Contacts of the helix formed by residues 484 - 502 (chain C) in PDB entry 1Z5S
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 ALA 484 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483C GLU* 1.3 92.1 + - - +
485C THR* 1.3 67.4 + - + +
487C ARG* 4.0 9.3 + - - +
488C MET* 3.6 26.1 + - - +
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Residues in contact with THR 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447C LEU* 4.1 11.4 - - - +
483C GLU* 2.5 23.0 + - - +
484C ALA* 1.3 80.1 - - + +
486C VAL* 1.3 62.2 + - - +
487C ARG 3.4 0.2 - - - -
488C MET* 3.6 11.2 - - - +
489C ALA* 3.0 26.9 + - - +
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Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C PRO* 3.7 19.3 - - + +
446C LEU* 5.5 1.3 - - + -
447C LEU* 3.6 31.9 - - + -
479C VAL 3.8 20.4 - - - +
481C LYS* 4.1 16.6 - - + +
483C GLU* 2.7 38.2 + - + +
485C THR* 1.3 72.9 - - - +
487C ARG* 1.3 61.5 + - - +
489C ALA* 3.2 2.9 + - - +
490C VAL* 3.0 27.9 + - + +
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Residues in contact with ARG 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C PHE* 3.5 31.8 - - + -
481C LYS 3.3 20.1 + - - +
482C ASP* 3.6 25.7 + - - -
483C GLU 3.3 17.1 + - - +
484C ALA* 4.0 9.4 + - - +
486C VAL* 1.3 77.2 - - - +
488C MET* 1.3 64.6 + - + +
490C VAL* 3.8 2.8 - - - +
491C GLN* 2.7 60.1 + - - +
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Residues in contact with MET 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ALA 3.6 15.0 - - - +
485C THR* 3.4 16.2 + - + +
487C ARG* 1.3 88.8 - - + +
489C ALA* 1.3 60.4 + - - +
491C GLN* 3.9 8.9 - - + +
492C ASP* 2.7 44.8 + - - +
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Residues in contact with ALA 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 3.8 20.9 - - + +
447C LEU* 4.0 18.6 - - + -
453C SER* 5.5 6.8 + - - +
454C SER* 5.5 2.1 - - - -
485C THR 3.0 13.5 + - - +
486C VAL 3.5 8.1 - - - +
487C ARG 3.2 0.2 - - - -
488C MET* 1.3 76.4 - - - +
490C VAL* 1.3 64.8 - - - +
492C ASP* 3.9 3.5 - - - +
493C ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 3.6 21.3 - - + -
476C VAL* 3.7 23.3 - - + +
477C SER* 4.2 6.1 - - - -
479C VAL* 3.8 27.6 - - + +
480C PHE* 3.9 27.4 - - + -
486C VAL* 3.0 21.3 + - + +
487C ARG* 3.8 6.1 - - - +
489C ALA* 1.3 75.9 - - - +
491C GLN* 1.3 65.0 + - - +
493C ALA* 3.1 4.7 + - - +
494C VAL* 3.0 26.0 + - + +
541C ALA* 5.0 4.5 - - + -
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Residues in contact with GLN 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C PHE* 4.7 13.0 - - + -
487C ARG* 2.7 62.3 + - - +
488C MET* 3.9 9.5 - - + +
490C VAL* 1.3 74.9 - - + +
492C ASP* 1.3 54.1 + - - +
494C VAL* 3.2 5.6 + - - +
495C ASP* 2.5 41.8 + - - +
541C ALA* 6.3 2.5 - - - +
544C HIS* 2.9 52.6 + - + +
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Residues in contact with ASP 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C SER* 3.4 28.5 + - - +
488C MET* 2.7 33.8 + - - +
489C ALA* 4.0 2.9 - - - +
491C GLN* 1.3 78.2 - - - +
493C ALA* 1.3 67.9 + - - +
495C ASP* 3.4 15.2 - - - +
496C ALA* 2.8 21.0 + - - +
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Residues in contact with ALA 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 5.0 4.0 - - + -
453C SER 5.4 0.7 - - - +
454C SER* 4.1 15.4 + - - +
457C ILE* 4.7 14.8 - - + -
458C ALA* 4.3 2.0 - - - +
476C VAL* 3.7 26.7 - - + -
489C ALA 3.0 15.1 + - - +
490C VAL* 3.2 10.5 - - - +
492C ASP* 1.3 77.4 - - - +
494C VAL* 1.3 58.4 + - - +
496C ALA* 3.1 2.3 + - - +
497C LEU* 2.9 31.5 + - - +
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Residues in contact with VAL 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C PHE* 3.9 26.7 - - + +
