Contacts of the helix formed by residues 200 - 204 (chain A) in PDB entry 1O6T
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 LEU 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ILE* 4.2 2.7 - - + -
193A PHE* 3.7 34.5 - - + -
197A VAL* 4.0 11.4 - - + -
198A THR 3.9 1.6 + - - +
199A ASP* 1.3 71.1 + - - +
201A LYS* 1.3 65.6 + - - +
202A PRO* 3.2 5.6 - - - -
203A LEU* 2.9 28.3 + - + +
214A ILE* 4.1 17.3 - - + -
219A VAL* 3.8 26.0 - - + -
221A ASP 3.8 22.9 + - - +
222A ILE* 4.1 10.8 - - + -
224A VAL* 3.5 17.7 - - + +
225A LEU* 4.4 13.0 - - + -
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Residues in contact with LYS 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 ASP* 3.0 17.3 + - - +
200A LEU* 1.3 76.3 - - - +
202A PRO* 1.4 65.3 - - + +
203A LEU 3.0 1.9 + - - -
204A ALA* 3.0 35.4 + - + +
224A VAL* 4.3 13.6 - - + +
227A LYS* 3.6 27.6 - - - +
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Residues in contact with PRO 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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178A ASP* 5.4 0.2 - - - +
179A ILE* 3.2 31.4 - - + +
180A SER* 3.7 32.1 - - - +
182A LEU* 4.4 0.8 - - + -
183A SER* 3.3 31.4 + - - +
199A ASP* 3.6 16.6 - - - +
200A LEU* 3.2 5.6 - - - -
201A LYS* 1.4 92.0 - - + +
203A LEU* 1.4 59.4 + - - +
204A ALA 3.2 2.0 + - - -
205A ASN 4.7 1.0 + - - -
206A LEU* 4.3 4.2 - - - +
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Residues in contact with LEU 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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179A ILE* 3.8 19.5 - - + -
182A LEU* 4.3 4.9 - - + -
191A LEU* 3.8 26.7 - - + -
193A PHE* 4.2 6.3 - - + -
200A LEU* 2.9 35.1 + - + +
202A PRO* 1.4 76.0 - - - +
204A ALA* 1.3 64.4 + - - +
205A ASN 3.2 2.5 - - - -
206A LEU* 2.9 33.0 + - + +
209A LEU* 4.9 1.3 - - + -
212A LEU* 3.9 28.9 - - + -
224A VAL* 4.2 7.4 - - + -
225A LEU* 4.2 12.6 - - + -
228A LEU* 3.5 17.3 - - + +
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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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201A LYS* 3.0 41.6 + - + +
202A PRO 3.2 2.0 - - - -
203A LEU* 1.3 77.3 - - - +
205A ASN* 1.3 68.6 + - - +
206A LEU 3.7 0.3 + - - -
207A THR* 4.1 7.3 - - - +
224A VAL* 3.6 15.1 - - + +
227A LYS* 3.9 28.5 - - + +
228A LEU* 4.4 0.5 - - - +
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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