Contacts of the helix formed by residues 357 - 365 (chain B) in PDB entry 1O9T
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 ARG 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLU* 3.1 46.5 + - - +
130B ASP* 2.8 31.6 + - - -
326B ALA* 3.8 7.6 - - + +
327B GLU* 3.6 48.6 + - - +
355B ASP* 2.9 37.2 + - - +
356B LEU* 1.3 77.1 - - - +
358B PRO* 1.3 73.2 - - + +
359B GLY 3.4 0.2 - - - -
360B VAL* 3.0 12.8 + - + +
361B ILE* 2.9 21.4 + - - +
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Residues in contact with PRO 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B VAL* 5.3 2.9 - - + -
132B GLY 5.0 6.3 - - - +
133B ALA* 3.9 32.8 - - + +
289B THR 5.9 2.2 - - - +
291B VAL* 4.2 13.2 - - + -
294B SER* 5.4 3.5 - - - -
321B TYR* 3.9 13.0 - - + -
326B ALA* 3.2 24.5 - - + +
356B LEU 3.6 0.6 - - - -
357B ARG* 1.3 81.3 - - + -
359B GLY* 1.3 64.9 + - - +
361B ILE* 3.1 22.0 + - + +
362B VAL* 3.2 20.7 + - + +
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 3.9 20.6 + - - -
131B VAL* 4.2 20.2 - - - +
357B ARG 3.2 0.8 + - - -
358B PRO* 1.3 78.7 - - - +
360B VAL* 1.3 60.5 + - - +
362B VAL* 3.1 27.0 - - - +
363B ARG* 3.2 8.2 + - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 3.6 28.7 + - + +
355B ASP* 3.1 49.1 - - + +
357B ARG* 3.0 16.3 + - + +
359B GLY* 1.3 72.2 - - - +
361B ILE* 1.3 61.4 + - - +
363B ARG* 3.2 18.9 + - - +
364B ASP* 2.8 53.5 + - - +
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Residues in contact with ILE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B SER* 3.7 17.9 - - - +
295B ALA* 4.1 9.9 - - + +
298B ALA* 3.6 22.4 - - + -
301B TRP* 6.0 3.6 - - + -
321B TYR* 3.4 13.0 - - + +
355B ASP 4.4 1.1 - - - +
356B LEU* 3.3 33.0 - - + +
357B ARG 2.9 17.2 + - - +
358B PRO* 3.2 11.9 - - + +
360B VAL* 1.3 76.1 - - - +
362B VAL* 1.3 56.3 + - - +
364B ASP* 4.8 2.5 - - - -
365B LEU* 2.8 62.8 + - + +
367B LEU* 3.8 8.3 - - + -
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TYR* 3.7 43.7 - - + +
289B THR* 5.6 0.9 - - + -
294B SER* 4.1 9.2 - - - +
358B PRO 3.2 16.5 + - - +
359B GLY* 3.1 16.6 - - - +
361B ILE* 1.3 74.9 - - - +
363B ARG* 1.3 63.1 + - + +
366B ASP* 3.0 7.6 + - - -
367B LEU* 2.8 43.0 + - + -
368B LYS* 4.6 14.8 + - + +
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Residues in contact with ARG 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 2.7 49.3 + - - +
359B GLY 3.2 8.5 + - - +
360B VAL* 3.2 21.8 + - - +
361B ILE 3.2 0.6 - - - -
362B VAL* 1.3 81.7 - - + +
364B ASP* 1.3 82.8 + - - +
366B ASP* 3.4 13.2 + - - +
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B TRP* 4.2 29.2 - - + -
355B ASP* 5.2 3.5 + - - +
360B VAL* 2.8 37.8 + - - +
361B ILE* 4.0 1.8 - - - +
363B ARG* 1.3 96.0 + - - +
365B LEU* 1.3 63.5 + - - +
366B ASP* 3.3 1.8 + - - +
387B PRO* 5.3 0.5 - - - +
392B LYS* 4.7 8.8 + - - -
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B TYR* 4.2 12.3 - - + -
298B ALA* 4.1 23.3 - - + +
301B TRP* 3.7 40.4 - - + -
361B ILE* 2.8 43.1 + - + +
364B ASP* 1.3 73.5 - - - +
366B ASP* 1.3 70.6 + - - +
367B LEU* 3.4 17.8 + - + +
387B PRO* 3.0 28.3 - - + +
388B TRP* 3.9 24.5 - - + +
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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