Contacts of the helix formed by residues 469 - 489 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A VAL* 3.6 3.4 - - - +
468A GLY* 1.3 81.4 - - - +
470A PRO* 1.3 77.9 - - - +
471A ASN* 3.9 6.6 + - - +
472A ALA* 3.1 21.0 + - - +
473A ALA* 2.9 24.0 + - - +
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Residues in contact with PRO 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A THR 4.6 1.5 - - - +
418A ALA* 3.8 13.0 - - + +
419A ALA* 3.7 27.3 - - - +
432A ALA* 4.4 19.7 - - + +
433A LYS* 5.5 2.9 - - + +
469A SER* 1.3 88.0 - - - +
471A ASN* 1.3 62.0 + - - +
473A ALA* 3.2 9.8 + - + +
474A VAL* 3.0 24.9 + - - +
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Residues in contact with ASN 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA* 3.6 7.4 - - - +
469A SER* 3.2 6.8 + - - +
470A PRO* 1.3 79.7 - - - +
472A ALA* 1.3 62.8 + - - +
474A VAL* 3.1 9.7 + - - +
475A LEU* 3.1 27.6 + - + +
528A LEU* 3.8 26.2 - - + +
532A LYS* 2.7 33.9 + - - +
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Residues in contact with ALA 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A VAL* 3.7 15.4 - - + +
468A GLY 4.0 5.8 - - - +
469A SER* 3.1 26.5 + - - +
471A ASN* 1.3 78.8 - - - +
473A ALA* 1.3 53.5 + - - +
475A LEU* 3.2 11.0 + - - +
476A TRP* 2.7 35.5 + - - +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A THR* 4.4 10.1 - - + +
435A VAL* 6.4 1.1 - - + -
436A LEU* 3.7 26.2 - - + +
467A VAL* 3.2 18.1 - - + +
469A SER 2.9 12.1 + - - +
470A PRO* 3.2 13.0 + - + +
472A ALA* 1.3 76.6 - - - +
474A VAL* 1.3 63.8 + - - +
476A TRP* 3.3 2.4 + - - +
477A LEU* 3.1 24.3 + - - +
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A HIS* 5.1 1.6 + - - -
415A THR* 3.4 43.6 + - - +
416A VAL* 3.8 22.2 - - + +
419A ALA* 3.9 10.1 - - + -
470A PRO 3.0 14.9 + - - +
471A ASN* 3.1 8.9 + - - +
473A ALA* 1.3 77.6 - - - +
475A LEU* 1.3 61.7 + - - +
477A LEU* 3.5 2.9 + - - +
478A TRP* 3.1 21.3 + - - +
528A LEU* 4.0 14.8 - - + -
531A LEU* 3.7 25.8 - - + -
532A LYS* 5.8 1.3 - - + +
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ASN* 3.1 19.7 + - + +
472A ALA* 3.7 10.1 - - - +
474A VAL* 1.3 74.4 - - - +
476A TRP* 1.3 60.3 + - - +
478A TRP* 3.4 28.1 - - + -
479A SER* 2.9 30.9 + - - -
524A VAL* 3.6 39.7 - - + +
527A THR* 4.5 2.0 - - + -
528A LEU* 4.2 20.0 - - + +
531A LEU* 4.0 17.0 - - + -
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Residues in contact with TRP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A LEU* 3.9 15.3 - - + -
456A PHE* 4.0 20.9 - + - -
459A MET* 3.8 9.6 - - + -
460A ALA* 3.7 31.9 - - - -
463A SER* 3.1 18.8 + - - -
464A MET* 3.3 34.7 - - + +
466A ARG* 3.8 27.2 - - - +
467A VAL* 3.7 25.8 - - + -
472A ALA 2.7 21.1 + - - +
473A ALA* 3.6 5.2 - - - +
474A VAL 3.3 0.2 - - - -
475A LEU* 1.3 74.9 - - - +
477A LEU* 1.3 69.1 + - + +
479A SER* 3.3 5.0 + - - -
480A SER* 2.9 61.2 + - - -
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 3.8 10.8 - - + -
411A PHE* 3.6 21.3 - - + +
412A HIS* 3.6 43.1 - - + +
415A THR* 3.8 14.4 - - + +
436A LEU* 4.5 7.0 - - + -
439A ILE* 4.5 4.5 - - + -
456A PHE* 3.8 30.7 - - + -
473A ALA 3.1 13.5 + - - +
474A VAL 3.9 3.1 - - - +
476A TRP* 1.3 88.7 - - + +
478A TRP* 1.3 59.9 + - - +
480A SER* 3.4 1.9 + - - -
481A HIS* 2.9 31.4 + - - +
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Residues in contact with TRP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A HIS* 3.8 11.8 - - + +
474A VAL 3.1 17.8 + - - +
475A LEU* 3.4 29.6 - - + +
477A LEU* 1.3 77.2 - - - +
479A SER* 1.3 83.8 + - - +
481A HIS 3.2 1.6 + - - -
482A ASN* 3.1 13.7 + - - +
503A TRP* 2.8 23.9 + + - -
504A PRO* 3.8 5.9 - - - +
522A TRP* 3.5 55.0 - + + -
524A VAL* 5.3 9.6 - - + -
527A THR* 3.5 19.7 - - + +
531A LEU* 3.9 26.7 - - + -
550A FAD 2.9 40.8 + + - +
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 4.6 11.4 + - - -
475A LEU 2.9 19.1 + - - -
476A TRP* 3.3 7.8 + - - -
478A TRP* 1.3 94.8 - - - +
480A SER* 1.3 69.3 + - - +
482A ASN* 3.1 8.5 + - - +
483A ARG* 3.0 30.8 + - - +
