Contacts of the helix formed by residues 536 - 546 (chain C) in PDB entry 6M17
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 VAL 536 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532C VAL* 3.1 18.7 + - + +
535C ARG* 1.3 89.3 - - + +
537C VAL* 1.3 77.6 + - + +
538C SER 3.8 0.7 - - - -
539C PRO* 4.0 2.3 - - - +
540C LEU* 3.5 22.7 + - + +
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Residues in contact with VAL 537 (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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80C LEU* 3.2 34.8 - - + +
532C VAL* 3.0 35.4 + - + +
533C THR* 3.9 11.9 - - + -
536C VAL* 1.3 80.6 - - + +
538C SER* 1.3 62.1 + - - +
540C LEU* 3.0 25.4 + - - +
541C LEU* 3.1 19.4 + - + +
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Residues in contact with SER 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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80C LEU 3.2 26.7 - - - -
81C GLU* 4.4 6.5 - - - +
84C PRO* 4.1 4.8 - - - +
502C MET* 3.4 24.6 - - - +
533C THR* 2.4 27.8 + - - -
537C VAL* 1.3 74.3 - - - +
539C PRO* 1.3 69.2 - - - +
540C LEU 3.3 0.3 + - - -
541C LEU* 4.2 5.7 - - - +
542C MET* 2.6 37.3 + - - +
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Residues in contact with PRO 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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499C PHE* 3.6 18.8 - - + -
502C MET* 4.1 11.7 - - + +
503C PHE* 6.3 1.6 - - + -
506C VAL* 5.5 3.1 - - + -
507C TYR* 5.6 5.6 - - + -
533C THR 3.2 8.7 - - - +
534C TRP 3.1 20.4 - - - +
535C ARG 3.6 15.7 - - - +
536C VAL 4.0 4.3 - - - +
537C VAL 3.6 2.9 - - - -
538C SER* 1.3 100.9 - - - +
540C LEU* 1.3 56.4 + - - +
542C MET* 3.4 11.2 + - + +
543C LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 540 (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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536C VAL* 3.5 15.4 + - + +
537C VAL* 3.0 12.0 + - - +
539C PRO* 1.3 78.2 - - - +
541C LEU* 1.3 71.7 + - + +
542C MET 3.1 1.3 - - - -
543C LEU* 3.2 18.8 + - + +
544C ILE* 2.9 42.3 + - + +
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Residues in contact with LEU 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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76C ILE* 5.2 4.9 - - + -
77C LEU* 3.5 24.9 - - + -
80C LEU* 3.8 31.4 - - + +
81C GLU* 2.3 37.5 - - - +
537C VAL* 3.1 18.8 + - + +
538C SER* 3.6 2.6 + - - +
540C LEU* 1.3 84.7 - - + +
542C MET* 1.3 56.3 + - - +
544C ILE* 3.2 10.7 + - + +
545C ILE* 2.9 36.1 + - + +
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Residues in contact with MET 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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81C GLU* 3.7 21.1 - - - +
85C LEU* 4.6 6.1 - - - -
276C PHE* 3.9 25.4 - - + -
495C LEU 5.7 1.3 - - - +
498C ALA* 4.0 21.3 - - - +
499C PHE* 4.1 22.2 - - + +
502C MET* 3.8 28.0 - - + -
538C SER* 2.6 41.3 + - - +
539C PRO* 3.4 12.1 - - + +
540C LEU 3.1 0.4 - - - -
541C LEU* 1.3 75.7 - - - +
543C LEU* 1.3 59.6 + - - +
544C ILE 2.7 10.1 + - - -
545C ILE* 3.2 6.4 + - - +
546C PHE* 3.1 22.9 + - - +
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Residues in contact with LEU 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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499C PHE* 4.5 24.1 - - + -
539C PRO 3.0 20.2 + - - +
540C LEU* 3.2 21.9 + - + +
542C MET* 1.3 75.1 - - - +
544C ILE* 1.3 62.2 + - + +
546C PHE* 3.8 24.6 - - + +
547C LEU* 4.0 15.9 + - + +
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Residues in contact with ILE 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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540C LEU* 2.9 39.6 + - + +
541C LEU* 3.3 12.8 - - + +
542C MET 2.7 2.0 + - - -
543C LEU* 1.3 79.6 - - + +
545C ILE* 1.3 58.9 + - + +
546C PHE 2.5 4.6 + - - -
547C LEU* 2.5 38.7 + - + +
548C PHE* 3.2 34.9 + - + -
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Residues in contact with ILE 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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77C LEU* 4.5 18.2 - - + -
81C GLU* 4.4 11.7 - - - +
268C TRP* 4.0 28.7 - - + +
269C LEU* 3.5 36.5 - - + +
272C GLY* 4.5 7.2 - - - -
276C PHE* 6.3 1.3 - - + -
495C LEU* 3.8 22.6 - - + +
541C LEU* 2.9 23.5 + - + +
542C MET* 3.2 5.4 + - - +
544C ILE* 1.3 80.2 - - + +
546C PHE* 1.3 59.2 + - - +
547C LEU 3.4 0.2 - - - -
548C PHE* 3.5 22.7 + - + +
549C PHE* 3.6 1.4 + - - +
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Residues in contact with PHE 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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492C ILE* 5.5 6.3 - - + -
495C LEU* 4.9 12.6 - - + -
496C ILE* 3.3 35.9 - - + -
499C PHE* 6.6 0.4 - - + -
542C MET 3.1 15.3 + - - +
543C LEU* 3.8 18.2 - - + +
544C ILE 2.5 4.9 + - - -
545C ILE* 1.3 74.4 - - - +
547C LEU* 1.3 77.8 + - + +
549C PHE* 3.7 10.1 + + + +
550C PHE* 3.4 47.5 - + - -
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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