Contacts of the helix formed by residues 541 - 550 (chain C) in PDB entry 3HN8
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 541 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C CYS* 5.1 1.9 - - - -
421C LEU* 5.7 0.9 - - - -
422C GLU* 3.4 35.4 + - - +
534C ARG* 6.1 0.8 - - - +
539C ALA* 3.4 4.0 - - - +
540C ALA* 1.3 79.0 - - + +
542C PRO* 1.3 77.9 - - - +
543C HIS* 3.0 26.2 + - - +
544C GLY* 2.7 33.3 + - - +
545C ARG* 3.3 6.4 + - - +
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Residues in contact with PRO 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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295C GLY* 5.3 3.4 - - - -
297C PRO* 3.9 41.7 - - + +
298C CYS* 4.7 11.2 - - + -
422C GLU* 6.6 0.2 - - - -
540C ALA 3.4 8.7 - - - +
541C ASP* 1.3 89.8 - - - +
543C HIS* 1.3 52.4 + - - +
545C ARG* 3.0 32.9 + - - +
546C GLU* 2.7 38.4 + - - +
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Residues in contact with HIS 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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298C CYS* 3.6 9.3 - - - -
419C ASP* 4.0 11.7 - - + -
420C ILE 6.1 0.2 - - - +
421C LEU* 3.5 20.9 - - + +
422C GLU 6.4 0.2 - - - +
541C ASP* 3.0 20.2 + - - +
542C PRO* 1.3 78.4 - - - +
544C GLY* 1.3 61.7 + - - +
546C GLU* 3.4 20.8 + - + +
547C HIS* 3.4 10.4 + - - +
561C HIS* 3.8 27.6 + + + -
562C TRP 2.7 29.1 + - - -
563C HIS* 3.4 21.8 + + - -
700C ZN 2.2 40.1 - - - -
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Residues in contact with GLY 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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534C ARG 3.8 17.9 - - - -
535C VAL* 2.9 34.4 - - - +
536C GLY 3.5 0.9 + - - -
539C ALA* 4.4 2.7 - - - -
541C ASP* 2.7 24.9 + - - +
543C HIS* 1.3 75.3 - - - +
545C ARG* 1.3 57.6 + - - -
547C HIS* 3.7 2.3 - - - +
548C TRP 3.7 0.3 + - - -
563C HIS* 4.0 9.6 - - - -
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Residues in contact with ARG 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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297C PRO* 5.5 6.5 - - - +
536C GLY 3.0 26.9 + - - +
537C PRO* 4.3 3.8 - - + -
538C GLU 4.7 4.9 - - - +
539C ALA* 2.9 30.5 + - + +
540C ALA 3.9 7.9 + - - -
541C ASP 3.3 3.0 + - - +
542C PRO* 3.4 39.0 - - - +
544C GLY* 1.3 73.1 - - - +
546C GLU* 1.3 60.9 + - - +
547C HIS 3.1 1.8 - - - -
548C TRP* 3.8 1.7 - - - +
549C ALA* 2.8 29.9 + - - +
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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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295C GLY* 2.9 40.2 + - - +
298C CYS* 3.9 3.5 - - - +
419C ASP* 2.9 10.6 - - - +
542C PRO 2.7 11.7 + - - +
543C HIS* 3.4 17.8 + - + +
545C ARG* 1.3 77.5 - - - +
547C HIS* 1.3 61.8 + - + +
549C ALA* 3.3 8.0 + - - +
550C GLU* 3.0 41.7 + - - +
561C HIS* 4.3 9.1 - - - +
700C ZN 2.6 32.1 - - - -
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Residues in contact with HIS 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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435C PHE* 3.2 41.4 - + - -
437C LEU* 3.6 12.0 - - + +
535C VAL* 3.6 5.3 - - + +
543C HIS* 3.4 15.4 + - + +
544C GLY 3.7 7.2 - - - +
546C GLU* 1.3 82.0 - - + +
548C TRP* 1.3 62.3 + - - +
550C GLU* 3.6 5.2 + - - +
551C MET* 3.2 18.9 + - - +
559C VAL* 3.0 36.9 + - + +
561C HIS* 3.3 26.9 - + + +
563C HIS* 2.7 24.2 + - + -
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Residues in contact with TRP 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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437C LEU* 3.7 11.7 - - + -
446C LEU* 3.8 13.3 - - + +
473C LEU* 5.7 0.2 - - + -
509C VAL* 2.6 49.8 - - + -
510C GLU* 3.9 4.0 - - - -
512C VAL* 3.4 31.9 - - + -
513C GLY* 4.1 2.7 - - - -
514C LEU* 3.2 20.4 - - + +
535C VAL* 3.7 28.4 + - + +
536C GLY* 3.3 24.7 - - - +
537C PRO* 3.9 13.5 - - + -
544C GLY 3.7 1.6 + - - -
545C ARG 3.5 5.3 + - - +
547C HIS* 1.3 77.7 - - - +
549C ALA* 1.3 64.1 + - - +
551C MET* 3.2 27.3 + - + +
552C LEU* 3.0 50.6 + - + +
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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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545C ARG 2.8 20.0 + - - +
546C GLU* 3.4 11.0 - - - +
547C HIS 3.2 0.2 - - - -
548C TRP* 1.3 80.2 - - - +
550C GLU* 1.3 58.5 + - - +
552C LEU* 2.8 23.9 + - - +
553C ALA* 4.0 5.2 - - - +
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Residues in contact with GLU 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 30.6 + - - +
547C HIS* 3.6 10.1 - - - +
549C ALA* 1.3 73.4 - - - +
551C MET* 1.3 58.0 + - - +
552C LEU 2.8 14.7 - - - +
553C ALA* 4.8 2.2 - - - -
554C ASN* 3.3 24.2 - - - +
559C VAL* 3.7 22.0 - - + +
561C HIS* 2.6 35.0 + - - -
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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