Contacts of the helix formed by residues 456 - 460 (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 GLY 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C PHE* 3.4 9.7 - - - -
233C PRO* 3.0 25.0 + - - +
455C PHE* 1.3 75.4 - - - +
457C ALA* 1.3 67.8 + - - -
458C GLU 3.1 3.1 - - - -
459C HIS* 3.0 18.5 + - - +
471C GLN* 5.1 0.9 - - - -
698C PRO 3.4 10.8 - - - -
699C ASN* 3.6 9.0 - - - -
700C TRP 4.3 0.7 - - - -
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Residues in contact with ALA 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PRO* 4.5 3.4 - - - -
456C GLY* 1.3 70.8 - - - -
458C GLU* 1.3 53.1 + - - +
459C HIS 2.7 11.6 + - - -
460C HIS* 2.7 26.8 + - - +
469C TRP* 3.8 10.7 - - + +
470C VAL 3.3 16.2 - - - +
471C GLN* 3.3 38.7 - - + +
642C TRP* 5.5 1.1 - - + -
649C MET* 4.1 19.8 - - + -
659C GLY* 4.5 2.0 - - - -
698C PRO 3.1 3.6 + - - -
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Residues in contact with GLU 458 (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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457C ALA* 1.3 76.3 - - - +
459C HIS* 1.3 81.7 + - + +
460C HIS 3.2 2.5 + - - -
468C PRO* 4.0 20.0 - - + +
469C TRP 3.6 13.1 + - - +
698C PRO* 2.9 38.1 + - + +
699C ASN* 2.9 23.4 + - - -
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Residues in contact with HIS 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PRO* 3.7 16.9 - - + +
234C PHE 4.5 3.7 - - - +
235C ASP* 3.7 30.9 + - + +
414C GLY 5.0 4.3 - - - +
453C ALA 2.8 26.0 + - - -
454C ALA* 3.3 24.4 - - - -
456C GLY* 3.4 26.2 + - - +
457C ALA 2.7 4.8 + - - -
458C GLU* 1.3 105.3 + - + +
460C HIS* 1.3 57.9 + - - +
461C LEU 4.0 1.3 + - - -
699C ASN* 4.4 0.8 - - - +
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Residues in contact with HIS 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PRO* 3.4 21.5 - - + +
415C LYS* 3.0 34.1 + - - -
457C ALA 2.7 8.2 + - - +
458C GLU 3.2 0.8 - - - -
459C HIS* 1.3 79.2 - - - +
461C LEU* 1.3 76.2 + - - +
462C ASP* 3.6 2.9 + - - -
463C GLY* 4.7 4.7 + - - -
468C PRO* 4.4 2.0 - - - -
469C TRP* 3.2 41.8 + + + -
642C TRP* 3.5 45.2 + + + +
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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