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Residues in contact with SER 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 4.8 1.1 - - - -
456A PHE* 5.5 0.2 - - - -
459A MET* 3.3 40.7 - - - +
466A ARG* 5.7 0.5 + - - -
476A TRP* 2.9 59.5 + - - -
477A LEU* 3.7 6.3 - - - -
479A SER* 1.3 78.6 + - - +
481A HIS* 1.3 62.0 + - - +
483A ARG* 3.2 13.7 + - - +
484A VAL* 3.2 8.7 + - - +
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Residues in contact with HIS 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP* 3.3 56.6 + + + -
412A HIS* 2.8 19.9 + - - +
477A LEU 2.9 19.2 + - - +
479A SER 3.2 0.2 - - - -
480A SER* 1.3 77.4 - - - +
482A ASN* 1.3 57.3 + - - +
484A VAL* 3.1 4.3 + - + +
485A ASN* 2.9 36.9 + - - -
550A FAD 2.8 69.8 + + + +
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Residues in contact with ASN 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A TRP* 3.1 28.0 + - - +
479A SER* 3.1 10.0 + - - +
481A HIS* 1.3 78.5 - - - +
483A ARG* 1.3 56.2 + - + +
485A ASN* 3.0 16.1 + - - +
486A ALA* 2.9 25.5 + - - +
502A GLN* 3.1 31.0 + - - +
503A TRP 2.8 47.4 + - - +
522A TRP* 4.0 10.9 - - - +
550A FAD 3.4 6.8 + - - -
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Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A MET* 3.5 37.8 - - - +
462A ALA* 5.7 3.6 - - - +
463A SER* 5.9 1.2 + - - -
479A SER* 3.0 18.5 + - - +
480A SER* 3.2 11.1 + - - +
482A ASN* 1.3 77.1 - - + +
484A VAL* 1.3 60.1 + - - +
486A ALA* 3.6 3.3 + - - +
487A ARG* 3.0 46.8 + - - +
547A FLC 2.9 53.7 + - + +
517B LEU* 3.2 30.4 + - + -
519B VAL 6.1 0.2 - - - -
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 4.2 13.7 - - + -
455A HIS* 5.1 1.3 - - + +
459A MET* 3.5 16.6 - - + -
480A SER 3.5 2.9 - - - +
481A HIS 3.1 9.5 + - - +
483A ARG* 1.3 76.4 - - - +
485A ASN* 1.3 68.2 + - - +
487A ARG* 3.2 5.3 + - - +
488A LEU* 3.1 35.0 + - + +
550A FAD 3.7 44.2 - - + +
517B LEU* 3.4 31.4 - - + -
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Residues in contact with ASN 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A HIS* 2.9 31.1 + - - -
482A ASN* 3.0 30.7 + - - +
484A VAL* 1.3 80.1 - - - +
486A ALA* 1.3 55.5 + - - +
488A LEU* 3.3 1.4 + - - +
489A ALA* 2.9 31.1 + - - +
500A LYS* 3.6 24.9 + - + +
501A VAL 3.3 21.6 + - - +
502A GLN* 3.9 3.8 - - - +
550A FAD 3.0 33.5 + - - -
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ASN 2.9 15.7 + - - +
483A ARG* 3.7 9.2 - - - +
484A VAL 3.2 0.4 - - - -
485A ASN* 1.3 78.6 - - - +
487A ARG* 1.3 62.0 + - - +
488A LEU 3.4 0.2 + - - -
489A ALA* 3.5 17.4 + - - +
502A GLN* 3.8 14.1 - - - +
547A FLC 5.3 1.1 - - - +
502B GLN* 6.4 2.5 - - + -
506B ARG* 5.2 1.2 + - - -
513B HIS* 5.3 3.8 + - - -
521B VAL* 4.3 27.2 - - + +
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A HIS* 5.8 2.5 - - + +
483A ARG* 3.0 35.9 + - - +
484A VAL* 3.2 9.2 + - + +
486A ALA* 1.3 79.1 - - - +
488A LEU* 1.3 62.7 + - + +
547A FLC 2.5 44.5 + - - -
506B ARG* 3.0 34.6 + - - +
513B HIS* 6.2 0.4 - - - -
514B ASN 4.3 9.0 - - - +
515B GLU* 3.5 34.3 - - - +
516B ARG 3.6 8.8 + - - +
517B LEU* 3.4 26.6 + - + +
519B VAL 3.0 24.0 + - - -
521B VAL* 3.4 31.3 - - + +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A HIS* 6.0 1.8 - - + +
484A VAL* 3.1 29.9 + - + +
485A ASN 4.0 2.7 - - - +
487A ARG* 1.3 81.3 - - + +
489A ALA* 1.3 66.1 + - - +
490A GLY 3.2 0.7 + - - -
491A ALA* 3.0 22.6 + - + +
493A SER* 4.5 12.1 + - - +
494A GLU* 4.0 5.4 - - - +
500A LYS* 3.9 23.5 - - + +
550A FAD 3.6 72.7 - - + +
515B GLU* 4.6 10.5 - - - +
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Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ASN 2.9 15.9 + - - +
486A ALA* 3.6 13.9 - - - +
487A ARG 3.5 1.0 - - - -
488A LEU* 1.3 74.5 - - - +
490A GLY* 1.3 63.4 + - - +
491A ALA 3.1 1.6 + - - -
494A GLU* 3.6 7.0 - - - -
500A LYS* 3.6 18.2 - - + +
502B GLN* 6.5 0.7 - - + -
506B ARG* 3.2 19.1 + - - +
513B HIS* 5.4 2.6 - - - -
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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
------------------------------------------------------------
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