Contacts of the strand formed by residues 416 - 423 (chain C) in PDB entry 2CKJ
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 GLU 416 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLN* 2.5 29.2 + - - +
325C GLU* 3.7 7.5 - - - +
326C VAL* 5.9 2.1 - - - +
411C TYR 4.6 1.9 - - - +
412C SER* 3.5 13.4 + - - +
413C ARG* 3.0 67.6 + - - +
415C GLY* 1.4 73.9 - - - +
417C TYR* 1.3 69.4 + - - +
439C ARG* 2.8 37.5 + - + +
440C VAL 3.7 10.1 - - - +
441C LEU* 4.2 13.1 - - + +
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Residues in contact with TYR 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLN* 3.3 20.9 - - - -
325C GLU* 3.4 13.2 - - - +
415C GLY* 3.9 27.8 + - - -
416C GLU* 1.3 88.3 - - - +
418C PHE* 1.4 59.8 + - - +
439C ARG* 3.5 7.4 - - - +
440C VAL* 2.9 39.8 + - + +
442C PHE* 4.3 19.7 - + - -
519C PHE* 4.5 3.9 - - + -
523C VAL* 4.2 27.4 - - + -
526C LYS* 3.0 47.6 + - + -
527C LEU* 3.9 24.8 - - + +
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Residues in contact with PHE 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C GLU* 2.8 40.7 + - + +
326C VAL* 3.6 41.5 - - + -
329C GLY* 5.5 6.4 + - - -
364C VAL* 3.6 31.9 - - + -
367C ALA* 4.2 11.9 - - + -
368C SER* 3.9 16.8 - - - -
417C TYR* 1.4 72.9 - - - +
419C SER* 1.3 94.5 + - - +
420C ALA* 5.0 1.1 - - + -
437C GLY* 4.0 4.5 - - - -
438C MET 2.7 32.8 - - - -
439C ARG* 4.5 13.9 - - + -
519C PHE* 4.4 3.9 - - - -
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Residues in contact with SER 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLY* 5.4 3.4 - - - -
418C PHE* 1.3 98.1 + - - +
420C ALA* 1.4 60.4 + - - +
421C PHE* 3.8 28.0 - - - -
438C MET* 3.0 20.7 + - - +
519C PHE* 3.8 18.5 - - - -
522C THR* 4.2 12.3 + - - -
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Residues in contact with ALA 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLY* 4.0 30.1 - - - +
332C GLU* 4.6 18.6 - - + +
333C GLN* 4.2 17.7 - - + +
364C VAL* 4.5 9.6 - - + -
418C PHE* 5.1 0.7 - - + -
419C SER* 1.4 74.1 - - - +
421C PHE* 1.4 74.6 + - - +
436C SER 3.4 11.2 - - - +
437C GLY* 4.6 0.2 - - - -
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Residues in contact with PHE 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C GLN* 3.9 4.5 - - - +
419C SER* 3.8 25.4 - - - -
420C ALA* 1.4 80.3 - - - +
422C LYS* 1.3 60.1 + - - +
435C THR* 3.4 4.5 + - - -
436C SER* 2.8 37.1 + - - +
438C MET* 4.1 15.9 - - + -
515C PHE* 3.4 68.4 - + + -
518C LYS* 4.1 26.5 - - + -
519C PHE* 4.0 16.8 - - + -
522C THR* 5.4 1.8 - - - -
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Residues in contact with LYS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C GLN* 3.7 16.5 + - - +
336C TRP* 3.3 42.9 + - + -
337C PHE* 4.0 3.0 - - - +
360C ASP* 3.1 45.2 + - + +
421C PHE* 1.3 75.5 - - - +
423C GLN* 1.3 71.0 + - - +
424C ALA* 5.0 4.9 - - - +
432C ALA* 4.6 12.6 - - + +
434C VAL 3.9 5.4 - - - +
435C THR* 4.3 4.0 - - - +
515C PHE* 4.0 4.9 - - - -
1169C THR* 6.0 0.2 - - - +
3006C FAD 3.5 13.9 + - - -
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Residues in contact with GLN 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C LYS* 1.3 80.1 - - - +
424C ALA* 1.3 94.3 + - - +
425C SER* 3.6 1.4 - - - +
426C ARG 5.4 1.2 + - - +
427C ARG* 6.0 2.8 - - - +
432C ALA 2.6 21.7 - - - +
433C LYS* 3.8 8.5 - - - +
434C VAL 3.1 14.7 + - - +
507C PHE* 4.3 6.3 - - + -
511C LEU* 4.1 19.5 - - + +
515C PHE* 3.9 16.7 - - + -
1169C THR* 3.2 27.2 + - + +
1170C GLY 4.0 1.7 - - - -
1171C ASP* 3.6 30.6 + - - +
1303C PRO* 4.6 6.1 - - - +
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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