Contacts of the helix formed by residues 469 - 489 (chain B) in PDB entry 3LLK
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 SER 469 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LYS* 6.5 1.3 - - - -
467B VAL* 3.8 4.0 - - - +
468B GLY* 1.3 80.8 - - - +
470B PRO* 1.3 71.1 - - - +
471B ASN* 3.5 8.4 + - - +
472B ALA* 3.0 24.0 + - - +
473B ALA* 2.8 29.4 + - - +
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Residues in contact with PRO 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR 4.5 1.1 - - - +
418B ALA* 4.1 6.5 - - + +
419B ALA* 3.5 31.7 - - - +
429B ALA* 5.7 0.9 - - - +
432B ALA* 3.8 29.8 - - + +
433B LYS* 5.4 2.2 - - + +
469B SER* 1.3 86.7 - - - +
471B ASN* 1.3 62.6 + - - +
473B ALA* 3.2 10.7 + - + +
474B VAL* 3.0 25.6 + - - +
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Residues in contact with ASN 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ALA* 3.6 9.3 + - - +
469B SER* 3.1 8.2 + - - +
470B PRO* 1.3 77.9 - - - +
472B ALA* 1.3 64.7 + - - +
474B VAL* 3.1 15.5 + - - +
475B LEU* 3.1 20.1 + - + +
528B LEU* 3.9 22.8 - - + +
532B LYS* 2.8 36.9 + - - +
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Residues in contact with ALA 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ARG 5.6 0.4 - - - +
467B VAL* 3.9 7.1 - - + +
468B GLY 4.0 11.2 - - - +
469B SER* 3.0 29.7 + - - +
471B ASN* 1.3 76.5 - - - +
473B ALA* 1.3 57.5 + - - +
475B LEU* 3.4 9.4 + - - +
476B TRP* 2.8 30.7 + - - +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 4.4 10.3 - - + +
432B ALA 5.9 3.1 - - - +
433B LYS* 6.6 0.2 - - - -
435B VAL* 6.1 2.5 - - + -
436B LEU* 3.7 29.6 - - + +
467B VAL* 3.5 13.0 - - + +
469B SER 2.8 12.4 + - - +
470B PRO* 3.2 14.6 - - + +
472B ALA* 1.3 79.3 - - - +
474B VAL* 1.3 62.4 + - - +
476B TRP* 3.7 1.7 - - - +
477B LEU* 3.2 22.3 + - - +
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B HIS* 5.1 2.0 + - - +
415B THR* 3.4 42.3 + - - +
416B VAL* 3.8 20.9 - - + +
419B ALA* 3.6 12.6 - - + -
470B PRO 3.0 15.8 + - - +
471B ASN* 3.1 6.9 + - - +
473B ALA* 1.3 79.1 - - - +
475B LEU* 1.3 63.5 + - - +
477B LEU* 3.4 2.9 + - - +
478B TRP* 3.1 19.9 + - - +
528B LEU* 4.1 15.9 - - + -
531B LEU* 3.7 24.7 - - + -
532B LYS* 5.6 2.2 - - + -
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Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASN* 3.1 18.6 + - + +
472B ALA* 3.9 7.4 - - - +
474B VAL* 1.3 72.3 - - - +
476B TRP* 1.3 59.9 + - - +
478B TRP* 3.3 29.8 + - + +
479B SER* 2.9 31.8 + - - -
524B VAL* 3.5 41.7 - - + +
527B THR* 4.6 1.3 - - + -
528B LEU* 4.2 24.2 - - + +
531B LEU* 4.1 16.8 - - + -
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Residues in contact with TRP 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU* 3.9 12.8 - - + -
456B PHE* 4.1 20.0 - + - -
459B MET* 3.6 25.8 - - + -
460B ALA* 3.7 17.5 - - + -
463B SER* 3.0 25.5 + - - -
464B MET* 3.2 42.5 - - + +
467B VAL* 3.6 26.0 - - + -
