Contacts of the strand formed by residues 189 - 196 (chain U) in PDB entry 3BT1
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 GLN 189 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188U PRO* 1.3 79.5 - - - +
190U ASN* 1.3 63.0 + - - +
191U GLY* 3.3 4.2 + - - +
214U ASP* 3.2 38.7 + - + +
215U CYS 3.4 10.3 - - - +
216U ARG* 3.5 35.1 - - - +
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Residues in contact with ASN 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188U PRO* 3.5 2.8 + - - -
189U GLN* 1.3 72.8 - - - +
191U GLY* 1.3 65.1 + - - +
192U ARG* 3.2 10.1 + - + +
215U CYS* 3.0 22.3 + - - +
216U ARG 3.1 10.7 + - - +
217U GLY* 2.8 27.3 + - - +
219U MET 2.6 31.5 + - - -
220U ASN* 3.5 16.9 - - + +
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Residues in contact with GLY 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189U GLN* 3.3 6.3 + - - +
190U ASN* 1.3 79.7 + - - +
192U ARG* 1.3 65.0 + - - +
193U GLN* 3.2 14.9 + - - +
215U CYS 4.5 0.2 + - - -
269U SER* 4.0 3.1 + - - -
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Residues in contact with ARG 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190U ASN* 3.2 9.2 + - - +
191U GLY* 1.3 78.5 + - - +
193U GLN* 1.3 69.7 + - - +
194U CYS* 4.6 4.9 - - - -
214U ASP* 3.6 0.9 - - - +
215U CYS* 3.0 36.2 + - + +
220U ASN* 2.9 40.7 + - + +
221U GLN* 4.7 3.7 + - - +
267U THR* 2.6 63.1 + - - +
268U LYS* 4.8 2.6 - - - +
269U SER* 3.1 14.5 - - - +
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Residues in contact with GLN 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191U GLY* 3.2 23.9 + - - +
192U ARG* 1.3 81.6 + - - +
194U CYS* 1.3 67.4 + - - +
212U LEU* 4.0 22.9 - - + +
213U ILE 3.3 9.0 - - - +
214U ASP* 2.8 31.6 + - - +
269U SER* 2.5 27.0 + - - +
270U GLY 2.8 24.8 + - - +
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Residues in contact with CYS 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192U ARG* 4.6 5.4 - - - -
193U GLN* 1.3 75.4 - - - +
195U TYR* 1.3 64.2 + - - +
212U LEU* 3.2 7.5 - - - -
213U ILE* 2.9 32.8 + - - +
215U CYS* 3.4 26.7 - - - -
221U GLN 4.1 0.7 - - - -
222U CYS* 2.0 58.1 - - - -
240U GLY 3.8 8.3 - - - +
241U CYS* 3.9 3.4 - - - -
270U GLY 4.4 1.3 - - - +
272U ASN* 3.4 8.3 - - - +
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Residues in contact with TYR 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194U CYS* 1.3 75.5 - - - +
196U SER* 1.3 58.9 + - - +
210U THR* 3.4 22.9 - - + -
211U PHE* 3.5 20.6 - - - -
212U LEU* 3.0 47.7 - - + +
213U ILE* 4.9 0.2 - - - +
239U ARG* 4.2 2.9 - - - -
240U GLY* 3.3 15.6 + - - -
270U GLY* 3.1 32.7 - - - -
272U ASN* 2.9 39.9 + - + +
273U HIS* 3.4 38.8 + + + -
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Residues in contact with SER 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161U ASN* 3.5 1.6 - - - +
162U ASN* 2.5 55.5 + - - +
195U TYR* 1.3 78.3 - - - +
197U CYS* 1.3 64.8 + - - +
209U GLU 4.0 2.8 - - - +
210U THR* 3.4 18.7 - - - +
211U PHE* 3.1 15.5 + - - -
213U ILE* 4.0 21.5 - - - -
239U ARG 3.3 8.5 - - - -
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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