Contacts of the strand formed by residues 226 - 231 (chain E) in PDB entry 3V56
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 LEU 226 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213E GLN* 3.5 36.3 - - + +
214E ARG 3.4 4.9 - - - +
215E LYS* 3.8 33.7 - - + +
224E LEU* 3.6 18.6 - - - +
225E SER* 1.4 77.4 - - - +
227E VAL* 1.3 67.7 + - - +
260E GLN* 3.9 22.0 - - - +
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Residues in contact with VAL 227 (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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213E GLN* 3.2 5.9 - - - -
214E ARG* 2.8 61.0 + - + +
216E LYS* 4.1 17.0 - - + -
224E LEU* 3.7 26.7 - - + +
226E LEU* 1.3 79.4 - - - +
228E THR* 1.3 64.0 - - - +
229E LEU* 3.5 8.9 + - + -
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Residues in contact with THR 228 (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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211E LEU* 3.7 25.1 - - + +
212E ILE 3.8 3.1 - - - +
213E GLN* 3.4 20.7 + - - -
227E VAL* 1.3 72.6 - - - +
229E LEU* 1.3 63.7 + - - +
230E PHE 3.7 20.4 - - - +
231E ARG* 4.0 1.3 - - + -
275F ASP* 3.4 30.2 - - + +
30K ARG* 3.4 20.5 + - - +
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Residues in contact with LEU 229 (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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195E ILE* 4.4 8.1 - - + -
212E ILE* 2.8 20.6 + - + +
214E ARG* 3.9 30.5 - - + +
227E VAL* 3.5 6.5 + - + +
228E THR* 1.3 71.8 - - - +
230E PHE* 1.4 84.1 + - + +
251E ALA* 4.1 28.7 - - + -
253E LEU* 4.4 2.5 - - + -
259E LEU* 3.9 28.0 - - + -
274F GLY 4.5 1.4 - - - +
275F ASP* 3.4 18.4 - - - +
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Residues in contact with PHE 230 (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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195E ILE* 4.3 18.6 - - + -
210E HIS* 4.1 0.7 - - - +
211E LEU* 3.5 2.8 - - - -
212E ILE* 2.8 52.4 + - + +
228E THR* 3.7 3.2 - - - +
229E LEU* 1.4 103.1 - - + +
231E ARG* 1.3 60.6 + - - +
247E SER* 3.9 20.4 - - - +
248E ALA 4.4 1.1 - - - +
249E GLY* 3.4 47.3 - - - -
250E ILE 3.7 15.7 - - - -
251E ALA* 4.6 2.9 - - + -
148F GLN* 4.5 9.9 - - - -
150F ILE* 6.5 0.4 - - + -
274F GLY 5.7 0.2 - - - -
275F ASP 3.2 6.5 - - - +
278F PHE* 3.9 25.4 - + + -
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Residues in contact with ARG 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E HIS* 3.4 5.2 - - - -
211E LEU* 3.5 29.8 - - + -
228E THR* 4.0 0.2 - - + -
230E PHE* 1.3 74.3 - - - +
232E CYS* 1.4 63.4 + - - +
233E ILE* 3.7 16.8 - - + +
247E SER* 4.6 3.4 - - - -
198F GLN* 2.8 28.4 + - - -
200F LEU* 4.3 4.0 - - - +
271F SER* 4.6 0.2 + - - -
273F ASP* 3.0 30.3 + - - +
275F ASP* 2.8 52.5 + - - +
276F VAL* 3.4 24.3 - - + +
28K LEU* 2.9 28.7 + - + -
29K VAL 4.1 11.9 + - - -
30K ARG* 3.3 21.9 - - - +
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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