Contacts of the helix formed by residues 482 - 499 (chain D) in PDB entry 3U1K
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 482 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D ARG* 4.1 3.4 - - - -
388D ARG* 2.8 29.4 + - - -
391D THR* 4.5 1.1 - - - -
481D GLY* 1.3 76.2 - - - -
483D SER* 1.3 57.8 + - - +
484D SER 3.3 2.7 - - - -
485D MET* 3.1 20.4 + - - +
486D ALA* 3.0 20.6 + - - +
510D ALA* 4.1 25.0 + - - +
532D ASP* 4.6 2.5 - - - -
533D ILE* 5.1 2.5 - - - +
546D LYS* 5.9 0.7 - - - -
670D CIT 2.4 23.8 + - - -
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Residues in contact with SER 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D THR* 4.2 13.7 - - - -
393D VAL* 3.8 2.8 - - - +
427D TYR* 2.7 23.2 + - - -
429D PHE* 3.9 3.7 - - - -
476D VAL* 3.5 35.4 - - - -
479D SER* 5.3 1.3 - - - -
481D GLY 3.5 1.4 - - - -
482D SER* 1.3 73.1 - - - +
484D SER* 1.3 57.1 + - - +
486D ALA* 3.3 3.1 + - - +
487D SER* 3.0 30.7 + - - -
670D CIT 2.6 31.3 + - - -
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Residues in contact with SER 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D TYR* 4.2 4.0 - - - -
450D HIS* 4.0 29.6 - - - -
453D LEU* 3.7 19.3 - - - +
454D ALA* 3.9 5.8 - - - +
483D SER* 1.3 71.0 + - - +
485D MET* 1.3 72.4 + - - +
487D SER* 3.3 9.5 + - - -
488D ALA 3.2 17.0 + - - -
546D LYS* 3.7 4.5 - - - +
670D CIT 2.4 43.4 + - - -
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Residues in contact with MET 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ARG* 4.0 2.2 - - - +
453D LEU* 3.7 37.2 - - + -
454D ALA 5.3 2.0 - - - +
457D ALA* 5.4 1.3 - - + -
482D SER* 3.1 24.3 + - - +
483D SER 3.3 0.4 - - - -
484D SER* 1.3 84.4 + - - +
486D ALA* 1.3 59.1 + - - +
488D ALA* 3.4 9.5 + - + +
489D CYS* 3.2 26.3 + - - -
508D GLY* 3.5 20.4 + - - +
509D VAL 3.5 16.8 - - - +
546D LYS* 4.0 17.0 - - + -
547D ILE 3.5 35.4 - - - +
548D ALA* 4.1 10.3 - - + -
556D ALA* 5.9 0.7 - - + -
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Residues in contact with ALA 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D PHE* 3.7 28.8 - - + +
388D ARG* 3.5 13.6 - - + +
391D THR* 4.3 9.4 - - + -
393D VAL* 3.7 25.3 - - + +
482D SER 3.0 18.0 + - - +
484D SER 3.3 0.2 - - - -
485D MET* 1.3 77.3 - - - +
487D SER* 1.3 55.0 + - - +
489D CYS* 3.7 1.4 - - - +
490D GLY* 2.9 27.2 + - - -
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Residues in contact with SER 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D VAL* 3.7 8.1 - - - +
395D CYS* 3.7 9.4 - - - -
425D LEU* 4.5 2.1 - - - +
427D TYR* 3.4 15.6 - - - -
454D ALA* 4.0 14.6 - - - -
474D SER* 3.3 33.6 + - - -
483D SER 3.0 14.8 + - - -
484D SER* 3.5 9.4 - - - -
485D MET 3.2 0.4 - - - -
486D ALA* 1.3 74.7 - - - +
488D ALA* 1.3 57.1 + - - +
491D GLY* 2.7 32.2 + - - -
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Residues in contact with ALA 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D ALA* 4.0 6.8 - - + +
457D ALA* 4.1 24.9 - - + -
458D LEU* 3.5 19.0 - - + +
484D SER 3.2 9.6 + - - +
485D MET* 3.5 13.2 - - + +
487D SER* 1.3 78.6 - - - +
489D CYS* 1.3 57.1 + - - +
491D GLY* 3.1 2.1 + - - -
492D SER* 2.8 26.5 + - - -
506D VAL* 4.4 13.0 - - + -
508D GLY 4.8 6.3 - - - +
548D ALA* 4.9 3.1 - - + -
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Residues in contact with CYS 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D PHE* 3.5 28.5 - - + -
388D ARG* 5.5 0.4 - - - -
485D MET 3.2 16.9 + - - -
486D ALA 3.7 4.9 - - - +
487D SER 3.3 0.2 - - - -
488D ALA* 1.3 78.2 - - - +
490D GLY* 1.3 63.8 + - - +
492D SER* 3.0 14.6 + - - -
493D LEU* 3.0 17.2 + - - +
506D VAL 3.7 8.7 - - - -
507D ALA* 3.5 15.7 - - - -
508D GLY 3.5 25.8 - - - -
585D ILE* 3.9 14.1 - - - -
589D MET* 3.8 5.2 - - - +
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Residues in contact with GLY 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D ALA* 3.7 6.4 - - - +
386D PHE* 4.0 16.0 - - - +
395D CYS* 3.5 18.4 - - - +
486D ALA 2.9 20.1 + - - -
489D CYS* 1.3 73.6 - - - +
491D GLY* 1.3 56.6 + - - +
493D LEU* 4.3 7.9 - - - -
494D ALA* 2.9 32.4 + - - +
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Residues in contact with GLY 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D CYS* 3.6 6.9 - - - -
