Contacts of the strand formed by residues 211 - 216 (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 PHE 211 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162U ASN* 3.2 42.4 - - + -
195U TYR* 3.6 10.1 - - - -
196U SER* 3.1 21.8 + - - -
208U GLU 5.5 1.3 - - - -
209U GLU* 3.2 31.0 - - - -
210U THR* 1.3 76.1 - - - +
212U LEU* 1.3 70.9 + - - +
213U ILE* 4.1 9.4 - - + -
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Residues in contact with LEU 212 (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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193U GLN* 4.0 24.5 - - + +
194U CYS* 3.2 14.4 - - - +
195U TYR* 3.0 65.2 - - + +
211U PHE* 1.3 83.2 - - - +
213U ILE* 1.3 67.0 + - - +
270U GLY* 4.4 4.0 - - - -
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Residues in contact with ILE 213 (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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160U HIS* 4.1 9.6 - - + +
161U ASN* 3.4 36.8 - - + -
162U ASN* 3.9 7.9 - - - +
193U GLN* 3.3 6.4 - - - -
194U CYS 2.9 36.7 + - - +
196U SER* 4.0 20.6 - - - +
211U PHE* 4.1 13.5 - - + -
212U LEU* 1.3 81.0 - - - +
214U ASP* 1.3 64.0 + - - +
215U CYS* 3.6 0.3 + - - -
240U GLY* 4.9 0.7 - - - -
241U CYS* 3.8 23.8 - - - +
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Residues in contact with ASP 214 (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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160U HIS* 3.8 5.5 + - - -
189U GLN* 3.2 37.6 + - + +
192U ARG 3.6 4.9 - - - +
193U GLN* 2.8 34.7 + - - +
213U ILE* 1.3 76.5 - - - +
215U CYS* 1.3 67.9 + - - +
216U ARG* 3.5 14.1 + - - +
241U CYS* 4.4 0.9 - - - -
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Residues in contact with CYS 215 (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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160U HIS* 3.6 1.1 - - - -
189U GLN* 3.4 7.1 - - - +
190U ASN* 3.0 35.7 + - - +
191U GLY 4.5 0.2 + - - -
192U ARG* 3.0 18.5 + - + +
194U CYS* 3.4 27.8 - - - -
214U ASP* 1.3 76.7 - - - +
216U ARG* 1.3 59.7 + - - +
219U MET 3.2 13.7 - - - +
220U ASN* 5.0 0.7 - - - -
221U GLN 4.9 1.1 - - - -
241U CYS* 2.0 49.8 - - - -
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Residues in contact with ARG 216 (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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160U HIS* 3.2 9.8 - - - +
184U LEU* 3.5 45.6 + - + +
185U GLU* 4.3 15.8 - - - +
186U ASN 4.4 2.6 - - - +
187U LEU* 2.6 35.0 + - + +
188U PRO* 3.1 11.4 - - - +
189U GLN* 3.5 36.3 - - + +
190U ASN* 3.1 6.8 + - - +
214U ASP 3.5 11.1 + - - +
215U CYS* 1.3 78.8 - - - +
217U GLY* 1.3 65.3 + - - +
219U MET* 2.7 28.8 - - - +
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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