Contacts of the strand formed by residues 200 - 205 (chain E) in PDB entry 4OA5
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 TYR 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E LEU* 4.5 1.0 - - + +
150E LYS* 3.4 26.9 - - + +
159E ILE* 4.1 14.8 - - + -
193E GLU* 2.8 56.9 + - + +
194E LEU* 3.6 28.6 - - + +
195E ALA 5.4 0.3 - - - -
196E ASN 2.9 15.2 + - - +
197E LYS* 3.4 16.8 - - - +
199E LYS* 1.3 105.0 - - + +
201E LEU* 1.3 60.2 + - - +
202E SER* 3.4 9.2 + - - +
214E SER* 3.3 17.3 - - - +
215E ILE 3.2 6.1 - - - +
216E LYS* 4.0 19.7 - - + -
217E LEU* 3.6 7.0 - - - +
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LYS* 6.1 5.6 - - + -
200E TYR* 1.3 73.4 - - - +
202E SER* 1.3 64.5 + - - +
213E VAL 4.0 0.9 - - - +
214E SER* 3.4 1.4 - - - -
215E ILE* 2.9 51.2 + - + +
217E LEU* 3.9 18.7 - - + +
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Residues in contact with SER 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E LEU 2.7 30.1 + - - -
195E ALA* 5.3 1.8 - - - -
200E TYR* 3.4 3.2 + - - +
201E LEU* 1.3 80.8 - - - +
203E THR* 1.3 66.0 + - - +
212E MET* 4.0 13.7 - - - -
213E VAL 3.4 5.2 - - - -
214E SER* 2.7 29.3 + - - -
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Residues in contact with THR 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E SER* 1.3 75.5 + - - +
204E ILE* 1.3 80.3 + - - +
205E ILE* 3.7 10.3 + - + +
206E PRO* 5.7 1.3 - - + -
212E MET* 3.7 2.6 - - - +
213E VAL* 2.9 37.3 + - - +
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Residues in contact with ILE 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E THR* 3.3 25.1 - - - +
165E PHE* 3.5 35.6 - - + -
170E VAL* 6.0 0.2 - - + -
191E ASN* 3.8 24.5 - - + +
203E THR* 1.3 80.5 - - - +
205E ILE* 1.3 64.2 + - - +
206E PRO* 3.2 9.4 - - - +
210E GLY* 3.6 16.4 - - - -
211E MET 3.6 3.6 - - - +
212E MET* 3.6 26.0 - - + -
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Residues in contact with ILE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E MET* 3.3 43.1 - - + -
51E LEU* 5.0 7.0 - - + -
203E THR* 3.7 9.8 + - + -
204E ILE* 1.3 69.4 - - - +
206E PRO* 1.4 64.3 - - + +
207E THR* 2.7 28.4 + - + +
210E GLY* 3.6 3.1 - - - -
211E MET* 2.8 34.4 + - + +
213E VAL* 3.6 27.8 - - + -
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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