Contacts of the helix formed by residues 198 - 205 (chain A) in PDB entry 1LSH
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A GLU 3.3 2.2 + - - +
197A ARG* 1.3 72.5 - - - +
199A PRO* 1.4 54.5 - - - +
200A THR* 3.9 3.4 - - - -
201A CYS* 2.1 51.3 - - - +
202A GLN* 2.8 34.8 + - - +
597A GLU* 3.8 27.8 - - + -
668A GLY 2.9 18.0 + - - +
669A TYR* 4.4 7.9 - - - -
670A ALA* 4.7 7.4 - - + +
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Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.3 23.7 - - + +
198A CYS* 1.4 82.9 - - - +
200A THR* 1.3 66.3 + - - +
202A GLN* 3.2 9.1 + - + +
203A LYS* 3.0 37.1 + - - +
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A CYS* 3.1 4.1 + - - -
199A PRO* 1.3 77.7 - - - +
201A CYS* 1.3 69.0 + - - +
203A LYS* 2.8 29.8 + - - +
204A MET* 3.2 13.1 + - + +
596A PRO* 3.4 38.4 + - + +
597A GLU* 5.1 1.4 + - - -
599A ARG* 3.9 26.4 - - + +
600A ASP* 4.4 19.2 + - - -
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Residues in contact with CYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A CYS* 2.1 47.5 + - + +
200A THR* 1.3 80.1 - - - +
202A GLN* 1.3 61.1 + - - +
204A MET* 3.1 22.9 + - - +
205A ASN 3.2 12.1 + - - +
596A PRO* 4.1 20.6 - - + -
597A GLU* 4.3 5.2 - - - -
632A PHE* 4.8 9.0 - - + -
637A MET* 3.9 10.2 - - + +
665A GLN* 4.9 9.6 - - - -
666A GLY 6.0 0.4 - - - -
668A GLY* 3.9 18.5 - - - +
669A TYR 5.3 0.9 - - - -
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Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 2.7 48.1 + - + +
198A CYS 2.8 22.6 + - - +
199A PRO* 3.8 7.4 - - + +
200A THR 3.0 0.4 - - - -
201A CYS* 1.3 74.6 - - - +
203A LYS* 1.3 67.5 + - + +
204A MET 3.2 0.2 - - - -
205A ASN 3.2 18.5 + - - +
206A LYS* 3.5 38.6 + - + +
207A ASN* 5.0 3.2 + - - -
667A MET 4.2 2.0 + - - -
668A GLY* 3.5 19.8 + - - +
669A TYR* 3.6 27.9 + - - -
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.2 22.9 + - - +
200A THR* 2.8 23.9 + - - +
202A GLN* 1.3 82.2 - - + +
204A MET* 1.3 63.0 + - + +
205A ASN* 4.7 0.2 - - - -
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A THR* 3.2 13.0 + - + +
201A CYS* 3.1 4.5 + - - +
203A LYS* 1.3 79.4 - - + +
205A ASN* 1.3 61.7 + - - +
242A ASP* 4.8 4.0 - - - +
596A PRO* 3.9 18.4 - - + -
599A ARG* 3.3 29.8 - - - +
632A PHE* 4.3 11.7 - - + -
634A ALA* 5.1 9.4 - - + -
637A MET* 3.2 40.1 - - + +
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Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A CYS 3.2 9.8 + - - +
202A GLN* 3.2 19.2 + - - +
203A LYS 3.3 1.4 - - - -
204A MET* 1.3 81.4 + - - +
206A LYS* 1.3 66.7 + - - +
207A ASN* 3.3 24.9 + - - +
209A ARG* 5.0 3.5 - - - +
239A SER* 4.3 1.4 - - - -
241A PHE 3.2 16.6 - - - +
242A ASP* 3.5 13.6 + - - +
243A ILE* 2.8 44.3 + - - +
637A MET* 3.8 22.2 - - + +
668A GLY* 5.4 1.6 - - - -
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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