476C VAL* 3.9 18.6 - - + +
477C SER* 4.1 7.4 - - - +
490C VAL* 3.0 12.3 + - + +
491C GLN* 3.5 9.2 - - - +
493C ALA* 1.3 75.2 - - - +
495C ASP* 1.3 69.8 + - - +
497C LEU* 4.4 7.0 - - - -
498C MET* 3.0 25.7 + - + +
541C ALA* 4.3 12.3 - - + +
544C HIS* 5.4 2.5 - - + -
545C MET* 3.5 36.6 - - + -
550C TYR* 4.1 5.6 - - - +
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Residues in contact with ASP 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C GLN* 2.5 33.7 + - - +
492C ASP* 3.2 19.2 + - - +
494C VAL* 1.3 71.7 - - - +
496C ALA* 1.3 57.2 + - - +
499C GLN* 3.0 29.5 + - - +
544C HIS* 2.7 26.2 + - - -
548C GLN* 2.8 35.8 - - - +
550C TYR* 3.1 17.1 + - + -
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Residues in contact with ALA 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C SER* 3.0 30.1 - - - +
455C VAL* 5.0 3.4 - - + -
458C ALA* 3.3 12.6 - - + -
492C ASP 2.8 15.5 + - - +
493C ALA 3.5 1.3 - - - +
495C ASP* 1.3 70.0 - - - +
497C LEU* 1.3 69.0 + - - +
498C MET 3.0 1.8 - - - -
499C GLN* 2.7 21.0 + - - +
500C LYS* 2.9 13.0 + - - +
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Residues in contact with LEU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C ILE* 4.4 3.8 - - + +
458C ALA* 3.2 21.6 - - + +
461C THR* 3.8 36.3 - - + +
463C THR* 4.8 8.0 + - - -
469C VAL* 4.0 16.7 - - + +
472C ALA* 3.4 9.2 - - + -
473C PHE* 3.4 39.7 - - + +
476C VAL* 5.6 5.6 - - + -
493C ALA 2.9 17.0 + - - +
494C VAL* 3.9 7.9 - - + +
496C ALA* 1.3 75.3 - - - +
498C MET* 1.3 62.4 + - - +
500C LYS* 3.4 17.0 - - + +
501C ALA* 3.4 10.4 + - - +
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Residues in contact with MET 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C VAL* 4.0 23.6 - - + -
473C PHE* 4.4 8.7 - - + -
494C VAL* 3.0 18.0 + - + +
496C ALA 2.8 4.2 + - - -
497C LEU* 1.3 73.4 - - + +
499C GLN* 1.3 65.6 + - - +
500C LYS 2.9 2.1 + - - -
501C ALA* 3.3 3.5 + - + +
502C PHE* 2.9 61.9 + - + +
507C PHE* 6.2 1.6 - - + -
512C PHE* 3.2 34.5 - - + -
545C MET* 3.3 30.5 - - + -
550C TYR* 3.3 23.1 - - + -
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Residues in contact with GLN 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ASP 3.0 22.2 + - - +
496C ALA* 2.7 12.2 + - - +
498C MET* 1.3 71.8 - - - +
500C LYS* 1.3 61.7 + - - +
503C ASN* 3.0 54.7 + - - +
550C TYR* 3.4 36.0 - - + +
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Residues in contact with LYS 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C ALA* 3.7 16.5 + - - +
459C GLN* 3.3 39.4 + - - +
461C THR 4.5 0.8 + - - +
463C THR* 3.3 36.7 - - + +
496C ALA 2.9 9.1 + - - +
497C LEU* 3.4 13.0 - - + +
498C MET 2.9 1.0 - - - -
499C GLN* 1.3 74.9 - - - +
501C ALA* 1.3 65.8 + - - +
503C ASN* 2.9 25.9 + - - +
504C SER* 4.1 1.6 + - - -
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Residues in contact with ALA 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C THR* 3.4 25.0 + - - +
469C VAL* 4.3 11.9 - - + -
497C LEU 3.4 10.4 + - - +
498C MET* 3.3 5.0 + - - +
500C LYS* 1.3 74.1 - - - +
502C PHE* 1.3 60.1 + - + +
503C ASN 2.9 10.0 + - - -
504C SER* 3.2 18.8 + - - -
507C PHE* 3.6 41.5 - - + +
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Residues in contact with PHE 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C MET* 2.9 59.1 + - + +
501C ALA* 1.3 73.1 - - + +
503C ASN* 1.3 64.6 + - - +
504C SER 3.7 2.5 + - - -
507C PHE* 4.8 9.6 - + - -
509C SER* 3.9 24.9 - - - -
512C PHE* 4.3 10.5 - + - -
545C MET* 4.4 1.1 - - - -
550C TYR* 3.6 32.5 - + + +
551C PHE* 3.9 15.7 - + - -
552C PRO* 3.4 36.7 - - + +
555C LEU* 4.0 11.2 - - + -
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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