472B ALA 2.8 17.8 + - - +
473B ALA 3.7 4.7 - - - +
474B VAL 3.3 0.2 - - - -
475B LEU* 1.3 77.2 - - - +
477B LEU* 1.3 62.4 + - + +
479B SER* 3.2 7.6 + - - -
480B SER* 2.6 59.2 + - - -
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 3.4 31.4 - - + -
411B PHE* 3.6 40.2 - - + +
412B HIS* 3.6 22.2 - - + +
415B THR* 3.7 12.3 - - + +
436B LEU* 4.1 14.6 - - + -
439B ILE* 4.7 2.5 - - + -
456B PHE* 4.1 20.6 - - + -
473B ALA 3.2 13.8 + - - +
474B VAL 3.9 3.1 - - - +
476B TRP* 1.3 84.0 - - + +
478B TRP* 1.3 60.9 + - - +
480B SER* 4.3 1.6 - - - -
481B HIS* 2.9 31.4 + - - +
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Residues in contact with TRP 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B HIS* 3.9 3.3 - - + +
474B VAL 3.1 12.2 + - - +
475B LEU* 3.5 33.7 - - + +
477B LEU* 1.3 76.4 - - - +
479B SER* 1.3 83.0 + - - +
481B HIS 3.2 0.9 + - - -
482B ASN* 3.0 15.1 + - - +
503B TRP* 2.9 20.2 + + - -
504B PRO* 3.8 6.3 - - - +
522B TRP* 3.5 53.8 - + + -
524B VAL* 5.1 10.1 - - + -
527B THR* 3.5 21.7 - - + +
531B LEU* 3.9 25.1 - - + -
550B FAD 3.0 52.8 + + - +
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LEU 2.9 19.4 + - - -
476B TRP* 3.2 11.8 + - - -
478B TRP* 1.3 92.1 - - - +
480B SER* 1.3 58.9 + - - +
482B ASN* 3.2 8.8 + - - +
483B ARG* 3.0 36.1 + - - +
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Residues in contact with SER 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 5.3 0.9 - - - -
456B PHE* 5.6 0.2 - - - -
459B MET* 3.3 38.8 - - - +
476B TRP* 2.6 55.0 + - - -
477B LEU* 3.7 7.9 - - - -
478B TRP 3.2 0.2 - - - -
479B SER* 1.3 80.7 + - - +
481B HIS* 1.3 62.3 + - - +
483B ARG* 3.2 5.8 + - - +
484B VAL* 3.1 17.5 + - - +
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Residues in contact with HIS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 3.4 50.1 + + + -
412B HIS* 2.9 20.1 + - - +
477B LEU 2.9 19.4 + - - +
478B TRP 3.2 0.2 + - - -
480B SER* 1.3 77.4 - - - +
482B ASN* 1.3 57.0 + - - +
484B VAL* 3.2 3.6 + - + +
485B ASN* 2.9 37.1 + - - -
550B FAD 2.7 75.3 + + + +
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Residues in contact with ASN 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B TRP* 3.0 32.3 + - - +
479B SER* 3.7 8.9 - - - +
480B SER 3.2 0.2 - - - -
481B HIS* 1.3 75.1 - - - +
483B ARG* 1.3 59.8 + - + +
485B ASN* 3.1 10.6 + - - +
486B ALA* 2.8 26.2 + - - +
502B GLN* 3.2 29.9 - - - +
503B TRP 2.8 46.3 + - - +
522B TRP* 4.2 8.3 - - - +
550B FAD 3.2 11.7 + - - -
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Residues in contact with ARG 483 (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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517A LEU* 2.7 30.2 + - + -
518A ASP 5.4 1.0 + - - -
459B MET* 3.6 39.3 + - - +
462B ALA* 5.5 5.7 - - - +
463B SER* 5.5 3.6 + - - -
479B SER* 3.0 21.9 + - - +
480B SER* 3.2 11.1 + - - +
482B ASN* 1.3 77.3 - - + +
484B VAL* 1.3 61.9 + - - +
486B ALA* 3.4 6.6 + - - +
