Contacts of the strand formed by residues 203 - 208 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H TRP* 3.4 8.9 - - - -
163H ASN* 2.8 46.4 + - - +
201H THR* 4.0 18.4 - - + +
202H TYR* 1.3 77.9 - - - +
204H CYS* 1.3 63.1 + - - +
205H ASN* 3.8 16.6 + - - +
216H ASP* 4.0 21.1 - - + -
217H LYS 3.4 13.0 - - - +
218H LYS* 3.9 23.3 - - + -
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Residues in contact with CYS 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H VAL* 4.1 13.9 - - - -
148H CYS* 2.0 50.0 - - + -
160H VAL* 4.7 4.0 - - + -
161H SER 3.5 5.6 - - - +
162H TRP* 3.5 26.1 - - + -
203H ILE* 1.3 73.7 - - - +
205H ASN* 1.3 59.9 - - - +
206H VAL* 4.2 8.7 - - - -
215H VAL 3.8 1.0 - - - +
216H ASP* 3.5 1.9 - - - -
217H LYS* 2.9 30.2 + - - -
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Residues in contact with ASN 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H THR 3.4 1.9 - - - +
160H VAL* 3.2 6.1 - - - -
161H SER* 2.7 56.0 + - - +
163H ASN 3.6 2.6 - - - +
164H SER* 2.9 38.2 + - - +
203H ILE* 3.8 13.6 - - - +
204H CYS* 1.3 74.6 - - - +
206H VAL* 1.3 62.8 + - - +
207H ASN* 5.4 0.6 - - - +
215H VAL 3.6 4.0 - - - -
216H ASP* 3.1 20.4 - - - +
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Residues in contact with VAL 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H PRO* 4.0 17.9 - - + -
129H VAL* 3.6 31.0 - - + -
150H VAL* 3.7 28.9 - - + -
158H VAL* 3.8 22.0 - - + -
159H THR 3.4 2.5 - - - -
160H VAL* 4.4 5.6 - - + -
204H CYS* 4.2 10.1 - - - -
205H ASN* 1.3 78.9 - - - +
207H ASN* 1.3 65.7 + - - +
208H HIS 4.2 0.4 - - - +
213H THR 4.0 0.7 - - - +
214H LYS* 3.4 5.4 - - - +
215H VAL* 2.8 41.1 + - + +
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Residues in contact with ASN 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PRO 4.3 0.5 - - - +
158H VAL* 3.4 3.6 - - - -
159H THR* 2.8 56.8 + - + +
205H ASN 5.4 0.7 - - - +
206H VAL* 1.3 78.2 - - - +
208H HIS* 1.3 64.0 + - - +
209H LYS* 3.4 42.7 + - - +
212H ASN* 6.2 0.2 - - - +
213H THR 3.6 8.7 + - - +
214H LYS* 3.8 25.2 - - + +
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Residues in contact with HIS 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H LYS 3.3 21.5 - - - -
127H PRO* 3.5 28.2 - - + +
153H TYR* 3.7 4.7 - + - -
154H PHE 3.4 16.4 - - - -
155H PRO* 2.7 23.5 + - + -
157H PRO 3.3 21.1 - - - -
158H VAL* 3.5 16.8 - - + -
206H VAL* 4.2 0.4 - - - +
207H ASN* 1.3 75.7 - - - +
209H LYS* 1.3 65.0 + - - +
210H PRO* 3.3 17.6 - - + +
211H SER* 2.8 37.4 + - - +
212H ASN 3.4 3.6 + - - -
213H THR 2.9 15.7 + - - +
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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