Contacts of the helix formed by residues 451 - 455 (chain C) in PDB entry 1SL0
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 CYS 451 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ILE* 4.4 3.8 - - - -
242C LEU* 4.1 17.3 - - - -
395C ARG* 4.6 10.1 - - - -
399C SER* 5.5 1.3 - - - -
406C TRP* 3.5 39.0 - - + -
440C ILE* 4.0 9.2 - - + -
441C PRO* 4.3 15.0 - - + -
447C TYR* 3.3 21.3 + - - +
448C GLY* 4.7 2.9 - - - -
450C GLN* 1.3 76.0 - - - +
452C ARG* 1.3 65.3 + - - +
454C ALA* 3.0 12.6 + - - +
455C PHE* 3.1 19.3 - - - -
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Residues in contact with ARG 452 (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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440C ILE* 2.3 65.8 + - - +
441C PRO 3.2 14.8 + - - -
442C GLY* 3.7 11.8 - - - -
443C VAL* 4.5 6.5 - - + +
448C GLY 3.7 15.3 + - - +
449C GLU 4.2 0.4 + - - +
451C CYS* 1.3 79.4 - - - +
453C ALA* 1.3 61.4 + - - +
454C ALA 3.0 1.8 + - - -
455C PHE* 3.2 23.2 + - - +
655C GLU* 5.1 2.8 + - - -
700C TRP* 3.6 58.2 - - + +
701C ALA* 3.5 22.1 + - + -
704C HIS* 6.0 1.8 - - - +
20Q C 3.8 5.9 + - - -
21Q 2DT 3.0 28.5 + - - -
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Residues in contact with ALA 453 (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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235C ASP* 5.3 0.3 - - - +
238C ALA* 6.0 1.8 - - - -
449C GLU 3.2 19.5 + - - +
450C GLN* 3.9 7.2 - - - +
451C CYS 3.2 0.8 - - - -
452C ARG* 1.3 79.0 - - - +
454C ALA* 1.3 56.8 + - - +
455C PHE 3.3 0.7 - - - -
459C HIS* 2.8 21.5 + - - -
699C ASN* 3.6 20.8 + - - +
701C ALA* 3.3 15.3 - - + +
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Residues in contact with ALA 454 (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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234C PHE* 3.2 12.5 - - + -
235C ASP* 2.8 36.8 + - + -
238C ALA* 4.7 4.0 - - + -
239C ILE* 3.4 42.6 - - + -
450C GLN 3.4 3.5 + - - +
451C CYS 3.0 10.2 + - - +
453C ALA* 1.3 78.9 - - - +
455C PHE* 1.3 60.1 + - - +
459C HIS* 3.3 8.3 - - - -
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Residues in contact with PHE 455 (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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232C PHE* 3.2 31.5 - + + -
233C PRO 3.5 5.4 - - - -
234C PHE* 3.2 31.9 - + + -
406C TRP* 3.6 30.5 - + - -
416C ILE* 3.6 21.8 - - + -
437C LEU* 3.8 28.5 - - + -
440C ILE* 3.9 18.6 - - + -
451C CYS 3.1 20.6 - - - -
452C ARG* 3.2 7.1 + - - +
454C ALA* 1.3 81.3 - - - +
456C GLY* 1.3 57.5 + - - +
459C HIS* 4.1 0.7 - - - -
699C ASN* 3.5 1.5 - - - +
700C TRP* 2.9 36.7 + + + +
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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