Contacts of the strand formed by residues 217 - 223 (chain H) in PDB entry 2OK0
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 THR 217 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H PRO* 3.9 19.6 - - + +
119H PRO* 4.9 3.4 - - + +
210H VAL 3.9 0.4 - - - +
211H ALA* 3.4 1.9 - - - +
212H HIS* 2.7 36.4 + - - +
215H SER* 3.0 29.5 + - - -
216H SER* 1.3 75.7 - - - +
218H LYS* 1.3 67.7 + - - +
219H VAL* 4.0 22.0 - - + -
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Residues in contact with LYS 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210H VAL 3.1 7.0 - - - +
211H ALA* 3.9 22.4 - - + -
216H SER 4.1 3.7 + - - +
217H THR* 1.3 82.2 - - - +
219H VAL* 1.3 68.2 + - - +
220H ASP* 4.2 11.4 - - - +
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Residues in contact with VAL 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 4.5 14.1 - - + +
121H VAL* 3.7 34.8 - - + +
208H CYS 3.6 1.9 - - - +
209H ASN* 3.5 0.5 - - - -
210H VAL* 2.6 40.9 + - - +
217H THR* 4.0 17.5 - - + -
218H LYS* 1.3 78.4 - - - +
220H ASP* 1.3 61.6 + - - +
221H LYS* 3.5 31.9 - - + +
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Residues in contact with ASP 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H THR* 4.7 5.3 - - - +
208H CYS 3.4 5.2 - - - -
209H ASN* 2.9 40.0 + - - +
210H VAL 4.4 0.2 + - - -
218H LYS* 5.0 10.7 - - - +
219H VAL* 1.3 74.8 + - - +
221H LYS* 1.3 63.2 + - - +
222H LYS* 3.8 2.4 + - - +
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Residues in contact with LYS 221 (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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121H VAL* 3.5 40.5 + - + +
123H PRO* 4.1 9.6 - - + -
142H CYS* 4.5 3.4 - - - -
207H THR* 3.1 4.0 - - - -
208H CYS* 2.8 42.7 + - - -
219H VAL* 3.5 21.4 - - + +
220H ASP* 1.3 71.7 + - - +
222H LYS* 1.3 66.6 + - - +
223H ILE* 3.6 1.9 + - - +
123L GLU* 2.8 40.8 - - - +
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Residues in contact with LYS 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 3.9 13.5 - - - +
205H THR* 3.5 40.7 + - + +
206H VAL 3.5 4.3 - - - -
207H THR* 3.7 8.5 - - + -
220H ASP 3.8 3.6 + - - +
221H LYS* 1.3 76.8 - - - +
223H ILE* 1.3 65.7 + - - +
226H VAL* 3.5 32.3 + - + +
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Residues in contact with ILE 223 (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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123H PRO* 3.3 26.0 - - + -
124H LEU 3.8 20.0 - - - +
125H ALA* 3.9 16.8 - - + -
140H LEU* 4.0 20.2 - - + -
141H GLY 3.5 18.2 - - - +
142H CYS* 3.5 16.6 - - - -
157H TRP* 3.8 20.2 - - + -
200H TRP* 3.0 23.6 + - + +
205H THR* 5.7 0.5 - - - -
206H VAL* 2.7 25.8 + - + +
221H LYS 3.9 4.0 - - - +
222H LYS* 1.3 74.6 - - - +
226H VAL* 1.3 62.9 + - - +
227H PRO* 4.4 0.3 - - - +
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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