Contacts of the strand formed by residues 232 - 240 (chain A) in PDB entry 5TOL
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 TYR 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ILE* 3.9 13.0 - - + -
228A ASP 4.0 3.6 - - - -
229A HIS* 2.6 66.3 + + + +
230A SER 3.2 2.3 - - - -
231A LEU* 1.3 80.1 - - - +
233A THR* 1.3 65.6 + - - +
234A GLY 3.3 24.4 - - - +
235A SER* 4.4 0.4 - - - -
236A LEU* 3.8 25.1 + - + +
390A TYR* 3.3 28.7 - + + -
403A ALA* 3.5 24.0 - - + -
404A VAL 3.2 13.9 - - - +
406A ALA* 4.0 2.9 - - - +
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Residues in contact with THR 233 (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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232A TYR* 1.3 83.1 - - - +
234A GLY* 1.3 69.1 + - - +
235A SER 3.7 0.9 + - - -
403A ALA* 4.1 0.2 - - - +
404A VAL* 2.9 48.7 + - - +
406A ALA* 4.6 17.0 - - + -
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Residues in contact with GLY 234 (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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232A TYR* 3.3 15.6 - - - -
233A THR* 1.3 78.1 - - - +
235A SER* 1.3 59.2 + - - -
404A VAL* 6.3 0.4 - - - -
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Residues in contact with SER 235 (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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232A TYR* 4.4 2.0 - - - -
233A THR 3.7 0.7 + - - +
234A GLY* 1.3 74.4 - - - -
236A LEU* 1.3 81.5 + - - +
237A TRP* 3.6 24.2 + - - +
402A PHE 3.6 1.7 - - - +
403A ALA* 3.5 18.4 - - - +
404A VAL 4.9 0.2 + - - -
418A VAL* 4.7 3.1 - - - +
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Residues in contact with LEU 236 (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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227A ILE* 4.1 12.1 - - + -
229A HIS* 5.4 1.1 - - + -
232A TYR* 3.8 29.1 + - + +
235A SER* 1.3 87.2 + - - +
237A TRP* 1.3 64.4 + - - +
238A TYR* 3.7 37.1 - - + +
390A TYR* 4.2 8.1 - - + +
392A VAL* 3.7 31.2 - - + -
401A GLY 4.1 1.6 - - - -
402A PHE 3.4 9.4 - - - +
403A ALA* 3.4 31.0 - - + +
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Residues in contact with TRP 237 (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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235A SER* 3.6 22.3 + - - +
236A LEU* 1.3 81.0 + - - +
238A TYR* 1.3 64.0 + - - +
342A GLN* 3.9 21.3 - - - -
344A PHE* 3.5 45.7 - + + -
400A ILE 3.7 1.0 - - - +
401A GLY* 3.0 1.6 - - - -
402A PHE 2.7 31.7 + - - -
418A VAL* 3.5 32.8 + - + -
420A GLY 3.2 36.6 - - - -
421A PRO* 3.4 20.0 - - + -
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Residues in contact with TYR 238 (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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227A ILE* 4.2 11.6 - - - +
236A LEU* 3.7 38.1 - - + +
237A TRP* 1.3 79.2 - - - +
239A THR* 1.3 58.3 + - - +
337A GLY* 3.8 0.9 - - - -
338A GLU* 3.6 52.5 + - + +
342A GLN* 5.5 0.3 + - - -
344A PHE* 3.2 13.8 - - - -
392A VAL* 4.5 11.0 - - + -
394A ASP* 4.1 8.9 + - + -
397A ARG* 5.6 0.3 + - - -
399A ARG* 3.5 51.4 + - + -
400A ILE 3.3 2.9 - - - -
401A GLY* 3.5 25.8 - - - -
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Residues in contact with THR 239 (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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238A TYR* 1.3 73.4 - - - +
240A PRO* 1.4 69.6 + - - +
249A VAL* 3.7 30.7 - - + +
250A ILE 4.4 3.5 + - - -
335A LEU* 3.5 15.1 - - + +
336A MET* 2.7 22.4 + - - +
338A GLU* 5.8 0.7 - - - -
344A PHE* 3.8 10.5 - - - -
399A ARG* 3.3 4.3 - - - -
400A ILE* 2.7 47.7 + - + +
402A PHE* 4.1 13.2 - - + -
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Residues in contact with PRO 240 (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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239A THR* 1.4 89.5 + - - +
241A ILE* 1.3 67.4 + - - +
242A ARG* 3.5 5.2 + - - +
248A GLU 3.8 4.9 - - - +
249A VAL* 4.1 13.0 - - - +
250A ILE 5.0 0.9 + - - +
336A MET* 3.4 36.1 - - + +
337A GLY 3.7 17.7 - - - +
338A GLU* 4.8 7.4 - - + +
398A LYS 3.5 8.7 - - - +
399A ARG* 4.2 3.6 - - + -
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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