Contacts of the strand formed by residues 211 - 216 (chain I) in PDB entry 5T0G
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 VAL 211 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I ALA* 5.7 2.9 - - + -
47I ALA 3.1 15.3 - - - +
48I GLU* 4.0 10.1 - - + -
49I ARG* 4.4 3.7 - - - +
197I LEU* 3.7 30.1 - - + -
206I LEU* 4.7 15.9 - - + -
207I SER 3.8 14.8 - - - +
208I ALA* 3.1 26.0 - - - +
209I GLU* 4.2 2.8 - - - +
210I LYS* 1.3 83.3 - - + +
212I GLU* 1.3 62.9 + - - +
213I ILE* 4.3 19.0 - - + +
233I VAL* 5.7 1.8 - - + -
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Residues in contact with GLU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ALA* 3.2 3.9 - - - -
47I ALA* 3.0 30.0 + - - +
49I ARG* 3.4 40.1 - - - +
61I PHE 6.2 0.2 - - - -
62I SER* 5.1 8.5 - - - -
65I ILE* 3.4 24.9 - - + +
211I VAL* 1.3 75.2 - - - +
213I ILE* 1.3 77.2 + - - +
214I ALA* 3.6 11.6 + - - +
227I VAL* 3.9 22.2 - - - +
228I LEU* 4.5 6.6 - - + +
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Residues in contact with ILE 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I LEU 3.4 9.6 - - - +
46I ALA* 3.9 15.3 - - + -
190I LEU* 4.2 18.6 - - + -
208I ALA 6.1 0.2 - - - +
211I VAL* 4.3 18.8 - - + +
212I GLU* 1.3 85.8 - - - +
214I ALA* 1.3 61.9 + - - +
215I THR* 4.0 16.4 - - + -
228I LEU* 3.1 53.7 + - + +
233I VAL* 3.9 28.9 - - + -
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Residues in contact with ALA 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I VAL 5.2 0.2 - - - -
44I LEU 3.9 0.3 - - - -
45I LEU* 2.8 38.8 + - + +
62I SER* 5.8 0.9 - - - +
65I ILE* 3.9 25.3 - - + +
212I GLU* 3.6 19.8 + - - +
213I ILE* 1.3 72.7 - - - +
215I THR* 1.3 62.1 + - - +
216I LEU 4.3 0.3 + - - -
225I ILE* 6.1 2.7 - - + -
226I ARG 3.9 6.5 - - - +
227I VAL* 5.0 8.7 - - + +
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Residues in contact with THR 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I VAL 3.4 7.4 - - - +
44I LEU* 3.8 24.7 - - + -
186I LEU* 5.5 6.5 - - + -
190I LEU* 4.5 13.5 - - + -
213I ILE* 4.0 16.7 + - + -
214I ALA* 1.3 76.2 - - - +
216I LEU* 1.3 57.5 + - - +
217I THR* 4.2 6.1 - - - +
225I ILE* 3.6 5.0 - - - +
226I ARG* 2.7 62.8 + - - +
228I LEU* 4.9 5.6 - - + +
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Residues in contact with LEU 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLY* 3.4 1.9 - - - -
43I VAL* 2.9 55.6 + - + +
71I ASP 4.0 21.3 - - - +
72I MET* 4.6 2.5 - - - +
73I ALA* 5.4 2.0 - - + -
137I ILE* 3.8 22.7 - - + -
138I GLY* 5.4 4.3 - - - -
139I TRP* 5.5 6.7 - - + -
145I PHE* 5.5 3.8 - - + -
215I THR* 1.3 73.9 - - - +
217I THR* 1.3 66.5 + - - +
218I ARG* 4.6 1.8 - - - +
223I THR* 3.7 23.3 - - + -
224I VAL 3.7 11.2 - - - +
225I ILE* 3.7 30.7 - - + +
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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