Contacts of the helix formed by residues 476 - 489 (chain Z) in PDB entry 5L4K
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 THR 476 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405Z HIS* 5.7 1.6 - - - +
408Z LEU* 5.7 2.0 - - + -
438Z ASP* 3.4 18.7 + - - +
439Z TYR* 4.0 29.2 - - + +
442Z SER* 2.8 30.6 + - - -
475Z ASN* 1.3 90.6 - - + +
477Z MET* 1.3 63.2 + - - +
478Z ARG 3.6 0.2 - - - -
479Z LEU* 3.9 3.2 - - - +
480Z GLY 3.1 21.0 + - - -
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Residues in contact with MET 477 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438Z ASP* 3.0 30.3 - - + +
441Z LYS* 3.5 32.8 - - + -
442Z SER* 3.8 5.2 - - - +
445Z LEU* 3.2 6.4 - - + +
469Z TYR* 3.6 22.2 - - + -
472Z HIS* 3.5 28.5 - - + +
474Z SER* 3.4 14.8 + - - +
476Z THR* 1.3 79.8 + - - +
478Z ARG* 1.3 61.9 + - - +
481Z SER* 2.5 35.2 + - - -
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Residues in contact with ARG 478 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469Z TYR 3.6 15.9 - - - +
470Z VAL 3.6 18.1 + - - -
471Z LEU 4.8 2.6 + - - -
472Z HIS* 3.2 21.4 + - - +
473Z ASN* 2.8 33.6 + - - +
474Z SER* 2.8 30.6 + - - +
477Z MET* 1.3 73.1 - - - +
479Z LEU* 1.3 56.7 + - - +
481Z SER* 3.3 0.6 + - - -
482Z ILE* 2.9 37.9 + - + +
501Z LEU* 4.5 3.0 - - - +
504Z VAL* 3.0 42.1 - - - +
512Z MET 3.9 11.2 - - - -
513Z GLU* 3.5 21.3 - - - +
514Z VAL* 4.6 5.4 - - + -
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Residues in contact with LEU 479 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475Z ASN* 3.0 30.8 + - - +
476Z THR* 3.7 4.8 + - - +
477Z MET 3.2 0.8 - - - -
478Z ARG* 1.3 79.7 - - - +
480Z GLY* 1.3 60.4 + - - +
482Z ILE* 3.5 7.2 - - - +
483Z PHE* 2.9 32.9 + - + +
514Z VAL* 3.6 27.8 - - + +
515Z ALA 4.8 7.9 - - - +
517Z VAL* 4.2 23.1 - - + -
518Z THR* 4.7 3.8 - - - +
796Z LEU* 3.9 32.3 - - + -
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Residues in contact with GLY 480 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442Z SER* 4.1 15.0 - - - -
445Z LEU* 4.0 14.4 - - - +
446Z LEU* 4.7 7.9 + - - +
476Z THR 3.1 16.9 + - - -
477Z MET 3.9 0.7 - - - -
479Z LEU* 1.3 81.0 - - - +
481Z SER* 1.3 55.0 + - - +
483Z PHE* 3.4 8.4 + - - +
484Z GLY* 2.9 24.3 + - - -
796Z LEU* 5.7 1.3 - - - -
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Residues in contact with SER 481 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445Z LEU* 3.0 22.9 - - - +
466Z LEU* 3.3 18.9 - - - +
469Z TYR* 2.7 39.0 - - - +
470Z VAL* 4.2 3.6 - - - -
477Z MET 2.5 23.9 + - - -
478Z ARG 3.5 4.5 - - - -
479Z LEU 3.2 0.2 - - - -
480Z GLY* 1.3 76.1 - - - +
482Z ILE* 1.3 58.2 + - - +
484Z GLY 2.9 3.6 + - - -
485Z LEU* 2.8 24.4 + - - +
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Residues in contact with ILE 482 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470Z VAL* 4.1 14.6 - - + -
478Z ARG* 2.9 27.9 + - + +
479Z LEU* 3.5 8.1 - - - +
481Z SER* 1.3 71.4 - - - +
483Z PHE* 1.3 62.1 + - - +
485Z LEU* 4.1 10.7 - - - +
486Z GLY* 2.9 23.1 + - - -
501Z LEU* 3.2 47.9 - - + +
504Z VAL* 4.5 1.3 - - + -
514Z VAL* 3.3 20.6 - - + -
518Z THR* 3.3 36.3 - - + +
521Z ALA* 4.1 5.8 - - + +
522Z CYS* 5.8 0.9 - - - -
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Residues in contact with PHE 483 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446Z LEU* 3.6 32.1 - - + -
