Contacts of the helix formed by residues 482 - 499 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C ARG* 4.3 5.2 - - - -
388C ARG* 3.2 37.5 + - - -
391C THR* 4.5 0.2 - - - -
481C GLY* 1.3 69.6 - - - +
483C SER* 1.3 61.6 + - - +
484C SER 3.5 0.2 - - - -
485C MET* 3.4 20.1 + - - +
486C ALA* 3.4 6.9 + - - +
510C ALA* 4.0 22.0 + - - +
532C ASP* 4.9 1.6 - - - -
533C ILE* 4.8 4.9 + - - +
546C LYS* 5.8 0.2 - - - -
670C CIT 2.1 33.2 + - - -
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Residues in contact with SER 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C THR* 4.5 10.3 - - - -
393C VAL* 3.9 2.6 - - - +
427C TYR* 2.2 35.4 + - - -
429C PHE* 4.0 4.0 - - - -
476C VAL* 3.9 24.5 - - - -
479C SER* 5.2 1.8 - - - -
481C GLY 3.4 2.1 - - - -
482C SER 1.3 65.3 - - - +
484C SER* 1.3 62.1 + - - -
486C ALA* 3.4 3.8 + - - +
487C SER* 2.9 28.0 + - - -
670C CIT 2.4 41.0 + - - -
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Residues in contact with SER 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C TYR* 4.1 4.7 - - - -
450C HIS* 4.0 22.9 - - - -
453C LEU* 3.5 18.8 - - - +
454C ALA* 3.7 6.8 - - - +
483C SER* 1.3 74.1 + - - +
485C MET* 1.3 76.8 + - - +
487C SER* 3.2 11.1 + - - -
488C ALA* 3.1 19.2 + - - +
546C LYS* 3.6 3.3 - - - +
670C CIT 2.7 37.0 + - - -
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Residues in contact with MET 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ARG* 3.9 3.1 - - - +
453C LEU* 3.6 32.1 - - + +
457C ALA* 5.6 0.7 - - + -
482C SER* 3.4 22.2 + - - +
483C SER 3.3 0.4 - - - -
484C SER* 1.3 98.5 + - - +
486C ALA* 1.3 66.0 + - - +
488C ALA* 3.2 8.9 + - + +
489C CYS* 3.2 26.2 + - - -
508C GLY* 3.6 33.2 + - - +
509C VAL 3.6 18.4 - - - +
510C ALA 4.2 0.2 - - - +
546C LYS* 4.0 14.8 - - + -
547C ILE 3.8 20.4 - - - +
548C ALA* 4.2 9.4 - - + -
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Residues in contact with ALA 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C PHE* 3.6 30.8 - - + +
388C ARG* 3.4 15.8 - - + +
391C THR* 4.2 9.4 - - + +
393C VAL* 3.5 26.8 - - + +
482C SER 3.4 6.8 + - - +
483C SER 3.4 3.7 + - - +
485C MET* 1.3 78.3 - - - +
487C SER* 1.3 52.3 + - - +
489C CYS* 3.3 2.0 + - - +
490C GLY* 2.8 33.1 + - - -
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Residues in contact with SER 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C VAL* 3.7 13.0 - - - +
395C CYS* 3.7 3.5 - - - -
425C LEU* 4.6 0.3 - - - +
427C TYR* 3.5 14.7 - - - -
454C ALA* 3.9 13.7 - - - -
458C LEU* 4.5 2.1 - - - +
474C SER* 3.4 32.9 + - - -
483C SER 2.9 18.7 + - - -
484C SER* 3.2 11.4 - - - -
485C MET 3.1 0.2 - - - -
486C ALA* 1.3 74.7 - - - +
488C ALA* 1.3 60.8 + - - +
491C GLY* 2.7 27.9 + - - -
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Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ALA* 4.0 6.9 - - - +
457C ALA* 4.0 27.1 - - + -
458C LEU* 3.3 20.7 - - + +
484C SER 3.1 11.3 + - - +
485C MET* 3.2 12.8 + - + +
487C SER* 1.3 77.6 - - - +
489C CYS* 1.3 55.7 + - - +
492C SER* 2.9 24.6 + - - -
506C VAL* 3.9 13.1 - - + +
508C GLY 4.9 2.0 - - - +
548C ALA* 4.8 6.1 - - + -
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Residues in contact with CYS 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C PHE* 3.6 37.7 - - + -
388C ARG* 5.6 0.2 - - - -
485C MET 3.2 17.9 + - - -
486C ALA 3.5 7.4 - - - +
487C SER 3.3 0.2 - - - -
488C ALA* 1.3 73.4 - - - +
490C GLY* 1.3 67.0 + - - +
492C SER* 3.0 14.2 + - - -
493C LEU* 3.0 14.1 + - - +
506C VAL 3.7 7.9 - - - -
507C ALA* 3.6 14.6 - - - -
508C GLY 3.5 27.8 - - - -
585C ILE* 4.0 2.7 - - - -
589C MET* 3.5 12.0 - - - +
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Residues in contact with GLY 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ALA* 3.5 6.7 - - - +
386C PHE* 4.0 16.5 - - - +
395C CYS* 3.5 17.0 - - - -
486C ALA 2.8 19.6 + - - -
489C CYS* 1.3 73.1 - - - +
491C GLY* 1.3 55.6 + - - +
493C LEU* 3.2 9.1 + - - +
494C ALA* 2.8 31.7 + - - +
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Residues in contact with GLY 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C CYS* 3.4 8.8 - - - -
