4 + - - +
420B GLU 3.2 2.6 - - - +
421B ARG* 1.3 78.5 - - - +
423B GLU* 1.3 66.0 + - - +
424B LEU 3.8 2.1 + - - -
440B ILE 3.4 4.7 - - - +
441B TYR* 3.3 42.4 - - + -
451B VAL* 4.5 1.3 - - + -
453B ILE* 3.9 24.5 - - + -
490B ILE* 3.8 12.1 - - + -
496B TRP* 3.7 29.5 - - + -
498B ILE* 4.1 18.8 - - + -
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B GLU 5.7 2.5 - - - +
422B ILE* 1.3 73.2 - - - +
424B LEU* 1.3 66.5 + - - +
425B GLY* 4.5 0.2 - - - -
439B GLY* 3.3 3.8 - - - -
440B ILE* 2.9 51.4 + - + +
442B MET* 3.3 33.5 - - + +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ILE* 3.8 5.2 + - - +
423B GLU* 1.3 74.8 - - - +
425B GLY* 1.3 68.6 + - - +
437B HIS* 3.6 42.6 - - + +
453B ILE* 3.9 20.4 - - + -
455B THR* 4.7 1.8 - - + -
496B TRP* 4.0 35.2 - - + -
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Residues in contact with GLY 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLU 3.5 2.5 + - - -
424B LEU* 1.3 78.6 - - - +
426B ARG* 1.3 72.0 + - - +
437B HIS* 3.2 15.6 - - - -
438B GLN* 2.8 19.3 + - - -
439B GLY* 4.6 1.6 - - - -
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B GLY* 1.3 77.4 - - - +
427B CYS* 1.3 75.6 + - - +
428B ILE* 4.6 9.7 - - - +
437B HIS* 3.3 2.1 - - - -
438B GLN* 2.8 64.7 + - + +
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Residues in contact with CYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ARG* 1.3 86.7 - - - +
428B ILE* 1.3 67.2 + - - +
429B GLY 3.7 17.5 - - - -
430B GLU* 5.8 1.6 - - - -
435B ASP* 3.9 20.9 - - - -
436B VAL 3.4 10.1 - - - -
437B HIS* 3.4 19.5 - - + +
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Residues in contact with ILE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ARG* 4.6 14.4 - - - +
427B CYS* 1.3 79.9 - - - +
429B GLY* 1.3 55.0 + - - +
436B VAL* 2.6 27.5 + - + +
437B HIS 3.8 20.6 - - - +
438B GLN* 4.0 24.7 - - + +
452B ALA* 4.5 1.3 - - + -
501B LEU* 3.7 24.0 - - + -
506B GLU* 5.8 0.3 - - - +
1687B 4ST 3.7 57.2 - - + +
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Residues in contact with GLY 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B CYS* 3.7 12.1 - - - -
428B ILE* 1.3 81.8 - - - +
430B GLU* 1.3 63.9 + - - +
435B ASP* 3.6 5.2 - - - -
436B VAL* 3.0 27.5 + - - +
1687B 4ST 3.3 19.7 - - - -
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B CYS* 5.8 1.3 - - - -
429B GLY* 1.3 73.4 - - - +
431B GLY* 1.3 65.6 + - - +
434B GLY 5.4 0.2 - - - -
435B ASP* 3.5 23.4 - - - +
457B LYS* 5.2 7.4 + - - -
1687B 4ST 3.8 12.7 - - - +
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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