Contacts of the helix formed by residues 535 - 546 (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 LEU 535 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520C MET* 3.7 41.7 - - + +
522C LEU* 3.9 15.0 - - + -
532C ILE* 3.6 30.3 - - + +
533C ALA 3.9 4.5 - - - +
534C ASN* 1.3 76.4 + - - +
536C TYR* 1.3 58.1 + - - +
538C PRO* 3.5 9.9 - - - -
539C LEU* 2.8 43.8 + - + +
569C ALA* 3.9 26.0 + - + +
570C LEU* 4.1 24.5 - - + +
573C CYS* 4.7 2.3 - - - -
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Residues in contact with TYR 536 (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* 4.0 30.2 - + - -
481C LYS* 5.4 0.9 - - - -
482C ASP* 4.3 15.0 - - + +
534C ASN* 2.5 35.5 + - - +
535C LEU* 1.3 68.1 - - - +
537C GLY* 1.3 68.8 + - - +
539C LEU 3.2 1.0 + - - -
540C MET* 2.8 65.0 + - + +
573C CYS* 3.8 13.7 - - + -
575C PHE* 4.5 15.2 - + + -
576C ALA* 3.4 26.7 - - + -
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Residues in contact with GLY 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C SER* 3.2 26.1 - - - +
478C SER* 4.9 2.2 - - - -
480C PHE* 4.0 15.0 - - - +
534C ASN* 3.8 5.1 - - - +
536C TYR* 1.3 81.2 - - - +
538C PRO* 1.3 56.7 - - - +
540C MET* 3.1 2.5 + - - +
541C ALA* 2.7 36.0 + - - +
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Residues in contact with PRO 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C PHE* 4.4 4.0 - - + -
474C LEU* 3.9 30.3 - - + +
477C SER* 3.8 19.7 - - - +
478C SER* 4.8 3.8 - - - +
520C MET* 3.7 24.7 - - + -
532C ILE* 5.4 5.4 - - + -
534C ASN 3.9 9.2 - - - +
535C LEU* 3.5 16.2 - - - +
537C GLY* 1.3 82.7 - - - +
539C LEU* 1.3 56.6 + - - +
540C MET 2.8 4.6 + - - -
541C ALA* 2.8 2.1 + - + -
542C LEU* 2.6 39.9 + - - +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C MET* 4.2 8.0 - - + +
535C LEU* 2.8 41.9 + - + +
538C PRO* 1.3 72.5 - - - +
540C MET* 1.3 58.1 + - - +
542C LEU* 4.4 5.4 - - + -
543C ASN* 3.1 23.4 + - - +
563C VAL* 4.2 4.0 - - + -
570C LEU* 3.4 38.1 - - + -
573C CYS* 4.5 9.4 - - + -
576C ALA* 3.7 30.0 - - + +
577C ARG* 4.2 17.7 - - + +
580C LEU* 3.4 30.8 - - + +
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Residues in contact with MET 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C PHE* 3.8 38.3 - - + -
482C ASP* 4.6 7.9 - - - +
536C TYR* 2.8 62.7 + - + +
537C GLY 3.5 3.1 - - - +
539C LEU* 1.3 76.8 - - - +
541C ALA* 1.3 67.6 + - - +
542C LEU 3.2 0.9 - - - -
543C ASN* 3.0 38.1 + - - +
544C HIS* 3.1 9.9 + - - +
575C PHE* 4.1 20.6 - - + -
576C ALA* 4.1 14.4 - - - +
579C SER* 4.9 3.4 - - - +
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Residues in contact with ALA 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C PHE* 3.6 13.7 - - + -
477C SER* 3.0 31.2 - - - +
480C PHE* 4.8 5.8 - - - -
490C VAL* 5.0 5.2 - - + -
491C GLN* 6.3 2.7 - - - +
494C VAL* 4.3 15.0 - - + +
537C GLY 2.7 17.6 + - - +
538C PRO 3.5 3.4 - - - +
540C MET* 1.3 73.8 - - - +
542C LEU* 1.3 61.9 + - - +
544C HIS* 3.2 9.2 + - - +
545C MET* 3.1 20.1 + - - +
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Residues in contact with LEU 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C PHE* 3.6 24.5 - - + -
512C PHE* 6.0 3.4 - - + -
516C LEU* 4.5 13.5 - - + -
520C MET* 4.1 28.0 - - + -
538C PRO 2.6 22.3 + - - +
539C LEU* 4.6 0.9 - - + -
541C ALA* 1.3 69.3 - - - +
543C ASN* 1.3 65.7 + - - +
544C HIS 3.0 1.6 + - - -
545C MET* 3.1 16.1 + - + -
546C VAL* 3.0 30.3 + - + +
551C PHE* 6.5 0.2 - - + -
559C LEU* 4.1 30.3 - - + -
563C VAL* 5.6 0.4 - - + -
580C LEU* 3.9 26.7 - - + -
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Residues in contact with ASN 543 (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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539C LEU 3.1 17.4 + - - +
540C MET* 3.0 35.1 + - - +
542C LEU* 1.3 79.3 - - - +
544C HIS* 1.3 54.9 + - - +
547C GLN* 2.9 28.5 + - - +
576C ALA 5.1 0.2 - - - +
579C SER* 4.2 16.0 - - - -
580C LEU* 4.1 17.5 + - + +
583C THR* 2.7 34.7 + - - +
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Residues in contact with HIS 544 (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* 6.4 0.4 - - + -
491C GLN* 2.9 46.8 + - + +
494C VAL* 5.4 2.9 - - + -
495C ASP* 2.7 41.0 + - - -
540C MET 3.1 10.7 + - - +
541C ALA* 3.4 9.9 - - - +
542C LEU 3.0 0.4 - - - -
543C ASN* 1.3 77.8 - - - +
545C MET* 1.3 57.2 - - - +
547C GLN* 2.8 43.3 + - - +
548C GLN* 2.8 36.2 + - + -
550C TYR* 5.3 0.4 - - - -
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Residues in contact with MET 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C PHE* 3.2 35.9 - - + -
494C VAL* 3.5 5.8 - - + -
498C MET* 3.3 46.4 - - + -
502C PHE* 4.4 0.2 - - - -
512C PHE* 5.0 2.7 - - + -
541C ALA 3.1 6.9 + - - +
542C LEU* 3.1 18.8 + - + +
544C HIS* 1.3 80.3 - - - +
546C VAL* 1.3 63.1 + - - +
547C GLN 3.1 1.0 + - - -
548C GLN* 3.1 25.4 + - - +
550C TYR* 3.9 18.8 - - + +
551C PHE* 3.5 35.9 - - + +
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Residues in contact with VAL 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LEU* 3.0 19.8 + - + +
544C HIS 3.2 0.2 + - - -
545C MET* 1.3 76.3 - - + +
547C GLN* 1.3 59.2 + - - +
548C GLN 3.6 5.3 - - - +
551C PHE* 4.1 31.9 - - + -
559C LEU* 4.1 18.6 - - + -
580C LEU* 4.3 4.9 - - + -
583C THR* 4.1 11.2 - - + -
584C LEU* 3.3 30.3 - - + -
587C VAL* 3.3 35.6 - - + +
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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
------------------------------------------------------------
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