Contacts of the strand formed by residues 416 - 423 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B GLN* 2.6 25.1 + - - +
325B GLU* 3.8 3.6 - - - +
326B VAL* 5.6 2.1 - - - +
411B TYR 4.6 2.1 - - - +
412B SER* 3.4 17.4 + - - +
413B ARG* 3.0 66.1 + - - +
415B GLY* 1.4 76.1 - - - +
417B TYR* 1.3 67.3 + - - +
439B ARG* 3.0 36.5 + - + +
440B VAL 3.6 9.4 - - - +
441B LEU* 4.2 15.6 - - + +
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Residues in contact with TYR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLN* 3.4 20.2 + - - -
325B GLU* 3.2 16.2 - - - -
415B GLY* 4.0 26.1 + - - -
416B GLU* 1.3 81.8 - - - +
418B PHE* 1.4 60.9 + - - +
438B MET 4.2 0.2 - - - +
439B ARG* 3.6 6.7 - - - +
440B VAL* 2.8 47.1 + - + +
442B PHE* 4.2 21.3 - + - -
519B PHE* 4.4 4.8 - - + -
523B VAL* 4.7 19.1 - - + -
526B LYS* 3.8 52.8 + - + -
527B LEU* 4.5 16.7 - - + +
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Residues in contact with PHE 418 (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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325B GLU* 2.8 40.3 + - + +
326B VAL* 3.7 42.4 - - + -
328B ARG* 6.2 0.2 - - - +
329B GLY* 5.7 4.9 + - - -
364B VAL* 3.7 31.4 - - + -
367B ALA* 4.2 13.0 - - + -
368B SER* 4.0 15.5 - - - -
417B TYR* 1.4 72.8 - - - +
419B SER* 1.3 92.7 + - - +
420B ALA* 5.1 1.3 - - + -
437B GLY* 4.0 4.0 - - - -
438B MET 2.7 34.5 - - - -
439B ARG* 4.6 12.6 - - + -
519B PHE* 4.4 2.6 - - - -
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLY* 5.5 3.1 - - - -
418B PHE* 1.3 84.1 + - - +
420B ALA* 1.3 63.5 + - - +
421B PHE* 3.9 26.8 - - - -
438B MET* 3.0 33.4 + - - +
519B PHE* 3.4 21.4 - - - -
522B THR* 4.5 8.1 + - - -
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Residues in contact with ALA 420 (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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329B GLY* 4.1 27.0 - - - +
332B GLU* 4.9 14.9 - - + +
333B GLN* 4.2 18.5 - - + +
364B VAL* 4.3 10.8 - - + -
418B PHE* 5.1 1.6 - - + -
419B SER* 1.3 77.3 - - - +
421B PHE* 1.3 74.6 + - - +
436B SER 3.4 10.1 - - - +
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN* 3.8 3.5 - - - +
419B SER* 3.9 25.8 - - - -
420B ALA* 1.3 84.6 - - - +
422B LYS* 1.3 63.0 + - - +
435B THR* 3.3 4.3 + - - -
436B SER* 2.7 36.3 + - - +
438B MET* 3.8 15.7 - - + -
515B PHE* 3.0 70.2 - + + -
518B LYS* 4.2 22.9 - - + -
519B PHE* 3.9 21.8 - - + -
522B THR* 5.3 1.6 - - - -
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Residues in contact with LYS 422 (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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332B GLU 6.1 0.2 - - - +
333B GLN* 3.7 17.4 + - - +
336B TRP* 3.3 42.0 + - + -
337B PHE* 3.9 2.6 - - - +
360B ASP* 2.9 46.7 + - + +
421B PHE* 1.3 78.1 - - - +
423B GLN* 1.3 68.8 + - - +
424B ALA* 5.4 4.9 - - + -
430B ASP 3.5 12.9 + - - -
432B ALA* 3.4 22.9 - - + -
434B VAL 4.1 4.9 - - - -
435B THR* 4.4 1.3 - - - +
515B PHE* 4.1 5.5 - - - -
1169B THR* 6.1 0.3 - - - +
3006B FAD 3.3 18.6 + - - -
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Residues in contact with GLN 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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422B LYS* 1.3 76.6 - - - +
424B ALA* 1.3 83.8 + - - +
425B SER* 3.3 15.8 - - - +
427B ARG* 6.0 2.0 - - - +
432B ALA* 3.7 22.8 - - - -
433B LYS* 4.0 10.3 + - + +
434B VAL* 3.7 10.1 + - + +
507B PHE* 4.4 8.1 - - + -
511B LEU* 3.7 31.9 - - + -
515B PHE* 4.0 11.7 - - + -
1169B THR* 3.4 34.3 + - - +
1171B ASP* 4.0 17.8 + - - +
1303B PRO* 4.1 16.0 - - - +
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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