Contacts of the helix formed by residues 534 - 551 (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 ASP 534 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497C HIS* 5.7 7.1 - - + +
532C ILE 4.0 0.8 + - - -
533C LEU* 1.3 78.6 - - - +
535C GLU* 1.3 60.0 + - - +
536C LYS* 3.3 11.4 + - - +
537C ASP* 2.9 40.0 + - - +
538C CYS* 2.9 25.7 + - - +
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Residues in contact with GLU 535 (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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534C ASP* 1.3 75.4 - - - +
536C LYS* 1.3 64.3 + - + +
538C CYS* 3.5 6.9 - - + +
539C ALA* 3.3 21.0 + - - +
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Residues in contact with LYS 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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534C ASP* 3.3 11.6 + - - +
535C GLU* 1.3 80.4 - - + +
537C ASP* 1.3 65.0 + - - +
539C ALA* 3.3 8.2 + - - +
540C VAL* 3.3 24.2 + - - +
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Residues in contact with ASP 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C HIS* 4.8 12.0 - - - -
498C LYS* 6.0 0.9 - - - +
501C CYS* 3.7 32.8 - - - +
505C PHE* 3.4 12.9 - - + -
533C LEU* 4.0 14.1 - - + +
534C ASP* 2.9 26.5 + - - +
536C LYS* 1.3 77.3 - - - +
538C CYS* 1.3 56.2 + - - +
540C VAL* 3.3 5.1 + - - +
541C SER* 2.8 35.3 + - - -
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Residues in contact with CYS 538 (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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530C ARG* 3.8 25.1 + - - +
533C LEU* 3.9 12.7 - - + +
534C ASP 2.9 20.9 + - - +
535C GLU* 3.5 9.9 - - - +
537C ASP* 1.3 76.9 - - - +
539C ALA* 1.3 59.5 + - - +
541C SER* 3.4 9.9 - - - -
542C GLU* 3.1 38.5 + - - +
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Residues in contact with ALA 539 (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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535C GLU 3.3 10.5 + - - +
536C LYS* 3.6 10.3 - - - +
537C ASP 3.3 0.4 - - - -
538C CYS* 1.3 76.0 - - - +
540C VAL* 1.3 64.8 + - + +
542C GLU* 3.0 18.7 + - - +
543C ASN* 3.0 26.9 + - - +
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Residues in contact with VAL 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C PHE* 3.4 30.1 - - + -
536C LYS 3.3 12.8 + - - +
537C ASP* 3.3 13.1 + - - +
539C ALA* 1.3 72.0 - - + +
541C SER* 1.3 67.2 + - - +
543C ASN* 3.0 12.6 + - - +
544C PHE* 3.0 40.6 + - + -
575C GLU* 4.1 26.0 - - + -
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Residues in contact with SER 541 (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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505C PHE* 3.5 16.7 - - - -
526C PHE* 3.5 20.6 + - - -
530C ARG* 3.0 27.4 + - - +
533C LEU* 3.8 18.2 - - - +
537C ASP 2.8 20.1 + - - -
538C CYS 3.4 7.6 - - - -
540C VAL* 1.3 73.4 - - - +
542C GLU* 1.3 57.5 + - - +
544C PHE* 3.3 2.8 + - - +
545C GLN* 2.9 24.4 + - - +
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Residues in contact with GLU 542 (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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530C ARG* 3.7 28.3 + - - +
538C CYS* 3.1 27.0 + - - +
539C ALA* 3.0 20.5 + - - +
541C SER* 1.3 73.3 - - - +
543C ASN* 1.3 66.3 + - - +
545C GLN* 3.8 4.0 - - - +
546C GLU* 3.1 33.6 + - - +
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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 ALA* 3.0 19.4 + - - +
540C VAL* 3.3 16.0 - - + +
542C GLU* 1.3 75.7 - - - +
544C PHE* 1.3 62.5 - - + +
546C GLU* 3.2 22.2 + - - +
547C PHE* 3.2 22.7 + - - +
570C GLU* 4.6 0.5 - - - +
573C THR 4.4 2.8 - - - +
574C SER* 3.4 27.2 + - - +
575C GLU* 3.5 20.3 + - - +
576C VAL* 3.8 8.2 - - + +
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Residues in contact with PHE 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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504C MET 4.1 5.8 - - - -