458D LEU* 4.0 10.5 - - - -
472D VAL* 4.3 13.5 - - - -
487D SER 2.7 23.5 + - - -
488D ALA 3.4 1.8 - - - -
489D CYS 3.0 0.2 - - - -
490D GLY* 1.3 72.3 - - - +
492D SER* 1.3 58.5 + - - +
494D ALA* 3.9 1.5 - - - +
495D LEU* 2.9 41.7 + - - +
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Residues in contact with SER 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D LEU* 3.8 11.1 - - - +
488D ALA 2.8 8.2 + - - -
489D CYS 3.2 9.4 - - - -
491D GLY* 1.3 75.5 - - - +
493D LEU* 1.3 62.6 + - - +
495D LEU* 3.2 7.7 + - - +
496D MET* 3.1 27.0 + - - +
502D ILE* 3.9 8.2 - - - +
505D ALA* 3.4 15.4 - - - +
506D VAL 3.0 41.1 + - - -
589D MET* 3.8 4.5 - - - +
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Residues in contact with LEU 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D CYS* 3.3 34.8 - - + -
373D GLU 4.8 1.6 - - - +
374D VAL* 3.9 10.1 - - + +
384D ALA* 3.6 22.4 - - + -
385D LEU 4.7 1.6 - - - +
386D PHE* 4.0 16.2 - - + -
489D CYS 3.0 14.9 + - - +
490D GLY* 3.8 4.0 - - - +
492D SER* 1.3 75.4 - - - +
494D ALA* 1.3 58.1 + - - +
496D MET* 3.4 5.9 + - - +
497D ASP* 3.0 28.1 + - - +
589D MET* 3.8 38.8 - - + +
592D THR* 4.9 2.0 - - - -
593D ILE* 3.8 26.2 - - + +
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D GLY* 4.0 1.6 - - - -
383D SER* 3.9 25.1 - - - -
384D ALA* 3.7 6.0 - - - +
395D CYS* 3.9 14.4 - - + +
397D VAL* 3.4 24.8 - - + +
472D VAL* 5.8 0.4 - - + -
490D GLY 2.9 18.8 + - - +
491D GLY* 3.9 2.9 - - - +
493D LEU* 1.3 73.0 - - - +
495D LEU* 1.3 61.5 + - - +
497D ASP* 3.4 3.8 + - - +
498D SER* 2.9 24.3 + - - -
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D VAL* 4.0 6.7 - - + -
423D PHE* 4.2 6.3 - - + -
458D LEU* 4.3 20.9 - - + -
461D VAL* 5.7 0.2 - - + -
462D ILE* 4.0 24.0 - - + -
470D ILE* 3.7 29.6 - - + -
472D VAL* 3.9 14.4 - - + -
491D GLY 2.9 33.1 + - - +
492D SER* 3.2 5.4 + - - +
494D ALA* 1.3 74.1 - - - +
496D MET* 1.3 64.3 + - - +
498D SER* 2.7 20.1 + - - -
500D VAL* 3.1 27.7 + - + -
502D ILE* 4.1 17.0 - - + -
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Residues in contact with MET 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D SER* 3.1 10.9 + - - +
493D LEU* 3.7 9.0 - - - +
495D LEU* 1.3 76.9 - - - +
497D ASP* 1.3 58.1 + - - +
499D GLY* 2.8 18.9 + - - -
500D VAL 4.3 2.7 + - - -
502D ILE* 3.8 27.8 - - + +
504D SER* 4.5 1.6 - - - -
505D ALA* 3.7 35.2 - - + +
593D ILE* 3.8 27.8 - - + +
594D SER* 3.7 34.3 - - - +
595D LYS 3.9 2.5 - - - +
596D PRO* 3.8 25.8 - - + -
597D ARG 3.0 18.7 + - - -
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Residues in contact with ASP 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D VAL* 4.0 16.0 - - + +
375D ASP* 3.3 27.1 + - - +
381D HIS 4.3 2.3 - - - +
382D GLY* 3.3 5.4 - - - -
383D SER 2.9 29.7 + - - +
493D LEU 3.0 17.7 + - - +
494D ALA 3.6 5.4 - - - +
496D MET* 1.3 76.3 - - - +
498D SER* 1.3 59.0 + - - +
499D GLY 3.4 0.3 + - - -
593D ILE* 3.8 10.1 - - + +
597D ARG* 3.0 55.4 + - - +
601D LYS* 4.7 3.0 + - - +
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Residues in contact with SER 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D HIS 3.2 23.5 - - - +
382D GLY* 3.8 2.4 - - - -
397D VAL* 3.6 21.7 - - - +
399D PHE* 3.5 10.2 - - - -
494D ALA 2.9 13.4 + - - -
495D LEU 2.7 19.8 + - - -
496D MET 3.0 0.2 - - - -
497D ASP* 1.3 76.7 - - - +
499D GLY* 1.3 59.4 + - - +
500D VAL* 3.2 18.2 - - - +
597D ARG* 5.2 0.7 - - - -
599D SER 4.8 0.2 - - - -
600D ARG* 3.6 26.2 - - - +
601D LYS 4.5 0.8 + - - -
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Residues in contact with GLY 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D PHE* 4.5 3.1 - - - -
496D MET 2.8 14.3 + - - -
497D ASP 3.2 0.8 + - - -
498D SER* 1.3 80.2 - - - +
500D VAL* 1.3 63.7 + - - +
501D PRO* 3.6 7.3 - - - +
596D PRO* 4.6 0.9 - - - -
597D ARG* 3.6 24.8 - - - +
598D ALA 5.6 0.2 - - - +
599D SER* 4.1 10.6 - - - -
600D ARG* 4.2 13.4 + - - +
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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
------------------------------------------------------------
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