Contacts of the helix formed by residues 482 - 499 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CIT 2.7 21.5 + - - -
368B ARG* 4.5 0.2 - - - -
388B ARG* 3.0 23.1 + - - -
391B THR* 4.4 0.4 - - - -
481B GLY* 1.3 76.1 - - - -
483B SER* 1.3 57.5 + - - +
484B SER 3.4 2.2 - - - -
485B MET* 2.9 30.0 - - - +
486B ALA* 3.0 20.8 + - - +
509B VAL 4.1 0.2 - - - -
510B ALA* 3.7 27.1 + - - +
532B ASP* 4.5 3.8 - - - -
533B ILE* 4.8 1.7 + - - +
546B LYS* 5.8 0.2 - - - -
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Residues in contact with SER 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CIT 2.9 25.5 + - - -
391B THR* 4.2 13.0 - - - -
393B VAL* 3.9 3.3 - - - +
427B TYR* 2.6 24.4 + - - -
429B PHE* 4.1 3.5 - - - -
476B VAL* 3.7 33.0 - - - -
479B SER* 5.5 2.0 - - - -
481B GLY 3.5 1.4 - - - -
482B SER* 1.3 73.7 - - - +
484B SER* 1.3 61.3 + - - +
486B ALA* 3.3 2.9 + - - +
487B SER* 2.9 32.0 + - - -
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Residues in contact with SER 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CIT 2.8 32.4 + - - -
427B TYR* 4.1 8.3 - - - -
450B HIS* 4.1 25.6 - - - -
453B LEU* 3.5 14.8 - - - +
454B ALA* 3.9 5.9 - - - +
483B SER* 1.3 78.9 + - - +
485B MET* 1.3 82.4 + - - +
487B SER* 3.1 7.0 + - - -
488B ALA* 3.1 17.3 + - - +
546B LYS* 3.7 2.9 - - - +
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Residues in contact with MET 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 4.1 2.0 - - - +
453B LEU* 3.6 30.3 - - + +
457B ALA* 5.5 0.7 - - + -
482B SER* 2.9 26.2 + - - +
483B SER 3.2 0.4 - - - -
484B SER* 1.3 102.7 + - - +
486B ALA* 1.3 61.0 + - - +
488B ALA* 3.3 8.8 + - + +
489B CYS* 3.2 27.2 + - - -
508B GLY* 3.5 18.8 + - - +
509B VAL 3.5 15.7 - - - +
510B ALA 4.2 0.2 - - - +
546B LYS* 3.9 12.8 - - + -
547B ILE 3.7 36.3 - - - +
548B ALA* 4.1 8.1 - - + -
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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
----------------------------------------------------------
386B PHE* 3.7 30.8 - - + +
388B ARG* 3.6 11.1 - - + +
391B THR* 4.2 9.9 - - + -
393B VAL* 3.7 21.2 - - + +
482B SER 3.0 17.4 + - - +
483B SER 3.6 5.2 - - - +
485B MET* 1.3 75.7 - - - +
487B SER* 1.3 58.2 + - - +
489B CYS* 3.6 1.2 - - - +
490B GLY* 2.8 27.5 + - - -
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Residues in contact with SER 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B VAL* 3.8 13.7 - - - +
395B CYS* 3.7 3.3 - - - -
425B LEU* 4.6 0.9 - - - +
427B TYR* 3.5 14.2 - - - -
454B ALA* 4.0 14.4 - - - -
458B LEU* 4.6 1.7 - - - +
474B SER* 3.4 31.8 + - - -
476B VAL* 5.0 0.3 - - - +
483B SER 2.9 18.7 + - - -
484B SER* 3.1 12.7 + - - -
486B ALA* 1.3 74.7 - - - +
488B ALA* 1.3 60.4 + - - +
491B GLY* 2.8 27.4 + - - -
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ALA* 4.3 7.5 - - - +
457B ALA* 4.0 27.1 - - + -
458B LEU* 3.5 18.2 - - + +
484B SER 3.1 10.9 + - - +
485B MET* 3.3 12.1 + - + +
487B SER* 1.3 78.1 - - - +
489B CYS* 1.3 57.5 + - - +
491B GLY 3.2 1.2 + - - -
492B SER* 2.9 26.2 + - - -
506B VAL* 4.2 12.8 - - + -
508B GLY 4.8 5.6 - - - +
548B ALA* 4.8 2.9 - - + -
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Residues in contact with CYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 3.6 37.7 - - + -
388B ARG* 5.6 0.2 - - - -
485B MET 3.2 16.9 + - - +
486B ALA 3.6 6.3 - - - +
488B ALA* 1.3 77.6 - - - +
490B GLY* 1.3 62.1 + - - +
492B SER* 3.1 5.5 + - - -
493B LEU* 3.0 27.6 + - - +
506B VAL 3.7 8.9 + - - -
507B ALA* 3.6 14.8 - - - -
508B GLY 3.5 25.1 - - - -
585B ILE* 3.9 7.4 - - - -
589B MET* 3.5 5.5 - - - +
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Residues in contact with GLY 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ALA* 3.7 5.1 - - - +
386B PHE* 4.1 16.5 - - - +
395B CYS* 3.5 19.6 - - - +
486B ALA 2.8 19.7 + - - -
489B CYS* 1.3 73.0 - - - +
491B GLY* 1.3 56.8 + - - +