479Z LEU* 2.9 20.6 + - + +
480Z GLY* 3.5 9.2 - - - +
481Z SER 3.2 0.2 - - - -
482Z ILE* 1.3 79.8 - - - +
484Z GLY* 1.3 57.4 + - - +
486Z GLY 3.6 1.0 - - - -
487Z LEU* 2.9 23.7 + - + +
517Z VAL* 4.4 22.0 - - + -
520Z LEU* 5.5 2.5 - - + -
521Z ALA* 3.9 20.5 - - + +
524Z MET* 3.9 25.8 - - + -
783Z SER* 5.4 2.9 - - - -
796Z LEU* 4.0 33.9 - - + -
799Z VAL* 3.9 31.2 - - + -
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Residues in contact with GLY 484 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445Z LEU 4.2 11.2 - - - -
446Z LEU* 5.0 5.8 - - - +
449Z GLY* 5.1 5.0 - - - -
462Z ALA* 4.4 1.0 - - - +
466Z LEU* 3.7 10.8 - - - -
480Z GLY 2.9 9.9 + - - -
481Z SER 2.9 8.3 + - - -
483Z PHE* 1.3 76.5 - - - +
485Z LEU* 1.3 59.3 + - - +
487Z LEU* 3.1 9.1 + - - +
488Z ALA* 2.9 30.8 + - - +
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Residues in contact with LEU 485 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462Z ALA* 5.0 0.7 - - - -
463Z LEU* 3.8 37.0 - - + -
466Z LEU* 3.3 13.8 - - + +
470Z VAL* 4.2 3.6 - - + -
481Z SER 2.8 17.0 + - - +
482Z ILE* 4.1 10.8 - - - +
484Z GLY* 1.3 71.7 - - - -
486Z GLY* 1.3 64.4 + - - +
487Z LEU 3.4 0.3 + - - -
488Z ALA* 3.5 10.0 + - - +
489Z TYR* 3.5 27.2 + - + -
497Z VAL* 3.7 11.4 - - + +
500Z LEU* 4.6 1.6 - - + -
501Z LEU* 3.7 37.9 - - + -
525Z ILE* 3.3 28.4 - - + +
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Residues in contact with GLY 486 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482Z ILE 2.9 21.2 + - - -
483Z PHE 3.5 3.1 + - - -
484Z GLY 3.2 0.2 - - - -
485Z LEU* 1.3 77.8 - - - +
487Z LEU* 1.3 58.9 + - - +
521Z ALA* 3.3 21.2 - - - +
524Z MET* 3.5 5.1 - - - +
525Z ILE* 2.9 40.9 + - - -
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Residues in contact with LEU 487 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446Z LEU* 4.1 25.8 - - + +
449Z GLY* 4.1 17.7 - - - +
450Z ILE* 5.1 10.8 - - + +
453Z SER* 4.0 20.4 - - - +
456Z ARG* 5.3 3.8 + - - +
483Z PHE* 2.9 18.0 + - + +
484Z GLY* 3.1 6.0 + - - +
486Z GLY* 1.3 78.3 - - - +
488Z ALA* 1.3 71.9 + - - +
489Z TYR 3.6 0.2 - - - -
490Z ALA* 3.2 17.9 - - - +
491Z GLY 4.6 0.2 + - - -
524Z MET* 4.2 17.5 - - + -
799Z VAL* 4.5 17.5 - - + -
802Z SER* 5.5 6.3 - - - +
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Residues in contact with ALA 488 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449Z GLY* 5.4 0.4 - - - -
452Z ASN* 5.0 7.2 - - - +
456Z ARG* 4.0 14.4 + - - +
462Z ALA* 3.0 37.7 - - + +
484Z GLY 2.9 10.8 + - - +
485Z LEU* 3.5 4.0 + - - +
487Z LEU* 1.3 86.9 - - + +
489Z TYR* 1.3 66.1 + - + +
490Z ALA 3.1 4.5 + - - -
491Z GLY 3.7 7.3 + - - -
492Z SER* 4.2 6.2 + - - -
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Residues in contact with TYR 489 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458Z GLU* 4.3 33.9 - - + -
461Z PRO* 3.7 19.6 - - + +
462Z ALA 4.8 3.8 - - - -
463Z LEU* 3.2 29.9 + - + +
485Z LEU* 3.5 34.3 + - + -
487Z LEU 3.6 0.4 - - - -
488Z ALA* 1.3 77.7 - - + +
490Z ALA* 1.3 56.3 - - - +
491Z GLY 3.3 2.5 - - - +
492Z SER* 2.9 28.2 - - - +
494Z ARG* 4.2 15.5 + - + +
497Z VAL* 3.2 46.5 - - + +
525Z ILE* 2.9 31.3 - - + +
529Z SER* 3.2 1.6 + - - -
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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