505C PHE* 3.5 27.4 - + + -
506C SER 3.5 19.1 - - - -
507C LEU* 4.3 7.6 - - + -
510C ILE* 3.4 27.1 - - + -
526C PHE* 3.6 24.9 - + + -
540C VAL* 3.0 38.7 + - + -
541C SER 3.8 1.3 - - - +
543C ASN* 1.3 75.1 - - + +
545C GLN* 1.3 64.2 + - - +
547C PHE* 3.3 4.7 + + - +
548C LEU* 3.0 27.7 + - - +
575C GLU* 4.2 9.9 - - + -
576C VAL* 3.8 28.7 - - + -
579C GLN* 3.8 15.3 - - - -
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Residues in contact with GLN 545 (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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523C ILE* 3.9 21.1 + - + +
526C PHE* 4.1 13.4 - - + -
527C VAL* 2.7 31.9 - - - +
530C ARG* 2.9 46.3 + - - +
541C SER 2.9 8.4 + - - +
542C GLU* 3.8 5.0 - - - +
543C ASN 3.3 0.6 - - - -
544C PHE* 1.3 76.9 - - - +
546C GLU* 1.3 60.1 + - + +
548C LEU* 3.3 8.4 + - - +
549C SER* 2.9 32.8 + - - +
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Residues in contact with GLU 546 (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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542C GLU* 3.1 21.9 + - - +
543C ASN* 3.2 32.1 + - - +
545C GLN* 1.3 76.2 - - + +
547C PHE* 1.3 59.6 + - - +
549C SER* 3.3 8.9 + - - +
550C LEU* 3.0 32.8 + - - +
570C GLU* 4.4 11.7 - - - +
571C PRO* 5.1 9.5 - - - +
574C SER* 5.0 2.9 + - - -
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Residues in contact with PHE 547 (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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507C LEU* 4.2 12.1 - - + -
510C ILE* 4.3 24.2 - - + -
543C ASN 3.2 14.6 + - - +
544C PHE 3.3 11.4 - - - +
546C GLU* 1.3 78.5 - - - +
548C LEU* 1.3 65.5 + - + +
550C LEU* 4.6 0.2 - - - -
551C ASN* 2.9 58.1 + - + +
555C LEU* 5.7 3.6 - - + -
563C ILE* 4.0 17.7 - - + -
566C LEU* 3.7 31.9 - - + -
567C GLY* 3.7 13.0 - - - -
570C GLU* 3.7 28.5 - - + +
576C VAL* 3.6 23.8 - - + -
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Residues in contact with LEU 548 (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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510C ILE* 3.6 38.4 - - + -
514C THR* 4.6 2.0 - - + -
519C PRO* 5.1 2.0 - - + -
522C LEU* 4.0 19.1 - - + -
523C ILE* 3.7 28.6 - - + +
526C PHE* 3.6 36.1 - - + -
544C PHE 3.0 15.4 + - - +
545C GLN* 3.7 4.7 - - - +
547C PHE* 1.3 79.7 - - + +
549C SER* 1.3 59.5 + - - +
551C ASN 3.4 0.7 + - - -
552C GLY* 2.9 31.2 + - - -
555C LEU* 3.9 19.9 - - + +
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Residues in contact with SER 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C ILE* 4.0 17.7 - - - +
545C GLN* 2.9 24.0 + - - +
546C GLU* 3.3 14.4 + - - +
548C LEU* 1.3 73.4 - - - +
550C LEU* 1.3 64.6 + - - +
551C ASN 3.4 0.5 + - - -
552C GLY* 3.4 9.3 + - - -
553C HIS* 5.1 0.7 + - - -
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Residues in contact with LEU 550 (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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546C GLU 3.0 18.7 + - - +
547C PHE 3.8 4.0 - - - +
549C SER* 1.3 79.0 + - - +
551C ASN* 1.3 79.5 + - - +
552C GLY 3.3 0.2 - - - -
553C HIS* 3.4 21.9 + - + -
569C CYS* 6.5 1.3 - - + -
570C GLU* 3.8 22.4 - - - +
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Residues in contact with ASN 551 (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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547C PHE* 2.9 50.4 + - + +
548C LEU 3.5 2.2 - - - -
550C LEU* 1.3 97.8 - - - +
552C GLY* 1.3 57.9 + - - +
553C HIS* 3.2 7.5 - - - -
554C LEU* 2.9 30.5 + - + +
555C LEU* 3.3 21.6 + - + +
566C LEU* 3.6 39.1 + - + +
570C GLU* 4.4 2.4 + - - -
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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
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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