Contacts of the strand formed by residues 210 - 213 (chain A) in PDB entry 5TQB
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A GLY 3.8 0.4 + - - -
209A PRO* 1.3 71.4 - - - +
211A ILE* 1.3 62.6 + - - +
212A VAL* 3.5 21.0 + - + -
233A GLU* 3.6 41.1 - - + +
235A CYS* 3.8 19.5 - - + -
240A LEU* 4.3 5.8 - - + -
244A GLN* 3.9 19.1 - - + +
245A LEU* 3.9 28.0 - - + -
253A ARG* 3.8 14.6 - - + +
254A PHE 2.7 14.1 + - - +
255A ILE* 3.3 10.1 - - + +
256A VAL 2.8 24.8 + - - -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.0 19.5 - - + -
209A PRO* 4.5 8.1 - - + +
210A LEU* 1.3 73.2 - - - +
212A VAL* 1.3 65.1 + - - +
213A TYR* 3.9 3.8 + - + -
222A LEU* 5.1 10.1 - - + -
226A PHE* 4.1 42.8 - - + -
232A VAL* 4.6 7.6 - - + -
233A GLU 2.8 21.0 + - - +
234A THR* 3.9 4.4 - - - -
235A CYS* 3.1 25.6 + - - +
256A VAL* 3.6 34.1 - - + +
258A THR* 5.2 8.7 - - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.0 12.8 - - + -
211A ILE* 1.3 73.5 - - - +
213A TYR* 1.3 62.2 + - - +
235A CYS 3.4 5.6 - - - +
237A VAL* 3.9 29.4 - - + +
240A LEU* 3.9 22.2 - - + -
255A ILE* 3.5 25.6 - - + -
256A VAL 2.9 10.1 + - - +
257A TRP* 3.6 33.0 - - + -
258A THR* 3.1 28.8 + - - +
261A ALA* 3.6 1.6 - - - +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.9 9.0 - - + -
212A VAL* 1.3 74.5 - - - +
214A SER* 1.3 65.4 + - - +
215A PRO* 3.4 10.0 - - + +
218A ASP* 3.6 7.4 - - - +
219A GLY 3.5 25.1 - - - -
220A LYS* 5.1 5.5 - - + +
222A LEU* 3.8 26.0 - - + -
223A VAL* 3.4 22.9 - - + +
234A THR* 3.4 17.3 + - - -
235A CYS 3.1 34.8 + - - -
236A PRO* 3.3 25.8 - - + +
237A VAL* 3.1 27.0 + - - -
258A THR* 3.6 14.8 - - + -
261A ALA* 4.1 0.2 - - - -
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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