487B ARG* 3.2 58.9 + - - +
502B GLN* 5.5 0.7 - - - +
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Residues in contact with VAL 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LEU* 3.4 29.2 - - + -
408B TRP* 4.2 14.4 - - + -
455B HIS* 5.2 0.7 - - + +
459B MET* 3.5 17.5 - - + -
480B SER 3.1 4.6 + - - +
481B HIS 3.4 8.3 - - - +
483B ARG* 1.3 74.1 - - - +
485B ASN* 1.3 68.1 + - - +
487B ARG* 3.1 6.8 + - - +
488B LEU* 3.0 45.1 + - + +
550B FAD 3.6 34.5 - - + +
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Residues in contact with ASN 485 (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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481B HIS* 2.9 30.6 + - - -
482B ASN* 3.2 23.2 + - - +
484B VAL* 1.3 79.4 - - - +
486B ALA* 1.3 57.0 + - - +
488B LEU* 3.2 1.8 + - - +
489B ALA* 2.8 32.3 + - - +
500B LYS* 3.6 25.4 + - + +
501B VAL 3.4 21.4 + - - +
502B GLN* 4.0 2.2 - - - +
550B FAD 3.0 38.8 + - - -
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Residues in contact with ALA 486 (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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502A GLN* 6.2 3.6 - - + -
506A ARG* 5.2 1.0 + - - -
513A HIS* 5.5 4.9 + - - -
521A VAL* 5.1 17.5 - - + +
482B ASN 2.8 15.5 + - - +
483B ARG* 3.6 9.0 - - - +
484B VAL 3.2 0.2 - - - -
485B ASN* 1.3 78.4 - - - +
487B ARG* 1.3 64.1 + - - +
488B LEU 3.5 0.3 + - - -
489B ALA* 3.6 16.6 + - - +
502B GLN* 3.8 15.9 + - - +
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Residues in contact with ARG 487 (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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506A ARG* 3.1 33.2 + - - +
513A HIS* 6.3 0.4 - - - -
514A ASN 4.2 12.5 + - - +
515A GLU* 3.9 12.8 - - - +
516A ARG 3.6 9.2 + - - -
517A LEU* 3.3 29.0 - - + +
519A VAL 2.9 27.9 + - - -
520A PRO* 3.7 1.4 + - - +
521A VAL* 3.3 45.7 - - + +
455B HIS* 5.9 1.6 - - + +
483B ARG* 3.2 63.0 + - - +
484B VAL* 3.1 9.0 + - + +
486B ALA* 1.3 79.5 - - - +
488B LEU* 1.3 64.0 + - + +
491B ALA* 4.8 0.3 - - - +
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B HIS* 5.9 1.1 - - + +
484B VAL* 3.0 40.4 + - + +
485B ASN* 4.0 3.1 - - - +
487B ARG* 1.3 81.7 - - + +
489B ALA* 1.3 67.2 + - - +
490B GLY 3.2 1.0 + - - -
491B ALA* 3.0 23.7 + - + +
493B SER* 4.9 8.7 - - - +
494B GLU* 4.0 5.1 - - - +
500B LYS* 4.0 22.2 - - + +
550B FAD 3.5 65.1 - - + +
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ARG* 3.4 18.2 + - - +
513A HIS* 5.6 1.7 - - - -
485B ASN 2.8 16.2 + - - +
486B ALA* 3.8 13.7 - - - +
487B ARG 3.5 1.0 - - - -
488B LEU* 1.3 75.1 - - - +
490B GLY* 1.3 58.9 + - - +
491B ALA 3.1 4.6 + - - -
494B GLU* 3.6 8.3 - - - +
500B LYS* 3.6 18.4 - - + +
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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
------------------------------------------------------------
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