Contacts of the strand formed by residues 203 - 208 (chain A) in PDB entry 2OSL
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 ILE 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A TRP* 3.3 11.1 - - - -
163A ASN* 3.1 38.0 + - - +
201A THR* 5.0 10.5 - - - +
202A TYR* 1.3 80.5 - - - +
204A CYS* 1.3 68.0 + - - +
205A ASN* 3.4 21.5 - - - +
216A ASP* 4.2 11.4 - - + +
217A LYS 3.1 18.4 - - - +
218A LYS* 3.9 19.3 - - + -
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Residues in contact with CYS 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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129A VAL* 3.9 8.5 - - - -
148A CYS* 2.0 49.8 - - + -
160A VAL* 3.9 11.2 - - + -
161A SER 3.3 3.8 - - - -
162A TRP* 3.8 18.9 - - + -
203A ILE* 1.3 75.3 - - - +
205A ASN* 1.3 61.4 + - - +
206A VAL* 3.7 8.6 + - - -
215A VAL 3.8 0.5 - - - +
216A ASP* 3.6 6.2 - - - -
217A LYS* 3.1 33.7 + - - -
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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
----------------------------------------------------------
159A THR 3.3 2.9 - - - +
160A VAL* 3.0 3.9 - - - -
161A SER* 2.6 62.4 + - - +
163A ASN* 3.6 3.9 - - - +
164A SER* 2.9 37.0 + - - +
203A ILE* 3.4 13.3 - - - +
204A CYS* 1.3 72.5 - - - +
206A VAL* 1.3 61.5 + - - +
207A ASN* 5.3 0.3 - - - +
215A VAL 4.1 3.4 - - - -
216A ASP* 3.4 22.6 - - - +
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Residues in contact with VAL 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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127A PRO* 4.9 9.6 - - + -
129A VAL* 3.8 26.2 - - + -
150A VAL* 3.8 11.7 - - + -
158A VAL* 4.5 9.4 - - + -
159A THR 3.3 5.6 - - - +
160A VAL* 3.8 18.2 - - + +
204A CYS* 4.3 11.9 - - - -
205A ASN* 1.3 78.2 - - - +
207A ASN* 1.3 65.2 + - - +
213A THR 4.7 2.7 - - - +
214A LYS* 3.6 6.2 - - - +
215A VAL* 3.1 52.7 + - + +
216A ASP* 4.9 0.9 - - - +
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Residues in contact with ASN 207 (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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157A PRO 4.6 0.5 - - - +
158A VAL* 3.7 5.7 - - - +
159A THR* 2.9 39.4 + - - +
205A ASN 5.3 0.2 - - - +
206A VAL* 1.3 77.7 - - - +
208A HIS* 1.3 67.7 + - - +
209A LYS* 3.4 39.3 + - - +
212A ASN* 5.4 0.8 - - - +
213A THR 3.3 9.7 + - - +
214A LYS* 3.3 40.6 - - + +
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Residues in contact with HIS 208 (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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125A LYS 3.0 26.3 + - - -
127A PRO* 3.6 25.0 - - + +
153A TYR* 3.9 5.1 - - + +
154A PHE 3.2 21.8 - - - -
155A PRO 2.8 20.0 + - - -
157A PRO 3.4 19.3 - - - -
158A VAL* 3.7 11.9 - - + +
206A VAL* 5.3 0.8 - - - +
207A ASN* 1.3 72.0 - - - +
209A LYS* 1.3 60.5 + - - +
210A PRO* 3.4 19.3 - - + +
211A SER* 2.9 21.1 + - - +
212A ASN 3.0 22.3 + - - -
213A THR 2.9 17.1 + - - +
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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