Contacts of the helix formed by residues 200 - 206 (chain A) in PDB entry 1S9C
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A PRO* 2.9 20.2 + - + +
199A ILE* 1.3 73.3 - - - +
201A PRO* 1.3 71.8 - - - +
202A ASN* 2.8 32.7 + - - +
203A PHE* 2.9 25.8 + - - +
204A ALA* 3.1 21.0 + - - +
212A PRO* 4.0 1.3 - - - -
44B LEU* 5.0 2.4 - - - +
48B TYR* 3.5 38.5 + - + +
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Residues in contact with PRO 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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199A ILE 3.1 11.2 - - - +
200A ASP* 1.3 91.4 - - - +
202A ASN* 1.3 66.8 + - - +
204A ALA* 3.3 12.2 - - + +
205A SER* 3.3 10.4 + - - -
210A ASP 5.6 0.5 - - - +
211A LYS* 5.5 1.4 - - - -
212A PRO* 4.1 17.9 - - + -
44B LEU* 4.0 20.9 - - + -
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Residues in contact with ASN 202 (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 ASP* 2.8 25.9 + - - +
201A PRO* 1.3 77.7 - - - +
203A PHE* 1.3 68.9 + - - +
204A ALA 2.8 1.3 + - - -
205A SER* 2.7 24.5 + - - -
206A LEU* 3.2 21.4 + - + +
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Residues in contact with PHE 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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195A ASN* 4.6 13.2 - - - -
196A PRO* 3.8 34.5 - - + +
197A LEU* 4.3 14.6 - - + -
200A ASP* 2.9 23.2 + - - +
202A ASN* 1.3 73.0 - - - +
204A ALA* 1.3 66.3 + - - +
206A LEU* 3.6 8.9 + - - +
207A ALA* 3.3 27.3 + - + +
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Residues in contact with ALA 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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196A PRO 4.9 0.6 + - - -
197A LEU* 4.3 15.5 - - - +
200A ASP 3.1 13.5 + - - +
201A PRO 3.3 14.1 - - - +
202A ASN 2.8 0.6 + - - -
203A PHE* 1.3 80.3 - - - +
205A SER* 1.3 64.5 + - - +
207A ALA* 3.0 13.0 + - - +
209A PHE* 3.2 19.6 + - + +
211A LYS* 3.9 7.2 - - - -
212A PRO* 3.7 31.4 - - + -
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Residues in contact with SER 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 PRO 3.3 9.1 + - - -
202A ASN* 2.7 22.7 + - - -
204A ALA* 1.3 71.6 - - - +
206A LEU* 1.3 64.3 + - - +
207A ALA 2.5 5.8 + - - -
208A GLY* 2.4 32.1 + - - -
209A PHE 3.2 17.0 + - - +
210A ASP 5.3 2.9 - - - -
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Residues in contact with LEU 206 (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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202A ASN* 3.2 29.0 + - + +
203A PHE* 3.8 8.3 - - + +
205A SER* 1.3 79.8 + - - +
207A ALA* 1.3 55.4 + - - +
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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