Contacts of the helix formed by residues 496 - 505 (chain C) in PDB entry 1Z6T
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 MET 496 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458C LYS* 4.0 36.1 - - + +
461C ILE* 3.8 37.5 - - + -
462C THR* 5.1 3.1 - - - +
465C GLN* 5.2 2.9 - - - +
491C MET* 2.8 18.8 + - - +
494C ALA* 3.6 29.4 - - + +
495C LYS* 1.3 69.5 - - - +
497C HIS* 1.3 58.8 + - - +
498C LYS 3.3 2.9 - - - -
499C GLU* 3.4 47.7 + - + +
500C LEU* 2.9 29.1 + - - +
532C ILE* 4.5 0.7 - - - -
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Residues in contact with HIS 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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495C LYS* 3.0 17.8 + - - +
496C MET* 1.3 68.1 - - - +
498C LYS* 1.3 96.9 + - + +
500C LEU* 3.6 3.1 - - - +
501C CYS* 3.0 32.6 + - - -
532C ILE* 4.0 35.4 + - + +
533C LEU* 4.0 12.8 - - + -
534C ASP* 5.8 6.5 - - + -
537C ASP* 4.8 11.0 - - - +
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Residues in contact with LYS 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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496C MET 3.3 0.4 - - - -
497C HIS* 1.3 100.9 - - + +
499C GLU* 1.3 65.4 + - - +
501C CYS* 3.5 5.2 + - - +
502C ALA* 3.0 27.9 + - - +
537C ASP* 6.0 0.9 - - - +
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Residues in contact with GLU 499 (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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465C GLN* 3.6 27.3 + - - +
491C MET* 3.6 21.9 - - + +
496C MET* 3.4 47.0 + - + +
498C LYS* 1.3 80.5 - - - +
500C LEU* 1.3 61.0 + - - +
502C ALA* 3.2 6.8 + - - +
503C LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 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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488C ALA* 3.7 31.9 - - + +
491C MET* 3.7 14.0 - - + -
492C ALA* 4.4 4.3 - - + +
496C MET 2.9 17.9 + - - +
497C HIS 3.6 4.7 - - - +
499C GLU* 1.3 77.4 - - - +
501C CYS* 1.3 56.7 + - - +
503C LEU* 3.3 1.6 + - - +
504C MET* 2.9 59.2 + - + +
529C TYR* 4.1 21.8 - - + +
532C ILE* 4.0 22.9 - - + -
533C LEU* 4.0 19.1 - - + -
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Residues in contact with CYS 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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497C HIS 3.0 25.2 + - - +
498C LYS* 3.7 5.8 - - - +
500C LEU* 1.3 73.3 - - - +
502C ALA* 1.3 62.3 + - - +
505C PHE* 2.9 75.5 + - + +
533C LEU* 3.8 15.5 - - - -
537C ASP* 3.7 24.9 - - - +
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Residues in contact with ALA 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 LYS 3.0 16.7 + - - +
499C GLU* 3.2 7.8 + - - +
501C CYS* 1.3 75.7 - - - +
503C LEU* 1.3 63.7 + - - +
505C PHE 4.8 1.4 - - - +
506C SER* 4.0 11.4 - - - -
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Residues in contact with LEU 503 (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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470C PRO* 3.7 38.4 - - + -
487C LEU* 3.9 16.8 - - + -
488C ALA* 4.0 30.5 - - + +
491C MET* 3.9 23.3 - - + -
499C GLU 2.9 17.4 + - - +
500C LEU* 3.5 3.6 - - + +
502C ALA* 1.3 79.9 - - - +
504C MET* 1.3 65.6 - - + +
506C SER* 3.4 4.0 - - - -
509C TRP* 3.3 54.2 - - + +
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Residues in contact with MET 504 (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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488C ALA* 4.1 9.2 - - + -
500C LEU* 2.9 42.8 + - + +
503C LEU* 1.3 86.8 - - + +
505C PHE* 1.3 64.1 + - + +
506C SER* 2.8 16.7 + - - +
509C TRP* 4.2 11.3 - - - +
510C ILE* 4.5 3.8 - - - +
522C LEU* 3.6 21.5 - - + -
525C GLU* 3.6 31.9 - - + +
526C PHE* 3.5 48.3 - - + +
529C TYR* 4.7 4.3 - - - -
544C PHE* 4.1 3.3 - - - -
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Residues in contact with PHE 505 (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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501C CYS* 2.9 54.0 + - + +
502C ALA* 4.8 1.4 - - - +
504C MET* 1.3 78.0 - - + +
506C SER* 1.3 55.8 + - - +
526C PHE* 3.8 16.2 - + - -
533C LEU* 4.3 4.7 - - + -
537C ASP* 3.4 29.6 - - - -
540C VAL* 3.4 28.7 - - + -
541C SER* 3.5 26.2 - - - -
544C PHE* 3.5 22.9 - + + -
579C GLN* 2.6 29.6 + - - +
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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
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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