493B LEU* 3.7 7.6 - - - +
494B ALA* 2.9 31.0 + - - +
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B CYS* 3.5 1.7 - - - -
458B LEU* 3.9 10.8 - - - -
472B VAL* 4.1 19.7 - - - -
487B SER 2.8 19.1 + - - -
488B ALA 3.6 1.8 - - - -
490B GLY* 1.3 75.0 - - - +
492B SER* 1.3 58.0 + - - +
494B ALA* 4.0 0.8 - - - +
495B LEU* 2.8 41.3 + - - +
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LEU* 3.8 11.7 - - - +
488B ALA 2.9 8.9 + - - -
489B CYS 3.1 10.1 + - - -
491B GLY* 1.3 74.8 - - - +
493B LEU* 1.3 63.2 + - - +
495B LEU* 3.4 3.4 + - - +
496B MET* 3.2 28.0 + - - +
502B ILE* 3.9 10.5 - - - +
505B ALA* 3.3 15.9 - - - +
506B VAL 2.8 40.9 + - - -
589B MET* 3.8 4.2 - - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B CYS* 3.7 29.2 - - + -
374B VAL* 3.8 12.7 - - + +
384B ALA* 3.6 18.8 - - + -
385B LEU 4.7 0.2 - - - +
386B PHE* 3.9 20.4 - - + -
489B CYS 3.0 18.3 + - - +
490B GLY* 3.7 7.6 - - - +
492B SER* 1.3 75.7 - - - +
494B ALA* 1.3 57.9 + - - +
496B MET* 3.3 6.3 + - - +
497B ASP* 2.9 26.9 + - - +
589B MET* 3.9 34.1 - - + +
592B THR* 5.0 1.3 - - - -
593B ILE* 3.6 26.3 - - + +
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Residues in contact with ALA 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLY* 3.9 1.4 - - - -
383B SER* 3.8 25.4 - - - -
384B ALA* 3.8 0.4 - - - +
395B CYS* 3.8 16.8 - - + +
397B VAL* 3.2 25.9 - - + +
472B VAL* 5.6 0.2 - - + -
490B GLY 2.9 20.5 + - - +
491B GLY* 4.0 2.5 - - - +
493B LEU* 1.3 73.3 - - - +
495B LEU* 1.3 57.3 + - - +
497B ASP* 3.3 8.9 + - - +
498B SER* 2.9 24.1 + - - -
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Residues in contact with LEU 495 (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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397B VAL* 3.9 5.4 - - + -
423B PHE* 4.2 7.9 - - + -
458B LEU* 4.3 17.3 - - + -
461B VAL* 5.7 0.2 - - + -
462B ILE* 3.7 28.0 - - + -
470B ILE* 3.6 31.2 - - + -
472B VAL* 4.1 12.3 - - + -
491B GLY 2.8 30.9 + - - +
492B SER* 3.8 5.6 - - - +
493B LEU 3.3 0.2 - - - -
494B ALA* 1.3 69.7 - - - +
496B MET* 1.3 65.0 + - - +
498B SER* 2.5 20.6 + - - -
500B VAL* 3.1 31.9 + - + -
502B ILE* 4.1 17.0 - - + -
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B SER* 3.2 13.2 + - - +
493B LEU* 3.6 8.5 - - - +
495B LEU* 1.3 77.9 - - - +
497B ASP* 1.3 60.9 + - - +
499B GLY 3.1 5.0 + - - -
500B VAL 4.4 0.9 + - - -
502B ILE* 3.9 27.1 - - + +
504B SER* 4.4 1.8 - - - -
505B ALA* 3.9 33.7 - - + +
590B ASN* 5.2 0.4 - - - +
593B ILE* 3.7 28.7 - - + +
594B SER 4.0 15.3 - - - +
595B LYS* 3.8 23.3 - - - +
596B PRO* 3.4 21.7 - - + +
597B ARG 2.7 27.9 + - - -
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 3.9 9.5 - - + +
375B ASP* 3.3 21.5 + - - +
382B GLY* 3.4 2.3 - - - -
383B SER* 2.9 30.6 + - - +
493B LEU 2.9 14.0 + - - +
494B ALA 3.5 8.7 - - - +
496B MET* 1.3 76.6 - - - +
498B SER* 1.3 60.2 + - - +
499B GLY 3.3 0.3 + - - -
593B ILE* 3.7 7.1 - - - +
597B ARG* 2.6 58.4 + - - +
601B LYS* 3.2 25.6 + - - -
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B HIS 3.2 22.2 - - - +
382B GLY* 3.9 0.7 - - - -
397B VAL* 3.4 27.1 - - - +
399B PHE* 3.6 11.1 - - - -
494B ALA 2.9 10.4 + - - -
495B LEU* 2.5 23.7 + - - -
497B ASP* 1.3 75.0 - - - +
499B GLY* 1.3 58.5 + - - +
500B VAL* 3.3 17.7 - - - +
597B ARG* 5.2 0.4 - - - -
599B SER 4.7 0.2 - - - -
600B ARG* 3.6 26.6 - - - +
601B LYS 4.5 0.8 + - - -
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Residues in contact with GLY 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PHE* 4.6 3.6 - - - -
496B MET 3.1 11.6 + - - -
497B ASP 3.1 1.4 + - - -
498B SER* 1.3 78.8 - - - +
500B VAL* 1.3 64.6 + - - +
501B PRO* 3.3 9.9 - - - +
596B PRO* 4.5 1.2 - - - +
597B ARG* 3.5 26.6 - - - +
598B ALA 5.9 0.2 - - - -
599B SER* 3.9 12.9 - - - -
600B ARG* 4.9 7.5 + - - +
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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