458C LEU* 4.0 17.0 - - - -
472C VAL* 4.2 14.1 - - - +
487C SER 2.7 23.7 + - - -
488C ALA 3.8 0.9 - - - -
490C GLY* 1.3 71.6 - - - +
492C SER* 1.3 62.6 + - - +
494C ALA* 4.1 1.4 - - - +
495C LEU* 3.0 29.6 + - - +
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Residues in contact with SER 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LEU* 3.8 10.4 - - - +
488C ALA 2.9 9.9 + - - -
489C CYS 3.0 9.6 + - - -
491C GLY* 1.3 77.4 - - - +
493C LEU* 1.3 63.6 + - - +
495C LEU* 3.2 6.5 + - - +
496C MET* 3.1 26.6 + - - +
502C ILE* 3.9 8.7 - - - +
505C ALA* 3.4 13.3 - - - +
506C VAL* 2.9 39.3 + - - +
589C MET* 3.7 5.1 - - - +
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Residues in contact with LEU 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C CYS* 3.5 35.0 - - + -
373C GLU 4.7 2.9 - - - +
374C VAL* 3.8 9.3 - - + +
384C ALA* 3.5 21.8 - - + -
385C LEU 4.7 1.1 - - - +
386C PHE* 4.1 12.1 - - + -
489C CYS 3.0 17.2 + - - +
490C GLY* 3.5 4.5 - - - +
492C SER* 1.3 75.4 - - - +
494C ALA* 1.3 57.4 + - - +
496C MET* 3.2 7.0 + - - +
497C ASP* 2.9 27.5 + - - +
589C MET* 4.0 33.4 - - + +
592C THR* 4.8 2.0 - - + -
593C ILE* 3.5 28.1 - - + +
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Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLY* 4.0 1.7 - - - -
383C SER* 3.8 29.2 - - - -
384C ALA* 3.6 6.0 - - - +
395C CYS* 3.9 13.5 - - + +
396C THR 4.8 0.2 - - - -
397C VAL* 3.4 18.3 - - + +
490C GLY 2.8 21.1 + - - +
491C GLY* 4.1 3.1 - - - +
493C LEU* 1.3 73.5 - - - +
495C LEU* 1.3 57.9 + - - +
497C ASP* 3.3 4.8 + - - +
498C SER* 2.9 30.1 + - - -
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Residues in contact with LEU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C VAL* 3.9 5.4 - - + -
423C PHE* 4.4 7.0 - - + -
458C LEU* 4.5 14.6 - - + -
461C VAL* 5.7 0.4 - - + -
462C ILE* 3.5 28.5 - - + -
470C ILE* 3.7 30.1 - - + -
472C VAL* 4.0 15.7 - - + -
491C GLY 3.0 27.9 + - - +
492C SER* 3.5 5.6 - - - +
493C LEU 3.2 0.2 - - - -
494C ALA* 1.3 73.6 - - - +
496C MET* 1.3 66.0 + - - +
498C SER* 2.7 21.2 + - - -
499C GLY 3.1 5.2 + - - -
500C VAL* 3.2 25.6 + - + -
502C ILE* 4.1 16.6 - - + -
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Residues in contact with MET 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C SER* 3.1 13.4 + - - +
493C LEU* 3.6 7.6 - - - +
495C LEU* 1.3 75.2 - - - +
497C ASP* 1.3 63.1 + - - +
499C GLY 2.9 6.1 + - - -
500C VAL 4.4 0.9 - - - -
502C ILE* 3.9 22.2 - - + +
504C SER* 4.3 1.6 - - - -
505C ALA* 3.8 39.7 - - + +
593C ILE* 3.8 30.1 - - + +
594C SER* 3.7 35.0 - - - +
595C LYS* 3.8 4.7 - - - +
596C PRO* 3.3 21.5 - - + +
597C ARG 2.9 25.3 + - - -
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Residues in contact with ASP 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C VAL* 4.0 16.9 - - + +
375C ASP* 3.5 26.7 + - - +
381C HIS 4.5 1.0 - - - +
382C GLY* 3.3 7.6 - - - -
383C SER 3.0 26.7 + - - +
493C LEU 2.9 14.0 + - - +
494C ALA 3.5 9.2 - - - +
495C LEU 3.2 0.2 - - - -
496C MET* 1.3 76.8 - - - +
498C SER* 1.3 58.9 + - - +
499C GLY 3.3 0.5 + - - -
593C ILE* 3.8 10.2 - - + +
597C ARG* 2.9 57.5 + - - +
601C LYS* 4.5 2.9 + - - -
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Residues in contact with SER 498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C HIS 3.2 25.2 - - - +
382C GLY* 3.8 6.3 - - - -
397C VAL* 3.7 15.3 - - - +
399C PHE* 3.6 12.2 - - - -
494C ALA 2.9 14.8 + - - -
495C LEU* 2.7 16.7 + - - -
497C ASP* 1.3 76.4 - - - +
499C GLY* 1.3 58.5 + - - +
500C VAL* 3.4 17.8 - - - +
597C ARG* 4.8 1.1 - - - -
600C ARG* 3.7 24.5 - - - +
601C LYS* 4.5 1.1 + - - -
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Residues in contact with GLY 499 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C PHE* 4.8 2.4 - - - -
496C MET 2.9 14.6 + - - -
497C ASP 3.1 1.2 + - - -
498C SER* 1.3 80.9 - - - +
500C VAL* 1.3 63.9 + - - +
501C PRO* 3.4 9.5 - - - +
596C PRO* 4.3 2.6 - - - +
597C ARG* 3.7 26.5 - - - +
599C SER* 4.3 6.9 - - - -
600C ARG* 4.6 10.4 + - - +
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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