Contacts of the helix formed by residues 535 - 550 (chain C) in PDB entry 2BT4
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 535 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C LEU* 4.4 4.5 - - + -
428C TYR 4.4 11.4 + - - +
429C GLY* 6.2 0.2 - - - -
431C ASP* 3.4 29.4 - - + +
436C VAL* 3.5 31.4 - - + -
439C LEU* 3.7 24.9 - - + +
507C ILE* 4.1 18.4 - - + +
534C GLY* 1.3 68.3 - - - -
536C GLN* 1.3 66.8 + - + +
537C GLY 3.0 2.2 - - - -
538C TYR* 3.1 29.1 + - + +
539C VAL 3.9 1.0 + - - -
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Residues in contact with GLN 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 5.2 1.8 - - - -
533C CYS 3.4 9.4 - - - +
534C GLY 3.1 0.8 - - - -
535C VAL* 1.3 83.0 - - + +
537C GLY* 1.3 61.8 + - - +
538C TYR 3.1 0.2 - - - -
539C VAL* 3.0 28.4 + - + +
540C PHE* 3.1 40.1 + - + -
1943J GLU* 3.4 24.0 + - - +
1944J ARG* 2.8 40.3 + - - +
1947J ALA* 3.2 15.9 - - - +
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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
----------------------------------------------------------
505C VAL* 3.6 18.7 - - - +
506C HIS 5.9 0.2 - - - -
530C VAL* 3.9 25.1 - - - +
533C CYS* 3.5 6.7 + - - +
534C GLY 3.1 11.8 + - - -
535C VAL 3.0 2.6 - - - -
536C GLN* 1.3 78.7 - - - +
538C TYR* 1.3 55.9 + - - +
540C PHE* 3.3 9.6 + - - +
541C GLY 2.9 23.0 + - - -
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Residues in contact with TYR 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ILE* 4.1 23.3 - - + -
413C ASN* 2.7 31.1 + - - -
417C LEU* 4.1 3.6 - - - +
433C LEU* 4.7 3.9 - - + +
436C VAL* 3.7 30.7 - - + -
439C LEU* 6.0 1.1 - - + -
440C CYS* 3.8 14.8 - - - -
477C VAL* 4.5 10.2 - - + +
479C ASN* 3.1 32.4 + - + +
505C VAL* 4.1 17.5 - - + -
507C ILE* 3.9 28.2 - - + +
535C VAL* 3.1 22.8 + - - +
537C GLY* 1.3 76.3 - - - +
539C VAL* 1.3 58.5 + - + +
541C GLY* 3.2 1.9 + - - -
542C VAL* 3.0 32.5 + - - +
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Residues in contact with VAL 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 4.2 43.1 - - + +
440C CYS* 5.2 0.7 - - - +
443C ALA* 4.2 17.7 - - + +
535C VAL 4.6 0.2 - - - +
536C GLN* 3.0 28.0 + - + +
538C TYR* 1.3 74.7 - - + +
540C PHE* 1.3 65.1 + - + +
542C VAL* 3.2 4.0 + - - +
543C GLU* 2.9 48.9 + - - +
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Residues in contact with PHE 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C VAL* 5.4 0.2 - - - -
530C VAL* 4.3 11.0 - - + -
533C CYS* 3.8 31.9 - - + -
536C GLN* 3.1 46.0 + - + -
537C GLY* 3.3 13.7 + - - +
539C VAL* 1.3 76.2 - - + +
541C GLY* 1.3 65.8 + - - +
543C GLU* 3.2 3.7 + - - -
544C ARG* 2.8 22.2 + - - +
1930J VAL* 5.1 1.1 - - + -
1940J PHE* 3.3 65.6 - + + -
1943J GLU* 3.1 30.5 - - + -
1944J ARG* 3.8 7.0 - - + -
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Residues in contact with GLY 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C VAL* 3.7 15.3 - - - -
503C VAL* 3.8 26.3 - - - +
537C GLY 2.9 15.4 + - - -
538C TYR 3.2 4.4 + - - -
540C PHE* 1.3 77.3 - - - +
542C VAL* 1.4 55.6 + - - +
544C ARG* 3.1 2.3 + - - +
545C ILE* 2.9 32.4 + - - +
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Residues in contact with VAL 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 5.5 1.6 - - + -
409C ILE* 3.8 18.5 - - + +
411C ILE* 4.0 27.4 - - + -
440C CYS* 4.6 18.4 - - - +
443C ALA* 3.8 11.7 - - + +
444C ALA* 3.5 34.5 - - - +
447C HIS* 5.2 2.7 - - + -
451C VAL* 4.8 1.1 - - + -
477C VAL* 4.0 3.3 - - + +
538C TYR 3.0 17.8 + - - +
539C VAL 3.2 6.5 + - - +
541C GLY* 1.4 73.6 - - - +
543C GLU* 1.3 64.6 + - - +
545C ILE* 3.2 3.2 + - - +
546C ALA* 2.9 22.9 + - - +
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Residues in contact with GLU 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ALA* 5.5 2.8 - - + +
447C HIS* 3.9 29.5 + - + +
539C VAL* 2.9 39.4 + - + +
540C PHE* 3.6 5.3 - - - +
542C VAL* 1.3 77.4 - - + +
544C ARG* 1.3 61.6 + - - +
546C ALA* 3.5 6.5 + - - +
547C ALA* 3.2 16.5 + - - +
1936J GLN* 3.4 14.4 + - - +
1940J PHE* 3.3 19.6 - - + -
1943J GLU* 2.7 36.3 - - - +
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Residues in contact with ARG 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C VAL* 4.0 22.0 - - + -
528C GLY* 5.8 0.9 - - - -
540C PHE 2.8 20.1 + - - +
541C GLY* 3.5 4.5 - - - +
543C GLU* 1.3 71.4 - - - +
545C ILE* 1.3 66.5 + - - +
547C ALA* 3.1 11.3 + - - +
548C LEU* 3.0 55.7 + - + +
1932J GLY 4.5 4.8 + - - +
1933J CYS* 3.1 50.4 + - - +
1934J GLY* 3.8 7.7 - - - +
1936J GLN* 2.7 39.1 + - - +
1940J PHE* 3.8 8.2 - - + -
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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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404C LEU* 4.1 7.9 - - + -
409C ILE* 4.1 28.9 - - + -
474C CYS* 4.3 1.8 - - - +
475C GLY* 4.3 13.0 - - - -
476C ILE 3.9 15.0 - - - +
477C VAL* 4.0 14.8 - - + -
501C PRO* 3.6 39.0 - - + +
503C VAL* 4.0 12.3 - - + -
541C GLY 2.9 19.5 + - - +
542C VAL 3.7 5.4 - - - +
544C ARG* 1.3 77.6 - - - +
546C ALA* 1.3 58.9 + - - +
548C LEU* 4.4 4.5 - - + +
549C ALA* 2.7 36.1 + - + +
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Residues in contact with ALA 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 3.5 32.5 - - + +
447C HIS* 3.9 26.5 - - + +
542C VAL* 2.9 16.2 + - + +
543C GLU 3.7 5.4 - - - +
544C ARG 3.2 0.2 - - - -
545C ILE* 1.3 78.6 - - - +
547C ALA* 1.3 61.7 + - - +
550C GLY* 3.2 20.3 + - - -
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Residues in contact with ALA 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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543C GLU 3.2 7.6 + - - +
544C ARG* 3.1 12.5 + - - +
545C ILE 3.1 0.6 - - - -
546C ALA* 1.3 79.8 - - - +
548C LEU* 1.3 61.2 + - - +
550C GLY 3.5 12.8 - - - +
1936J GLN* 3.2 32.3 - - - +
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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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501C PRO* 4.0 30.6 - - + +
503C VAL* 5.7 1.1 - - + -
527C ASP* 5.1 14.8 - - + -
544C ARG* 3.0 59.8 + - + +
545C ILE* 3.9 3.4 - - + +
547C ALA* 1.3 78.8 - - - +
549C ALA* 1.3 60.3 + - - +
550C GLY 3.2 9.0 - - - +
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Residues in contact with ALA 549 (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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402C ARG 4.2 11.9 - - - +
403C SER* 3.6 23.2 - - - -
404C LEU* 3.5 22.2 + - + +
474C CYS* 4.1 22.2 - - + +
501C PRO* 4.6 4.5 - - + -
545C ILE* 2.7 24.1 + - + +
546C ALA 4.1 0.4 - - - -
548C LEU* 1.3 71.7 - - - +
550C GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 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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403C SER* 5.8 0.9 - - - -
404C LEU* 5.9 0.7 - - - -
546C ALA 3.2 15.9 + - - -
547C ALA 3.5 11.2 - - - +
548C LEU 3.5 12.1 - - - +
549C ALA* 1.3 81.0 - - - +
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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